From dcc42555289d949964653650911d377b3a9c6bf9 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Wed, 19 Jun 2024 08:00:16 -0400 Subject: [PATCH 01/21] Project updated --- src/main/java/org/snpeff/vcf/VcfEntry.java | 45 +++++++++++----------- 1 file changed, 22 insertions(+), 23 deletions(-) diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index 8dfce352..feda374a 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -1521,6 +1521,11 @@ List variants(Chromosome chromo, int start, String reference, String al if (alt == null || alt.isEmpty() || alt.equals(reference)) { // Non-variant list = Variant.factory(chromo, start, reference, null, id, false); + } else if (reference.length() == 1 && alt.length() == 1) { + // The most common case: SNPs + // SNPs + // 20 3 . C G . PASS DP=100 + list = Variant.factory(chromo, start, reference, alt, id, vcfFileIterator.isExpandIub()); } else if (alt.charAt(0) == '<') { // Structural variants if (alt.startsWith(" variants(Chromosome chromo, int start, String reference, String al list = new LinkedList<>(); list.add(var); } else if (reference.length() == alt.length()) { - // Case: SNP, MNP - if (reference.length() == 1) { - // SNPs - // 20 3 . C G . PASS DP=100 - list = Variant.factory(chromo, start, reference, alt, id, vcfFileIterator.isExpandIub()); - } else { - // MNPs - // 20 3 . TC AT . PASS DP=100 - // Sometimes the first bases are the same and we can trim them - int startDiff = Integer.MAX_VALUE; - for (int i = 0; i < reference.length(); i++) - if (reference.charAt(i) != alt.charAt(i)) startDiff = Math.min(startDiff, i); - - // MNPs - // Sometimes the last bases are the same and we can trim them - int endDiff = 0; - for (int i = reference.length() - 1; i >= 0; i--) - if (reference.charAt(i) != alt.charAt(i)) endDiff = Math.max(endDiff, i); - - String newRef = reference.substring(startDiff, endDiff + 1); - String newAlt = alt.substring(startDiff, endDiff + 1); - list = Variant.factory(chromo, start + startDiff, newRef, newAlt, id, vcfFileIterator.isExpandIub()); - } + // Case: MNP (note that SNPs were covers at the beginning of this if/else clause) + // MNPs + // 20 3 . TC AT . PASS DP=100 + // Sometimes the first bases are the same and we can trim them + int startDiff = Integer.MAX_VALUE; + for (int i = 0; i < reference.length(); i++) + if (reference.charAt(i) != alt.charAt(i)) startDiff = Math.min(startDiff, i); + + // MNPs + // Sometimes the last bases are the same and we can trim them + int endDiff = 0; + for (int i = reference.length() - 1; i >= 0; i--) + if (reference.charAt(i) != alt.charAt(i)) endDiff = Math.max(endDiff, i); + + String newRef = reference.substring(startDiff, endDiff + 1); + String newAlt = alt.substring(startDiff, endDiff + 1); + list = Variant.factory(chromo, start + startDiff, newRef, newAlt, id, vcfFileIterator.isExpandIub()); } else { // Short Insertions, Deletions or Mixed Variants (substitutions) VcfRefAltAlign align = new VcfRefAltAlign(alt, reference); From 8c52183b1a540778d5c4474bd93ef0831c7d57e4 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Mon, 22 Jul 2024 14:19:05 -0400 Subject: [PATCH 02/21] Project updated --- src/main/java/org/snpeff/vcf/VcfEntry.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index feda374a..7f6bdd84 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -312,7 +312,6 @@ public void addInfo(String key, String value) { if (!infoStr.endsWith(SUB_FIELD_SEP)) infoStr += SUB_FIELD_SEP; // Do we need to add a semicolon? infoStr += addInfoStr; // Add info string } - } /** From f8e1026ab94d51ead2b037b8bbdaf13d5b27ce31 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Thu, 1 Aug 2024 13:37:42 -0400 Subject: [PATCH 03/21] Project updated --- .classpath | 8 +- galaxy/tool-data/snpEff_genomes.loc | 317 ------------------ galaxy/tool-data/snpEff_genomes.loc.sample | 317 ------------------ pom.xml | 2 +- src/main/java/org/snpeff/interval/Genome.java | 3 - 5 files changed, 5 insertions(+), 642 deletions(-) diff --git a/.classpath b/.classpath index c5ab3fb9..14901ab0 100644 --- a/.classpath +++ b/.classpath @@ -24,7 +24,7 @@ - + @@ -36,18 +36,18 @@ - + - - + + diff --git a/galaxy/tool-data/snpEff_genomes.loc b/galaxy/tool-data/snpEff_genomes.loc index bcc00d93..9f417ef7 100644 --- a/galaxy/tool-data/snpEff_genomes.loc +++ b/galaxy/tool-data/snpEff_genomes.loc @@ -15,13 +15,11 @@ Abyssibacter_profundi_gca_003151135 Abyssibacter_profundi_gca_003151135 Abys Abyssicoccus_albus_gca_003815035 Abyssicoccus_albus_gca_003815035 Abyssicoccus_albus_gca_003815035 Acanthamoeba_castellanii_str_neff_gca_000313135 Acanthamoeba_castellanii_str_neff_gca_000313135 Acanthamoeba_castellanii_str_neff_gca_000313135 Acanthaster_planci_gca001949145v1 Acanthaster_planci_gca001949145v1 Acanthaster_planci_gca001949145v1 -ASM210954v1.110 Acanthochromis_polyacanthus ASM210954v1.110 ASM210954v1.99 Acanthochromis_polyacanthus ASM210954v1.99 Acaromyces_ingoldii_gca_003144295 Acaromyces_ingoldii_gca_003144295 Acaromyces_ingoldii_gca_003144295 Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017_gca_000018105 Acaryochloris_marina_mbic11017_gca_000018105 Acaryochloris_marina_mbic11017_gca_000018105 Acaryochloris_thomasi_rcc1774_gca_003231495 Acaryochloris_thomasi_rcc1774_gca_003231495 Acaryochloris_thomasi_rcc1774_gca_003231495 -Accipiter_nisus_ver1.0.110 Accipiter_nisus Accipiter_nisus_ver1.0.110 Accipiter_nisus_ver1.0.99 Accipiter_nisus Accipiter_nisus_ver1.0.99 Acetanaerobacterium_elongatum_gca_900103835 Acetanaerobacterium_elongatum_gca_900103835 Acetanaerobacterium_elongatum_gca_900103835 Acetatifactor_muris_gca_900248245 Acetatifactor_muris_gca_900248245 Acetatifactor_muris_gca_900248245 @@ -3205,7 +3203,6 @@ Ahrensia_sp__gca_002706335 Ahrensia_sp__gca_002706335 Ahrensia_sp__gca_00270 Ahrensia_sp_r2a130 Ahrensia_sp_r2a130 Ahrensia_sp_r2a130 Ahrensia_sp_r2a130_gca_000179775 Ahrensia_sp_r2a130_gca_000179775 Ahrensia_sp_r2a130_gca_000179775 Aidingimonas_halophila_gca_900106955 Aidingimonas_halophila_gca_900106955 Aidingimonas_halophila_gca_900106955 -ASM200744v2.110 Ailuropoda_melanoleuca ASM200744v2.110 ailMel1.75 Ailuropoda_melanoleuca ailMel1.75 ailMel1.99 Ailuropoda_melanoleuca ailMel1.99 Akanthomyces_lecanii_gca_001653215 Akanthomyces_lecanii_gca_001653215 Akanthomyces_lecanii_gca_001653215 @@ -3737,7 +3734,6 @@ Amanita_muscaria_koide_bx008_gca_000827485 Amanita_muscaria_koide_bx008_gca_00 Amanita_thiersii_skay4041_gca_002554575 Amanita_thiersii_skay4041_gca_002554575 Amanita_thiersii_skay4041_gca_002554575 Amantichitinum_ursilacus Amantichitinum_ursilacus Amantichitinum_ursilacus Amantichitinum_ursilacus_gca_001294205 Amantichitinum_ursilacus_gca_001294205 Amantichitinum_ursilacus_gca_001294205 -ASM394721v1.110 Amazona_collaria ASM394721v1.110 ASM394721v1.99 Amazona_collaria ASM394721v1.99 Amborella_trichopoda Amborella_trichopoda Amborella_trichopoda Amedibacillus_dolichus_dsm_3991_gca_000154285 Amedibacillus_dolichus_dsm_3991_gca_000154285 Amedibacillus_dolichus_dsm_3991_gca_000154285 @@ -3773,14 +3769,11 @@ Amphibacillus_marinus_gca_900110345 Amphibacillus_marinus_gca_900110345 Amph Amphibacillus_xylanus_nbrc_15112 Amphibacillus_xylanus_nbrc_15112 Amphibacillus_xylanus_nbrc_15112 Amphibacillus_xylanus_nbrc_15112_gca_000307165 Amphibacillus_xylanus_nbrc_15112_gca_000307165 Amphibacillus_xylanus_nbrc_15112_gca_000307165 Amphibalanus_amphitrite_gca019059575v1 Amphibalanus_amphitrite_gca019059575v1 Amphibalanus_amphitrite_gca019059575v1 -Midas_v5.110 Amphilophus_citrinellus Midas_v5.110 Midas_v5.99 Amphilophus_citrinellus Midas_v5.99 Amphimedon_queenslandica Amphimedon_queenslandica Amphimedon_queenslandica Amphimedon_queenslandica_gca000090795v2rs Amphimedon_queenslandica_gca000090795v2rs Amphimedon_queenslandica_gca000090795v2rs Amphiplicatus_metriothermophilus_gca_900199215 Amphiplicatus_metriothermophilus_gca_900199215 Amphiplicatus_metriothermophilus_gca_900199215 -AmpOce1.0.110 Amphiprion_ocellaris AmpOce1.0.110 AmpOce1.0.99 Amphiprion_ocellaris AmpOce1.0.99 -Nemo_v1.110 Amphiprion_percula Nemo_v1.110 Nemo_v1.99 Amphiprion_percula Nemo_v1.99 Amphritea_atlantica_gca_900111095 Amphritea_atlantica_gca_900111095 Amphritea_atlantica_gca_900111095 Amphritea_balenae_gca_003858655 Amphritea_balenae_gca_003858655 Amphritea_balenae_gca_003858655 @@ -3877,7 +3870,6 @@ Anabaena_sp_wa113_gca_001672155 Anabaena_sp_wa113_gca_001672155 Anabaena_sp_ Anabaena_variabilis_atcc_29413 Anabaena_variabilis_atcc_29413 Anabaena_variabilis_atcc_29413 Anabaenopsis_circularis_nies_21_gca_002367975 Anabaenopsis_circularis_nies_21_gca_002367975 Anabaenopsis_circularis_nies_21_gca_002367975 fAnaTes1.1.99 Anabas_testudineus fAnaTes1.1.99 -fAnaTes1.2.110 Anabas_testudineus fAnaTes1.2.110 Anaerobacillus_alkalidiazotrophicus_gca_001866055 Anaerobacillus_alkalidiazotrophicus_gca_001866055 Anaerobacillus_alkalidiazotrophicus_gca_001866055 Anaerobacillus_alkalilacustris_gca_001866005 Anaerobacillus_alkalilacustris_gca_001866005 Anaerobacillus_alkalilacustris_gca_001866005 Anaerobacillus_alkaliphilus_gca_004116265 Anaerobacillus_alkaliphilus_gca_004116265 Anaerobacillus_alkaliphilus_gca_004116265 @@ -4057,11 +4049,8 @@ Anaplasma_phagocytophilum_str_mrk Anaplasma_phagocytophilum_str_mrk Anaplasm Anaplasma_phagocytophilum_str_nch_1 Anaplasma_phagocytophilum_str_nch_1 Anaplasma_phagocytophilum_str_nch_1 Anaplasma_phagocytophilum_str_norway_variant2 Anaplasma_phagocytophilum_str_norway_variant2 Anaplasma_phagocytophilum_str_norway_variant2 Anaplasma_phagocytophilum_str_webster Anaplasma_phagocytophilum_str_webster Anaplasma_phagocytophilum_str_webster -ASM874695v1.110 Anas_platyrhynchos ASM874695v1.110 BGI_duck_1.0.75 Anas_platyrhynchos BGI_duck_1.0.75 -CAU_duck1.0.110 Anas_platyrhynchos_platyrhynchos CAU_duck1.0.110 CAU_duck1.0.99 Anas_platyrhynchos_platyrhynchos CAU_duck1.0.99 -ASM222487v1.110 Anas_zonorhyncha ASM222487v1.110 Ancrocorticia_populi_gca_003123745 Ancrocorticia_populi_gca_003123745 Ancrocorticia_populi_gca_003123745 Ancylobacter_aquaticus_gca_003963445 Ancylobacter_aquaticus_gca_003963445 Ancylobacter_aquaticus_gca_003963445 Ancylobacter_aquaticus_gca_004339465 Ancylobacter_aquaticus_gca_004339465 Ancylobacter_aquaticus_gca_004339465 @@ -4097,7 +4086,6 @@ Anncaliia_algerae_pra339_gca_000385875 Anncaliia_algerae_pra339_gca_000385875 Anneissia_japonica_gca011630105v1 Anneissia_japonica_gca011630105v1 Anneissia_japonica_gca011630105v1 AnoCar2.0.75 Anolis_carolinensis AnoCar2.0.75 AnoCar2.0.99 Anolis_carolinensis AnoCar2.0.99 -AnoCar2.0v2.110 Anolis_carolinensis AnoCar2.0v2.110 Anopheles_albimanus Anopheles_albimanus Anopheles_albimanus Anopheles_arabiensis Anopheles_arabiensis Anopheles_arabiensis Anopheles_atroparvus Anopheles_atroparvus Anopheles_atroparvus @@ -4162,9 +4150,7 @@ Anoxybacillus_thermarum_gca_000836725 Anoxybacillus_thermarum_gca_000836725 Anoxybacillus_vitaminiphilus_gca_003259935 Anoxybacillus_vitaminiphilus_gca_003259935 Anoxybacillus_vitaminiphilus_gca_003259935 Anoxybacter_fermentans_gca_003991135 Anoxybacter_fermentans_gca_003991135 Anoxybacter_fermentans_gca_003991135 Anseongella_ginsenosidimutans_gca_004346135 Anseongella_ginsenosidimutans_gca_004346135 Anseongella_ginsenosidimutans_gca_004346135 -ASM259213v1.110 Anser_brachyrhynchus ASM259213v1.110 ASM259213v1.99 Anser_brachyrhynchus ASM259213v1.99 -GooseV1.0.110 Anser_cygnoides GooseV1.0.110 GooseV1.0.99 Anser_cygnoides GooseV1.0.99 Antarcticibacterium_flavum_gca_006159205 Antarcticibacterium_flavum_gca_006159205 Antarcticibacterium_flavum_gca_006159205 Antarcticimicrobium_luteum_gca_004358185 Antarcticimicrobium_luteum_gca_004358185 Antarcticimicrobium_luteum_gca_004358185 @@ -4176,7 +4162,6 @@ Anthracocystis_flocculosa_gca_900322975 Anthracocystis_flocculosa_gca_90032297 Anthracocystis_flocculosa_pf_1_gca_000417875 Anthracocystis_flocculosa_pf_1_gca_000417875 Anthracocystis_flocculosa_pf_1_gca_000417875 Antricoccus_suffuscus_gca_003003235 Antricoccus_suffuscus_gca_003003235 Antricoccus_suffuscus_gca_003003235 Antrodiella_citrinella_gca_004802725 Antrodiella_citrinella_gca_004802725 Antrodiella_citrinella_gca_004802725 -Anan_2.0.110 Aotus_nancymaae Anan_2.0.110 Anan_2.0.99 Aotus_nancymaae Anan_2.0.99 Aphanizomenon_flos_aquae_2012_km1_d3 Aphanizomenon_flos_aquae_2012_km1_d3 Aphanizomenon_flos_aquae_2012_km1_d3 Aphanizomenon_flos_aquae_2012_km1_d3_gca_000789435 Aphanizomenon_flos_aquae_2012_km1_d3_gca_000789435 Aphanizomenon_flos_aquae_2012_km1_d3_gca_000789435 @@ -4231,11 +4216,8 @@ Apis_florea_gca000184785v2rs Apis_florea_gca000184785v2rs Apis_florea_gca000 Apis_mellifera Apis_mellifera Apis_mellifera Aplosporella_prunicola_cbs_121167_gca_010093885 Aplosporella_prunicola_cbs_121167_gca_010093885 Aplosporella_prunicola_cbs_121167_gca_010093885 Aplysia_californica_gca000002075v2 Aplysia_californica_gca000002075v2 Aplysia_californica_gca000002075v2 -aptHaa1.110 Apteryx_haastii aptHaa1.110 aptHaa1.99 Apteryx_haastii aptHaa1.99 -aptOwe1.110 Apteryx_owenii aptOwe1.110 aptOwe1.99 Apteryx_owenii aptOwe1.99 -aptRow1.110 Apteryx_rowi aptRow1.110 aptRow1.99 Apteryx_rowi aptRow1.99 Aquabacter_spiritensis_gca_004346185 Aquabacter_spiritensis_gca_004346185 Aquabacter_spiritensis_gca_004346185 Aquabacterium_commune_gca_004362855 Aquabacterium_commune_gca_004362855 Aquabacterium_commune_gca_004362855 @@ -4260,7 +4242,6 @@ Aquifex_aeolicus_vf5_gca_000008625 Aquifex_aeolicus_vf5_gca_000008625 Aquife Aquifex_sp__gca_003978875 Aquifex_sp__gca_003978875 Aquifex_sp__gca_003978875 Aquificae_bacterium_gca_003697005 Aquificae_bacterium_gca_003697005 Aquificae_bacterium_gca_003697005 Aquiflexum_balticum_dsm_16537_gca_900176595 Aquiflexum_balticum_dsm_16537_gca_900176595 Aquiflexum_balticum_dsm_16537_gca_900176595 -bAquChr1.2.110 Aquila_chrysaetos_chrysaetos bAquChr1.2.110 bAquChr1.2.99 Aquila_chrysaetos_chrysaetos bAquChr1.2.99 Aquimarina_aggregata_gca_001632745 Aquimarina_aggregata_gca_001632745 Aquimarina_aggregata_gca_001632745 Aquimarina_amphilecti_gca_900109375 Aquimarina_amphilecti_gca_900109375 Aquimarina_amphilecti_gca_900109375 @@ -4779,7 +4760,6 @@ Aspergillus_versicolor_cbs_583_65_gca_001890125 Aspergillus_versicolor_cbs_583 Aspergillus_violaceofuscus_cbs_115571_gca_003184705 Aspergillus_violaceofuscus_cbs_115571_gca_003184705 Aspergillus_violaceofuscus_cbs_115571_gca_003184705 Aspergillus_welwitschiae_gca_003344945 Aspergillus_welwitschiae_gca_003344945 Aspergillus_welwitschiae_gca_003344945 Aspergillus_wentii_dto_134e9_gca_001890725 Aspergillus_wentii_dto_134e9_gca_001890725 Aspergillus_wentii_dto_134e9_gca_001890725 -fAstCal1.2.110 Astatotilapia_calliptera fAstCal1.2.110 fAstCal1.2.99 Astatotilapia_calliptera fAstCal1.2.99 Aster_yellows_witches_broom_phytoplasma_aywb Aster_yellows_witches_broom_phytoplasma_aywb Aster_yellows_witches_broom_phytoplasma_aywb Aster_yellows_witches_broom_phytoplasma_aywb_gca_000012225 Aster_yellows_witches_broom_phytoplasma_aywb_gca_000012225 Aster_yellows_witches_broom_phytoplasma_aywb_gca_000012225 @@ -4802,13 +4782,10 @@ Asticcacaulis_sp_ybe204 Asticcacaulis_sp_ybe204 Asticcacaulis_sp_ybe204 Asticcacaulis_sp_ybe204_gca_000495855 Asticcacaulis_sp_ybe204_gca_000495855 Asticcacaulis_sp_ybe204_gca_000495855 Asticcacaulis_taihuensis_gca_900100255 Asticcacaulis_taihuensis_gca_900100255 Asticcacaulis_taihuensis_gca_900100255 AstMex102.75 Astyanax_mexicanus AstMex102.75 -Astyanax_mexicanus-2.0.110 Astyanax_mexicanus Astyanax_mexicanus-2.0.110 Astyanax_mexicanus-2.0.99 Astyanax_mexicanus Astyanax_mexicanus-2.0.99 -Astyanax_mexicanus-1.0.2.110 Astyanax_mexicanus_pachon Astyanax_mexicanus-1.0.2.110 Astyanax_mexicanus-1.0.2.99 Astyanax_mexicanus_pachon Astyanax_mexicanus-1.0.2.99 Athalia_rosae_gca000344095v2 Athalia_rosae_gca000344095v2 Athalia_rosae_gca000344095v2 Athalia_rosae_gca917208135v1 Athalia_rosae_gca917208135v1 Athalia_rosae_gca917208135v1 -athCun1.110 Athene_cunicularia athCun1.110 athCun1.99 Athene_cunicularia athCun1.99 Atlantibacter_hermannii_gca_900635495 Atlantibacter_hermannii_gca_900635495 Atlantibacter_hermannii_gca_900635495 Atlantibacter_hermannii_nbrc_105704 Atlantibacter_hermannii_nbrc_105704 Atlantibacter_hermannii_nbrc_105704 @@ -7303,7 +7280,6 @@ Bactrocera_latifrons_gca001853355v1 Bactrocera_latifrons_gca001853355v1 Bact Bactrocera_tryoni_gca016617805v2 Bactrocera_tryoni_gca016617805v2 Bactrocera_tryoni_gca016617805v2 Baia_soyae_gca_004341445 Baia_soyae_gca_004341445 Baia_soyae_gca_004341445 Bailinhaonella_thermotolerans_gca_003594875 Bailinhaonella_thermotolerans_gca_003594875 Bailinhaonella_thermotolerans_gca_003594875 -mBalMus1.v2.110 Balaenoptera_musculus mBalMus1.v2.110 Balneicella_halophila_gca_003096835 Balneicella_halophila_gca_003096835 Balneicella_halophila_gca_003096835 Balneola_sp__gca_002694685 Balneola_sp__gca_002694685 Balneola_sp__gca_002694685 Balneola_sp__gca_002696035 Balneola_sp__gca_002696035 Balneola_sp__gca_002696035 @@ -7568,7 +7544,6 @@ Betaproteobacteria_bacterium_scgc_ag_212_j23 Betaproteobacteria_bacterium_scgc Betaproteobacteria_bacterium_sg8_41_gca_001303585 Betaproteobacteria_bacterium_sg8_41_gca_001303585 Betaproteobacteria_bacterium_sg8_41_gca_001303585 Betaproteobacteria_bacterium_ukl13_2 Betaproteobacteria_bacterium_ukl13_2 Betaproteobacteria_bacterium_ukl13_2 Betaproteobacteria_bacterium_ukl13_2_gca_001602455 Betaproteobacteria_bacterium_ukl13_2_gca_001602455 Betaproteobacteria_bacterium_ukl13_2_gca_001602455 -fBetSpl5.2.110 Betta_splendens fBetSpl5.2.110 fBetSpl5.2.99 Betta_splendens fBetSpl5.2.99 Beutenbergia_cavernae_dsm_12333 Beutenbergia_cavernae_dsm_12333 Beutenbergia_cavernae_dsm_12333 Beutenbergia_cavernae_dsm_12333_gca_000023105 Beutenbergia_cavernae_dsm_12333_gca_000023105 Beutenbergia_cavernae_dsm_12333_gca_000023105 @@ -8077,7 +8052,6 @@ Bipolaris_sorokiniana_nd90pr_gca_000338995 Bipolaris_sorokiniana_nd90pr_gca_00 Bipolaris_victoriae_fi3_gca_000527765 Bipolaris_victoriae_fi3_gca_000527765 Bipolaris_victoriae_fi3_gca_000527765 Bipolaris_zeicola_26_r_13_gca_000523435 Bipolaris_zeicola_26_r_13_gca_000523435 Bipolaris_zeicola_26_r_13_gca_000523435 Bisgaardia_hudsonensis_gca_004345785 Bisgaardia_hudsonensis_gca_004345785 Bisgaardia_hudsonensis_gca_004345785 -Bison_UMD1.0.110 Bison_bison_bison Bison_UMD1.0.110 Bison_UMD1.0.99 Bison_bison_bison Bison_UMD1.0.99 Bizionia_argentinensis_jub59 Bizionia_argentinensis_jub59 Bizionia_argentinensis_jub59 Bizionia_echini_gca_900115185 Bizionia_echini_gca_900115185 Bizionia_echini_gca_900115185 @@ -8775,16 +8749,11 @@ Borreliella_spielmanii_a14s_gca_000181895 Borreliella_spielmanii_a14s_gca_0001 Borreliella_valaisiana_tom4006 Borreliella_valaisiana_tom4006 Borreliella_valaisiana_tom4006 Borreliella_valaisiana_vs116 Borreliella_valaisiana_vs116 Borreliella_valaisiana_vs116 Borreliella_valaisiana_vs116_gca_000170955 Borreliella_valaisiana_vs116_gca_000170955 Borreliella_valaisiana_vs116_gca_000170955 -LU_Bosgru_v3.0.110 Bos_grunniens LU_Bosgru_v3.0.110 LU_Bosgru_v3.0.99 Bos_grunniens LU_Bosgru_v3.0.99 -UOA_Brahman_1.110 Bos_indicus_hybrid UOA_Brahman_1.110 UOA_Brahman_1.99 Bos_indicus_hybrid UOA_Brahman_1.99 -BosGru_v2.0.110 Bos_mutus BosGru_v2.0.110 BosGru_v2.0.99 Bos_mutus BosGru_v2.0.99 -ARS-UCD1.2.110 Bos_taurus ARS-UCD1.2.110 ARS-UCD1.2.99 Bos_taurus ARS-UCD1.2.99 UMD3.1.75 Bos_taurus UMD3.1.75 -UOA_Angus_1.110 Bos_taurus_hybrid UOA_Angus_1.110 UOA_Angus_1.99 Bos_taurus_hybrid UOA_Angus_1.99 Bosea_caraganae_gca_003351325 Bosea_caraganae_gca_003351325 Bosea_caraganae_gca_003351325 Bosea_lathyri_gca_900108245 Bosea_lathyri_gca_900108245 Bosea_lathyri_gca_900108245 @@ -9667,7 +9636,6 @@ KJ473813.1 BtRf-BetaCoV/SX2013, KJ473813.1 KJ473815.1 BtRs-BetaCoV/GX2013, KJ473815.1 KJ473814.1 BtRs-BetaCoV/HuB2013, KJ473814.1 KJ473816.1 BtRs-BetaCoV/YN2013, KJ473816.1 -BubBub1.0.110 Bubo_bubo BubBub1.0.110 Buchananella_hordeovulneris_gca_001907235 Buchananella_hordeovulneris_gca_001907235 Buchananella_hordeovulneris_gca_001907235 Buchananella_hordeovulneris_gca_003858505 Buchananella_hordeovulneris_gca_003858505 Buchananella_hordeovulneris_gca_003858505 Buchnera_aphidicola_aphis_glycines_ Buchnera_aphidicola_aphis_glycines_ Buchnera_aphidicola_aphis_glycines_ @@ -10485,7 +10453,6 @@ Burkholderiales_bacterium_rifoxyc12_full_65_23_gca_001770995 Burkholderiales_b Burkholderiales_bacterium_rifoxyd12_full_59_19_gca_001771065 Burkholderiales_bacterium_rifoxyd12_full_59_19_gca_001771065 Burkholderiales_bacterium_rifoxyd12_full_59_19_gca_001771065 Burkholderiales_bacterium_yl45 Burkholderiales_bacterium_yl45 Burkholderiales_bacterium_yl45 Burkholderiales_bacterium_yl45_gca_001688905 Burkholderiales_bacterium_yl45_gca_001688905 Burkholderiales_bacterium_yl45_gca_001688905 -ButJap1.0.110 Buteo_japonicus ButJap1.0.110 Buttiauxella_agrestis_atcc_33320 Buttiauxella_agrestis_atcc_33320 Buttiauxella_agrestis_atcc_33320 Buttiauxella_agrestis_atcc_33320_gca_000735355 Buttiauxella_agrestis_atcc_33320_gca_000735355 Buttiauxella_agrestis_atcc_33320_gca_000735355 Buttiauxella_agrestis_gca_900446255 Buttiauxella_agrestis_gca_900446255 Buttiauxella_agrestis_gca_900446255 @@ -10599,12 +10566,10 @@ Caenispirillum_salinarum_ak4_gca_000315795 Caenispirillum_salinarum_ak4_gca_00 Caenorhabditis_brenneri Caenorhabditis_brenneri Caenorhabditis_brenneri Caenorhabditis_briggsae Caenorhabditis_briggsae Caenorhabditis_briggsae Caenorhabditis_elegans Caenorhabditis_elegans Caenorhabditis_elegans -WBcel235.110 Caenorhabditis_elegans WBcel235.110 WBcel235.75 Caenorhabditis_elegans WBcel235.75 WBcel235.99 Caenorhabditis_elegans WBcel235.99 Caenorhabditis_japonica Caenorhabditis_japonica Caenorhabditis_japonica Caenorhabditis_remanei Caenorhabditis_remanei Caenorhabditis_remanei -CaiMos1.0.110 Cairina_moschata_domestica CaiMos1.0.110 Cajanus_cajan Cajanus_cajan Cajanus_cajan Caldalkalibacillus_thermarum_ta2_a1 Caldalkalibacillus_thermarum_ta2_a1 Caldalkalibacillus_thermarum_ta2_a1 Caldalkalibacillus_thermarum_ta2_a1_gca_000218765 Caldalkalibacillus_thermarum_ta2_a1_gca_000218765 Caldalkalibacillus_thermarum_ta2_a1_gca_000218765 @@ -10681,14 +10646,10 @@ Caldivirga_sp_mg_3 Caldivirga_sp_mg_3 Caldivirga_sp_mg_3 Calidifontibacter_indicus_gca_003386865 Calidifontibacter_indicus_gca_003386865 Calidifontibacter_indicus_gca_003386865 Calidithermus_roseus_gca_003574095 Calidithermus_roseus_gca_003574095 Calidithermus_roseus_gca_003574095 Calidithermus_terrae_gca_003574345 Calidithermus_terrae_gca_003574345 Calidithermus_terrae_gca_003574345 -ASM143184v1.110 Calidris_pugnax ASM143184v1.110 ASM143184v1.99 Calidris_pugnax ASM143184v1.99 -ASM369795v1.110 Calidris_pygmaea ASM369795v1.110 ASM369795v1.99 Calidris_pygmaea ASM369795v1.99 ASM275486v1.99 Callithrix_jacchus ASM275486v1.99 C_jacchus3.2.1.75 Callithrix_jacchus C_jacchus3.2.1.75 -mCalJac1.pat.X.110 Callithrix_jacchus mCalJac1.pat.X.110 -Callorhinchus_milii-6.1.3.110 Callorhinchus_milii Callorhinchus_milii-6.1.3.110 Callorhinchus_milii-6.1.3.99 Callorhinchus_milii Callorhinchus_milii-6.1.3.99 Calocera_cornea_hhb12733_gca_001632435 Calocera_cornea_hhb12733_gca_001632435 Calocera_cornea_hhb12733_gca_001632435 Calocera_viscosa_tufc12733_gca_001630345 Calocera_viscosa_tufc12733_gca_001630345 Calocera_viscosa_tufc12733_gca_001630345 @@ -10720,10 +10681,8 @@ Calothrix_sp_pcc_6303 Calothrix_sp_pcc_6303 Calothrix_sp_pcc_6303 Calothrix_sp_pcc_6303_gca_000317435 Calothrix_sp_pcc_6303_gca_000317435 Calothrix_sp_pcc_6303_gca_000317435 Calothrix_sp_pcc_7507 Calothrix_sp_pcc_7507 Calothrix_sp_pcc_7507 Calothrix_sp_pcc_7507_gca_000316575 Calothrix_sp_pcc_7507_gca_000316575 Calothrix_sp_pcc_7507_gca_000316575 -Camarhynchus_parvulus_V1.1.110 Camarhynchus_parvulus Camarhynchus_parvulus_V1.1.110 Camelimonas_lactis_gca_004342915 Camelimonas_lactis_gca_004342915 Camelimonas_lactis_gca_004342915 Camelina_sativa Camelina_sativa Camelina_sativa -CamDro2.110 Camelus_dromedarius CamDro2.110 CamDro2.99 Camelus_dromedarius CamDro2.99 Caminibacter_mediatlanticus_tb_2 Caminibacter_mediatlanticus_tb_2 Caminibacter_mediatlanticus_tb_2 Caminibacter_mediatlanticus_tb_2_gca_005843985 Caminibacter_mediatlanticus_tb_2_gca_005843985 Caminibacter_mediatlanticus_tb_2_gca_005843985 @@ -12896,15 +12855,9 @@ Candidimonas_sp_syp_b2681_gca_003971065 Candidimonas_sp_syp_b2681_gca_00397106 Canicola_haemoglobinophilus_gca_900450725 Canicola_haemoglobinophilus_gca_900450725 Canicola_haemoglobinophilus_gca_900450725 CanFam3.1.75 Canis_familiaris CanFam3.1.75 CanFam3.1.99 Canis_familiaris CanFam3.1.99 -ASM325472v1.110 Canis_lupus_dingo ASM325472v1.110 ASM325472v1.99 Canis_lupus_dingo ASM325472v1.99 -ROS_Cfam_1.0.110 Canis_lupus_familiaris ROS_Cfam_1.0.110 -Basenji_breed-1.1.110 Canis_lupus_familiarisbasenji Basenji_breed-1.1.110 Basenji_breed-1.1.99 Canis_lupus_familiarisbasenji Basenji_breed-1.1.99 -Dog10K_Boxer_Tasha.110 Canis_lupus_familiarisboxer Dog10K_Boxer_Tasha.110 -UMICH_Zoey_3.1.110 Canis_lupus_familiarisgreatdane UMICH_Zoey_3.1.110 UMICH_Zoey_3.1.99 Canis_lupus_familiarisgreatdane UMICH_Zoey_3.1.99 -UU_Cfam_GSD_1.0.110 Canis_lupus_familiarisgsd UU_Cfam_GSD_1.0.110 Cannabis_sativa_female Cannabis_sativa_female Cannabis_sativa_female Capitella_teleta Capitella_teleta Capitella_teleta Capnocytophaga_canimorsus Capnocytophaga_canimorsus Capnocytophaga_canimorsus @@ -12973,16 +12926,13 @@ Capnocytophaga_sputigena_gca_002302595 Capnocytophaga_sputigena_gca_002302595 Capnocytophaga_sputigena_gca_002312885 Capnocytophaga_sputigena_gca_002312885 Capnocytophaga_sputigena_gca_002312885 Capnocytophaga_sputigena_gca_900638125 Capnocytophaga_sputigena_gca_900638125 Capnocytophaga_sputigena_gca_900638125 Capnocytophaga_stomatis_gca_002302635 Capnocytophaga_stomatis_gca_002302635 Capnocytophaga_stomatis_gca_002302635 -ARS1.110 Capra_hircus ARS1.110 ARS1.99 Capra_hircus ARS1.99 -CVASU_BBG_1.0.110 Capra_hircus_blackbengal CVASU_BBG_1.0.110 Caproiciproducens_sp_njn_50_gca_004103755 Caproiciproducens_sp_njn_50_gca_004103755 Caproiciproducens_sp_njn_50_gca_004103755 Capronia_coronata_cbs_617_96_gca_000585585 Capronia_coronata_cbs_617_96_gca_000585585 Capronia_coronata_cbs_617_96_gca_000585585 Capronia_epimyces_cbs_606_96_gca_000585565 Capronia_epimyces_cbs_606_96_gca_000585565 Capronia_epimyces_cbs_606_96_gca_000585565 Capsaspora_owczarzaki_atcc_30864_gca_000151315 Capsaspora_owczarzaki_atcc_30864_gca_000151315 Capsaspora_owczarzaki_atcc_30864_gca_000151315 Capsicum_annuum Capsicum_annuum Capsicum_annuum Capsulimonas_corticalis_gca_003574315 Capsulimonas_corticalis_gca_003574315 Capsulimonas_corticalis_gca_003574315 -ASM336829v1.110 Carassius_auratus ASM336829v1.110 Carbonactinospora_thermoautotrophica_gca_001543895 Carbonactinospora_thermoautotrophica_gca_001543895 Carbonactinospora_thermoautotrophica_gca_001543895 Carbonactinospora_thermoautotrophica_gca_001543925 Carbonactinospora_thermoautotrophica_gca_001543925 Carbonactinospora_thermoautotrophica_gca_001543925 Carboxydocella_sporoproducens_dsm_16521_gca_900167165 Carboxydocella_sporoproducens_dsm_16521_gca_900167165 Carboxydocella_sporoproducens_dsm_16521_gca_900167165 @@ -13000,7 +12950,6 @@ Cardiobacterium_valvarum_f0432 Cardiobacterium_valvarum_f0432 Cardiobacteriu Cardiobacterium_valvarum_f0432_gca_000239355 Cardiobacterium_valvarum_f0432_gca_000239355 Cardiobacterium_valvarum_f0432_gca_000239355 Cardiobacterium_valvarum_gca_900460955 Cardiobacterium_valvarum_gca_900460955 Cardiobacterium_valvarum_gca_900460955 Carideicomes_alvinocaridis_gca_005473895 Carideicomes_alvinocaridis_gca_005473895 Carideicomes_alvinocaridis_gca_005473895 -Tarsius_syrichta-2.0.1.110 Carlito_syrichta Tarsius_syrichta-2.0.1.110 Tarsius_syrichta-2.0.1.99 Carlito_syrichta Tarsius_syrichta-2.0.1.99 Carnobacterium_alterfunditum_gca_900143105 Carnobacterium_alterfunditum_gca_900143105 Carnobacterium_alterfunditum_gca_900143105 Carnobacterium_divergens_dsm_20623 Carnobacterium_divergens_dsm_20623 Carnobacterium_divergens_dsm_20623 @@ -13030,10 +12979,8 @@ Caryophanon_tenue Caryophanon_tenue Caryophanon_tenue Caryophanon_tenue_gca_001700315 Caryophanon_tenue_gca_001700315 Caryophanon_tenue_gca_001700315 Castellaniella_defragrans_65phen Castellaniella_defragrans_65phen Castellaniella_defragrans_65phen Castellaniella_defragrans_65phen_gca_000612685 Castellaniella_defragrans_65phen_gca_000612685 Castellaniella_defragrans_65phen_gca_000612685 -C.can_genome_v1.0.110 Castor_canadensis C.can_genome_v1.0.110 C.can_genome_v1.0.99 Castor_canadensis C.can_genome_v1.0.99 Catabacter_hongkongensis Catabacter_hongkongensis Catabacter_hongkongensis -CatWag_v2_BIUU_UCD.110 Catagonus_wagneri CatWag_v2_BIUU_UCD.110 CatWag_v2_BIUU_UCD.99 Catagonus_wagneri CatWag_v2_BIUU_UCD.99 Catalinimonas_alkaloidigena_gca_900100765 Catalinimonas_alkaloidigena_gca_900100765 Catalinimonas_alkaloidigena_gca_900100765 Catellatospora_citrea_gca_003610235 Catellatospora_citrea_gca_003610235 Catellatospora_citrea_gca_003610235 @@ -13051,7 +12998,6 @@ Catenovulum_agarivorans_ds_2_gca_000568405 Catenovulum_agarivorans_ds_2_gca_00 Catenovulum_maritimum_gca_001050375 Catenovulum_maritimum_gca_001050375 Catenovulum_maritimum_gca_001050375 Catenulispora_acidiphila_dsm_44928 Catenulispora_acidiphila_dsm_44928 Catenulispora_acidiphila_dsm_44928 Catenulispora_acidiphila_dsm_44928_gca_000024025 Catenulispora_acidiphila_dsm_44928_gca_000024025 Catenulispora_acidiphila_dsm_44928_gca_000024025 -bCatUst1.pri.110 Catharus_ustulatus bCatUst1.pri.110 Catonella_morbi_atcc_51271 Catonella_morbi_atcc_51271 Catonella_morbi_atcc_51271 Catonella_morbi_atcc_51271_gca_000160035 Catonella_morbi_atcc_51271_gca_000160035 Catonella_morbi_atcc_51271_gca_000160035 Caulobacter_crescentus_cb15 Caulobacter_crescentus_cb15 Caulobacter_crescentus_cb15 @@ -13109,14 +13055,11 @@ Caulobacterales_bacterium_rifcsphigho2_01_full_70_19_gca_001794825 Caulobacter Caulochytrium_protostelioides_gca_003615035 Caulochytrium_protostelioides_gca_003615035 Caulochytrium_protostelioides_gca_003615035 Caulochytrium_protostelioides_gca_003615045 Caulochytrium_protostelioides_gca_003615045 Caulochytrium_protostelioides_gca_003615045 Cavenderia_fasciculata_gca_000203815 Cavenderia_fasciculata_gca_000203815 Cavenderia_fasciculata_gca_000203815 -CavAp1.0.110 Cavia_aperea CavAp1.0.110 CavAp1.0.99 Cavia_aperea CavAp1.0.99 -Cavpor3.0.110 Cavia_porcellus Cavpor3.0.110 Cavpor3.0.99 Cavia_porcellus Cavpor3.0.99 cavPor3.75 Cavia_porcellus cavPor3.75 Caviibacterium_pharyngocola_gca_002795405 Caviibacterium_pharyngocola_gca_002795405 Caviibacterium_pharyngocola_gca_002795405 Cebus_imitator-1.0.99 Cebus_capucinus Cebus_imitator-1.0.99 -Cebus_imitator-1.0.110 Cebus_imitator Cebus_imitator-1.0.110 Cecembia_calidifontis_gca_004216715 Cecembia_calidifontis_gca_004216715 Cecembia_calidifontis_gca_004216715 Cecembia_lonarensis_lw9 Cecembia_lonarensis_lw9 Cecembia_lonarensis_lw9 Cecembia_lonarensis_lw9_gca_000298295 Cecembia_lonarensis_lw9_gca_000298295 Cecembia_lonarensis_lw9_gca_000298295 @@ -13244,7 +13187,6 @@ Ceraceosorus_guamensis_gca_003144195 Ceraceosorus_guamensis_gca_003144195 Ce Ceratitis_capitata_gca000347755v4 Ceratitis_capitata_gca000347755v4 Ceratitis_capitata_gca000347755v4 Ceratobasidium_theobromae_gca_009078325 Ceratobasidium_theobromae_gca_009078325 Ceratobasidium_theobromae_gca_009078325 Ceratocystis_platani_gca_000978885 Ceratocystis_platani_gca_000978885 Ceratocystis_platani_gca_000978885 -Caty_1.0.110 Cercocebus_atys Caty_1.0.110 Caty_1.0.99 Cercocebus_atys Caty_1.0.99 Cercospora_berteroae_gca_002933655 Cercospora_berteroae_gca_002933655 Cercospora_berteroae_gca_002933655 Cercospora_beticola_gca_002742065 Cercospora_beticola_gca_002742065 Cercospora_beticola_gca_002742065 @@ -13261,7 +13203,6 @@ Cereibacter_sphaeroides_f_sp_denitrificans_gca_003363065 Cereibacter_sphaeroid Cereibacter_sphaeroides_gca_003243455 Cereibacter_sphaeroides_gca_003243455 Cereibacter_sphaeroides_gca_003243455 Cereibacter_sphaeroides_gca_003846425 Cereibacter_sphaeroides_gca_003846425 Cereibacter_sphaeroides_gca_003846425 Cereibacter_sphaeroides_kd131_gca_000021005 Cereibacter_sphaeroides_kd131_gca_000021005 Cereibacter_sphaeroides_kd131_gca_000021005 -CEY_v1.110 Cervus_hanglu_yarkandensis CEY_v1.110 Cesiribacter_andamanensis_amv16 Cesiribacter_andamanensis_amv16 Cesiribacter_andamanensis_amv16 Cesiribacter_andamanensis_amv16_gca_000348925 Cesiribacter_andamanensis_amv16_gca_000348925 Cesiribacter_andamanensis_amv16_gca_000348925 Cetobacterium_ceti_gca_900167275 Cetobacterium_ceti_gca_900167275 Cetobacterium_ceti_gca_900167275 @@ -13290,15 +13231,12 @@ Chelatococcus_sp_co_6 Chelatococcus_sp_co_6 Chelatococcus_sp_co_6 Chelatococcus_sp_co_6_gca_001271345 Chelatococcus_sp_co_6_gca_001271345 Chelatococcus_sp_co_6_gca_001271345 Chelonobacter_oris Chelonobacter_oris Chelonobacter_oris Chelonobacter_oris_gca_000772535 Chelonobacter_oris_gca_000772535 Chelonobacter_oris_gca_000772535 -ASM359739v1.110 Chelonoidis_abingdonii ASM359739v1.110 ASM359739v1.99 Chelonoidis_abingdonii ASM359739v1.99 Chelonus_insularis_gca013357705v1rs Chelonus_insularis_gca013357705v1rs Chelonus_insularis_gca013357705v1rs -Chelydra_serpentina-1.0.110 Chelydra_serpentina Chelydra_serpentina-1.0.110 Chenopodium_quinoa Chenopodium_quinoa Chenopodium_quinoa Chimaeribacter_arupi_gca_002858825 Chimaeribacter_arupi_gca_002858825 Chimaeribacter_arupi_gca_002858825 Chimaeribacter_californicus_gca_002858675 Chimaeribacter_californicus_gca_002858675 Chimaeribacter_californicus_gca_002858675 Chimaeribacter_coloradensis_gca_002858715 Chimaeribacter_coloradensis_gca_002858715 Chimaeribacter_coloradensis_gca_002858715 -ChiLan1.0.110 Chinchilla_lanigera ChiLan1.0.110 ChiLan1.0.99 Chinchilla_lanigera ChiLan1.0.99 Chishuiella_changwenlii_gca_900142565 Chishuiella_changwenlii_gca_900142565 Chishuiella_changwenlii_gca_900142565 Chitinasiproducens_palmae_gca_900095735 Chitinasiproducens_palmae_gca_900095735 Chitinasiproducens_palmae_gca_900095735 @@ -13621,7 +13559,6 @@ Chlorobium_phaeovibrioides_gca_003968655 Chlorobium_phaeovibrioides_gca_003968 Chlorobium_sp_gbchlb Chlorobium_sp_gbchlb Chlorobium_sp_gbchlb Chlorobium_sp_n1_gca_004332115 Chlorobium_sp_n1_gca_004332115 Chlorobium_sp_n1_gca_004332115 Chlorobium_tepidum_tls Chlorobium_tepidum_tls Chlorobium_tepidum_tls -ChlSab1.1.110 Chlorocebus_sabaeus ChlSab1.1.110 ChlSab1.1.99 Chlorocebus_sabaeus ChlSab1.1.99 Chloroflexi_bacterium_13_1_40cm_65_17_gca_001917815 Chloroflexi_bacterium_13_1_40cm_65_17_gca_001917815 Chloroflexi_bacterium_13_1_40cm_65_17_gca_001917815 Chloroflexi_bacterium_44_23_gca_001899005 Chloroflexi_bacterium_44_23_gca_001899005 Chloroflexi_bacterium_44_23_gca_001899005 @@ -13735,7 +13672,6 @@ Chloroherpeton_thalassium_atcc_35110 Chloroherpeton_thalassium_atcc_35110 Ch Chloroherpeton_thalassium_atcc_35110_gca_000020525 Chloroherpeton_thalassium_atcc_35110_gca_000020525 Chloroherpeton_thalassium_atcc_35110_gca_000020525 Choanephora_cucurbitarum_gca_001683725 Choanephora_cucurbitarum_gca_001683725 Choanephora_cucurbitarum_gca_001683725 Choiromyces_venosus_120613_1_gca_003788595 Choiromyces_venosus_120613_1_gca_003788595 Choiromyces_venosus_120613_1_gca_003788595 -choHof1.110 Choloepus_hoffmanni choHof1.110 choHof1.75 Choloepus_hoffmanni choHof1.75 choHof1.99 Choloepus_hoffmanni choHof1.99 Chondrocystis_sp_nies_4102_gca_002368355 Chondrocystis_sp_nies_4102_gca_002368355 Chondrocystis_sp_nies_4102_gca_002368355 @@ -13800,7 +13736,6 @@ Chroococcidiopsis_thermalis_pcc_7203 Chroococcidiopsis_thermalis_pcc_7203 Ch Chroococcidiopsis_thermalis_pcc_7203_gca_000317125 Chroococcidiopsis_thermalis_pcc_7203_gca_000317125 Chroococcidiopsis_thermalis_pcc_7203_gca_000317125 Chroogloeocystis_siderophila_5_2_s_c_1_gca_001904655 Chroogloeocystis_siderophila_5_2_s_c_1_gca_001904655 Chroogloeocystis_siderophila_5_2_s_c_1_gca_001904655 Chroomonas_mesostigmatica_ccmp1168_gca_000286095 Chroomonas_mesostigmatica_ccmp1168_gca_000286095 Chroomonas_mesostigmatica_ccmp1168_gca_000286095 -Chrysemys_picta_bellii-3.0.3.110 Chrysemys_picta_bellii Chrysemys_picta_bellii-3.0.3.110 Chrysemys_picta_bellii-3.0.3.99 Chrysemys_picta_bellii Chrysemys_picta_bellii-3.0.3.99 Chryseobacterium_angstadtii Chryseobacterium_angstadtii Chryseobacterium_angstadtii Chryseobacterium_angstadtii_gca_001045465 Chryseobacterium_angstadtii_gca_001045465 Chryseobacterium_angstadtii_gca_001045465 @@ -13978,7 +13913,6 @@ Chryseolinea_serpens_gca_900129725 Chryseolinea_serpens_gca_900129725 Chryse Chryseolinea_soli_gca_003589925 Chryseolinea_soli_gca_003589925 Chryseolinea_soli_gca_003589925 Chryseomicrobium_excrementi_gca_002798305 Chryseomicrobium_excrementi_gca_002798305 Chryseomicrobium_excrementi_gca_002798305 Chryseotalea_sanaruensis_gca_003990915 Chryseotalea_sanaruensis_gca_003990915 Chryseotalea_sanaruensis_gca_003990915 -Chrysolophus_pictus_GenomeV1.0.110 Chrysolophus_pictus Chrysolophus_pictus_GenomeV1.0.110 Chrysolophus_pictus_GenomeV1.0.99 Chrysolophus_pictus Chrysolophus_pictus_GenomeV1.0.99 Chrysosporum_ovalisporum Chrysosporum_ovalisporum Chrysosporum_ovalisporum Chrysosporum_ovalisporum_gca_001458455 Chrysosporum_ovalisporum_gca_001458455 Chrysosporum_ovalisporum_gca_001458455 @@ -13995,10 +13929,8 @@ Ciceribacter_lividus_gca_003337715 Ciceribacter_lividus_gca_003337715 Ciceri Ciceribacter_naphthalenivorans_gca_900492205 Ciceribacter_naphthalenivorans_gca_900492205 Ciceribacter_naphthalenivorans_gca_900492205 Ciceribacter_selenitireducens_atcc_baa_1503_gca_900492185 Ciceribacter_selenitireducens_atcc_baa_1503_gca_900492185 Ciceribacter_selenitireducens_atcc_baa_1503_gca_900492185 Cimex_lectularius Cimex_lectularius Cimex_lectularius -KH.110 Ciona_intestinalis KH.110 KH.75 Ciona_intestinalis KH.75 KH.99 Ciona_intestinalis KH.99 -CSAV2.0.110 Ciona_savignyi CSAV2.0.110 CSAV2.0.75 Ciona_savignyi CSAV2.0.75 CSAV2.0.99 Ciona_savignyi CSAV2.0.99 Citreicella_sp_357 Citreicella_sp_357 Citreicella_sp_357 @@ -15107,7 +15039,6 @@ Clostridium_tyrobutyricum_divetgp_gca_000577845 Clostridium_tyrobutyricum_dive Clostridium_tyrobutyricum_gca_004924375 Clostridium_tyrobutyricum_gca_004924375 Clostridium_tyrobutyricum_gca_004924375 Clostridium_uliginosum_gca_900112485 Clostridium_uliginosum_gca_900112485 Clostridium_uliginosum_gca_900112485 Clostridium_vincentii_gca_002995745 Clostridium_vincentii_gca_002995745 Clostridium_vincentii_gca_002995745 -Ch_v2.0.2.110 Clupea_harengus Ch_v2.0.2.110 Ch_v2.0.2.99 Clupea_harengus Ch_v2.0.2.99 Clytia_hemisphaerica_gca902728285 Clytia_hemisphaerica_gca902728285 Clytia_hemisphaerica_gca902728285 Cnuella_takakiae_gca_900129015 Cnuella_takakiae_gca_900129015 Cnuella_takakiae_gca_900129015 @@ -15200,7 +15131,6 @@ Collinsella_intestinalis_dsm_13280 Collinsella_intestinalis_dsm_13280 Collin Collinsella_sp_4_8_47faa Collinsella_sp_4_8_47faa Collinsella_sp_4_8_47faa Collinsella_stercoris_dsm_13279 Collinsella_stercoris_dsm_13279 Collinsella_stercoris_dsm_13279 Collinsella_tanakaei_yit_12063 Collinsella_tanakaei_yit_12063 Collinsella_tanakaei_yit_12063 -Cang.pa_1.0.110 Colobus_angolensis_palliatus Cang.pa_1.0.110 Cang.pa_1.0.99 Colobus_angolensis_palliatus Cang.pa_1.0.99 Colwellia_chukchiensis_gca_900109795 Colwellia_chukchiensis_gca_900109795 Colwellia_chukchiensis_gca_900109795 Colwellia_marinimaniae_gca_002207865 Colwellia_marinimaniae_gca_002207865 Colwellia_marinimaniae_gca_002207865 @@ -15450,7 +15380,6 @@ Coriobacteriaceae_bacterium_gca_004793925 Coriobacteriaceae_bacterium_gca_0047 Coriobacteriales_bacterium_dnf00809 Coriobacteriales_bacterium_dnf00809 Coriobacteriales_bacterium_dnf00809 Coriobacterium_glomerans_pw2 Coriobacterium_glomerans_pw2 Coriobacterium_glomerans_pw2 Corticibacter_populi_gca_003703815 Corticibacter_populi_gca_003703815 Corticibacter_populi_gca_003703815 -bCorMon1.pri.110 Corvus_moneduloides bCorMon1.pri.110 Corylus_avellana Corylus_avellana Corylus_avellana Corymbia_citriodora Corymbia_citriodora Corymbia_citriodora Corynebacterium_accolens_atcc_49725 Corynebacterium_accolens_atcc_49725 Corynebacterium_accolens_atcc_49725 @@ -15820,9 +15749,7 @@ Corynebacterium_yudongzhengii_gca_003113335 Corynebacterium_yudongzhengii_gca_ Corynespora_cassiicola_philippines_gca_003016335 Corynespora_cassiicola_philippines_gca_003016335 Corynespora_cassiicola_philippines_gca_003016335 Cosenzaea_myxofaciens_atcc_19692 Cosenzaea_myxofaciens_atcc_19692 Cosenzaea_myxofaciens_atcc_19692 Cotesia_glomerata_gca020080835v1 Cotesia_glomerata_gca020080835v1 Cotesia_glomerata_gca020080835v1 -fCotGob3.1.110 Cottoperca_gobio fCotGob3.1.110 fCotGob3.1.99 Cottoperca_gobio fCotGob3.1.99 -Coturnix_japonica_2.0.110 Coturnix_japonica Coturnix_japonica_2.0.110 Coturnix_japonica_2.0.99 Coturnix_japonica Coturnix_japonica_2.0.99 Couchioplanes_caeruleus_gca_003751945 Couchioplanes_caeruleus_gca_003751945 Couchioplanes_caeruleus_gca_003751945 Couchioplanes_caeruleus_subsp_caeruleus_gca_001884705 Couchioplanes_caeruleus_subsp_caeruleus_gca_001884705 Couchioplanes_caeruleus_subsp_caeruleus_gca_001884705 @@ -15865,12 +15792,9 @@ Criblamydia_sequanensis_crib_18 Criblamydia_sequanensis_crib_18 Criblamydia_ Criblamydia_sequanensis_crib_18_gca_000750955 Criblamydia_sequanensis_crib_18_gca_000750955 Criblamydia_sequanensis_crib_18_gca_000750955 Cribrihabitans_marinus_gca_900109035 Cribrihabitans_marinus_gca_900109035 Cribrihabitans_marinus_gca_900109035 Cricetibacter_osteomyelitidis_gca_004340985 Cricetibacter_osteomyelitidis_gca_004340985 Cricetibacter_osteomyelitidis_gca_004340985 -CHOK1GS_HDv1.110 Cricetulus_griseus_chok1gshd CHOK1GS_HDv1.110 CHOK1GS_HDv1.99 Cricetulus_griseus_chok1gshd CHOK1GS_HDv1.99 -CriGri_1.0.110 Cricetulus_griseus_crigri CriGri_1.0.110 CriGri_1.0.99 Cricetulus_griseus_crigri CriGri_1.0.99 CriGri-PICR.99 Cricetulus_griseus_picr CriGri-PICR.99 -CriGri-PICRH-1.0.110 Cricetulus_griseus_picr CriGri-PICRH-1.0.110 Criibacterium_bergeronii_gca_001693775 Criibacterium_bergeronii_gca_001693775 Criibacterium_bergeronii_gca_001693775 Crinalium_epipsammum_pcc_9333 Crinalium_epipsammum_pcc_9333 Crinalium_epipsammum_pcc_9333 Crinalium_epipsammum_pcc_9333_gca_000317495 Crinalium_epipsammum_pcc_9333_gca_000317495 Crinalium_epipsammum_pcc_9333_gca_000317495 @@ -15895,7 +15819,6 @@ Crocinitomicaceae_bacterium_gca_002713215 Crocinitomicaceae_bacterium_gca_0027 Crocinitomicaceae_bacterium_gca_002723085 Crocinitomicaceae_bacterium_gca_002723085 Crocinitomicaceae_bacterium_gca_002723085 Crocinitomicaceae_bacterium_tmed16_gca_002167775 Crocinitomicaceae_bacterium_tmed16_gca_002167775 Crocinitomicaceae_bacterium_tmed16_gca_002167775 Crocinitomicaceae_bacterium_tmed209_gca_002170625 Crocinitomicaceae_bacterium_tmed209_gca_002170625 Crocinitomicaceae_bacterium_tmed209_gca_002170625 -CroPor_comp1.110 Crocodylus_porosus CroPor_comp1.110 CroPor_comp1.99 Crocodylus_porosus CroPor_comp1.99 Crocosphaera_subtropica_atcc_51142_gca_000017845 Crocosphaera_subtropica_atcc_51142_gca_000017845 Crocosphaera_subtropica_atcc_51142_gca_000017845 Crocosphaera_watsonii_wh_0003 Crocosphaera_watsonii_wh_0003 Crocosphaera_watsonii_wh_0003 @@ -16272,7 +16195,6 @@ Cutibacterium_granulosum_tm11 Cutibacterium_granulosum_tm11 Cutibacterium_gr Cutibacterium_modestum_hl044pa1_gca_000144085 Cutibacterium_modestum_hl044pa1_gca_000144085 Cutibacterium_modestum_hl044pa1_gca_000144085 Cutibacterium_modestum_p08_gca_000204235 Cutibacterium_modestum_p08_gca_000204235 Cutibacterium_modestum_p08_gca_000204235 Cyanidioschyzon_merolae Cyanidioschyzon_merolae Cyanidioschyzon_merolae -cyaCae2.110 Cyanistes_caeruleus cyaCae2.110 cyaCae2.99 Cyanistes_caeruleus cyaCae2.99 Cyanobacteria_bacterium_j003_gca_003696925 Cyanobacteria_bacterium_j003_gca_003696925 Cyanobacteria_bacterium_j003_gca_003696925 Cyanobacteria_bacterium_j007_gca_003695985 Cyanobacteria_bacterium_j007_gca_003695985 Cyanobacteria_bacterium_j007_gca_003695985 @@ -16335,7 +16257,6 @@ Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_m_gca_002101225 Cycloclasticu Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_n_gca_002101205 Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_n_gca_002101205 Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_n_gca_002101205 Cycloclasticus_zancles_78_me Cycloclasticus_zancles_78_me Cycloclasticus_zancles_78_me Cycloclasticus_zancles_78_me_gca_000442595 Cycloclasticus_zancles_78_me_gca_000442595 Cycloclasticus_zancles_78_me_gca_000442595 -fCycLum1.pri.110 Cyclopterus_lumpus fCycLum1.pri.110 Cyclospora_cayetanensis_gca_000769155 Cyclospora_cayetanensis_gca_000769155 Cyclospora_cayetanensis_gca_000769155 Cylindrobasidium_torrendii_fp15055_ss_10_gca_000934385 Cylindrobasidium_torrendii_fp15055_ss_10_gca_000934385 Cylindrobasidium_torrendii_fp15055_ss_10_gca_000934385 Cylindrospermopsis_raciborskii_cena303_gca_002114155 Cylindrospermopsis_raciborskii_cena303_gca_002114155 Cylindrospermopsis_raciborskii_cena303_gca_002114155 @@ -16349,17 +16270,11 @@ Cylindrospermum_sp_nies_4074_gca_003994795 Cylindrospermum_sp_nies_4074_gca_00 Cylindrospermum_stagnale_pcc_7417 Cylindrospermum_stagnale_pcc_7417 Cylindrospermum_stagnale_pcc_7417 Cylindrospermum_stagnale_pcc_7417_gca_000317535 Cylindrospermum_stagnale_pcc_7417_gca_000317535 Cylindrospermum_stagnale_pcc_7417_gca_000317535 Cynara_cardunculus Cynara_cardunculus Cynara_cardunculus -Cse_v1.0.110 Cynoglossus_semilaevis Cse_v1.0.110 Cse_v1.0.99 Cynoglossus_semilaevis Cse_v1.0.99 Cyphellophora_europaea_cbs_101466_gca_000365145 Cyphellophora_europaea_cbs_101466_gca_000365145 Cyphellophora_europaea_cbs_101466_gca_000365145 -C_variegatus-1.0.110 Cyprinodon_variegatus C_variegatus-1.0.110 C_variegatus-1.0.99 Cyprinodon_variegatus C_variegatus-1.0.99 -Cypcar_WagV4.0.110 Cyprinus_carpio_carpio Cypcar_WagV4.0.110 -German_Mirror_carp_1.0.110 Cyprinus_carpio_germanmirror German_Mirror_carp_1.0.110 German_Mirror_carp_1.0.99 Cyprinus_carpio_germanmirror German_Mirror_carp_1.0.99 -Hebao_red_carp_1.0.110 Cyprinus_carpio_hebaored Hebao_red_carp_1.0.110 Hebao_red_carp_1.0.99 Cyprinus_carpio_hebaored Hebao_red_carp_1.0.99 -Hunaghe_carp_2.0.110 Cyprinus_carpio_huanghe Hunaghe_carp_2.0.110 Hunaghe_carp_2.0.99 Cyprinus_carpio_huanghe Hunaghe_carp_2.0.99 Cystobacter_ferrugineus_gca_001887355 Cystobacter_ferrugineus_gca_001887355 Cystobacter_ferrugineus_gca_001887355 Cystobacter_fuscus_dsm_2262 Cystobacter_fuscus_dsm_2262 Cystobacter_fuscus_dsm_2262 @@ -16398,7 +16313,6 @@ Daejeonella_lutea_gca_900168015 Daejeonella_lutea_gca_900168015 Daejeonella_ Daejeonella_rubra_gca_900103545 Daejeonella_rubra_gca_900103545 Daejeonella_rubra_gca_900103545 Daldinia_sp_ec12_gca_002120325 Daldinia_sp_ec12_gca_002120325 Daldinia_sp_ec12_gca_002120325 Danaus_plexippus Danaus_plexippus Danaus_plexippus -GRCz11.110 Danio_rerio GRCz11.110 GRCz11.99 Danio_rerio GRCz11.99 Zv9.75 Danio_rerio Zv9.75 Dankookia_rubra_gca_004355005 Dankookia_rubra_gca_004355005 Dankookia_rubra_gca_004355005 @@ -16407,7 +16321,6 @@ Daphnia_magna_gca020631705v2 Daphnia_magna_gca020631705v2 Daphnia_magna_gca0 Daphnia_pulex Daphnia_pulex Daphnia_pulex Daphnia_pulex_gca021134715v1rs Daphnia_pulex_gca021134715v1rs Daphnia_pulex_gca021134715v1rs Daphnia_pulicaria_gca021234035v2rs Daphnia_pulicaria_gca021234035v2rs Daphnia_pulicaria_gca021234035v2rs -Dasnov3.0.110 Dasypus_novemcinctus Dasnov3.0.110 Dasnov3.0.75 Dasypus_novemcinctus Dasnov3.0.75 Dasnov3.0.99 Dasypus_novemcinctus Dasnov3.0.99 Daucus_carota Daucus_carota Daucus_carota @@ -16548,7 +16461,6 @@ Delftia_tsuruhatensis_gca_004353655 Delftia_tsuruhatensis_gca_004353655 Delf Delftia_tsuruhatensis_gca_900111975 Delftia_tsuruhatensis_gca_900111975 Delftia_tsuruhatensis_gca_900111975 Dellaglioa_algida_dsm_15638_gca_001434695 Dellaglioa_algida_dsm_15638_gca_001434695 Dellaglioa_algida_dsm_15638_gca_001434695 Dellaglioa_algida_gca_900206325 Dellaglioa_algida_gca_900206325 Dellaglioa_algida_gca_900206325 -ASM228892v3.110 Delphinapterus_leucas ASM228892v3.110 Delta_proteobacterium_ml8_d_gca_002029965 Delta_proteobacterium_ml8_d_gca_002029965 Delta_proteobacterium_ml8_d_gca_002029965 Delta_proteobacterium_mlms_1 Delta_proteobacterium_mlms_1 Delta_proteobacterium_mlms_1 Delta_proteobacterium_mlms_1_gca_000168275 Delta_proteobacterium_mlms_1_gca_000168275 Delta_proteobacterium_mlms_1_gca_000168275 @@ -16607,7 +16519,6 @@ Denitrobacterium_detoxificans Denitrobacterium_detoxificans Denitrobacterium Denitrovibrio_acetiphilus_dsm_12809 Denitrovibrio_acetiphilus_dsm_12809 Denitrovibrio_acetiphilus_dsm_12809 Denitrovibrio_acetiphilus_dsm_12809_gca_000025725 Denitrovibrio_acetiphilus_dsm_12809_gca_000025725 Denitrovibrio_acetiphilus_dsm_12809_gca_000025725 Denitrovibrio_sp__gca_002869145 Denitrovibrio_sp__gca_002869145 Denitrovibrio_sp__gca_002869145 -fDenClu1.1.110 Denticeps_clupeoides fDenClu1.1.110 fDenClu1.1.99 Denticeps_clupeoides fDenClu1.1.99 Dentipellis_fragilis_gca_004679275 Dentipellis_fragilis_gca_004679275 Dentipellis_fragilis_gca_004679275 Dentipellis_sp_kuc8613_gca_002286715 Dentipellis_sp_kuc8613_gca_002286715 Dentipellis_sp_kuc8613_gca_002286715 @@ -16992,7 +16903,6 @@ Diaphorobacter_sp_j5_51_gca_001023515 Diaphorobacter_sp_j5_51_gca_001023515 Diaphorobacter_sp_lr2014_1_gca_002916785 Diaphorobacter_sp_lr2014_1_gca_002916785 Diaphorobacter_sp_lr2014_1_gca_002916785 Diaporthe_ampelina_gca_001006365 Diaporthe_ampelina_gca_001006365 Diaporthe_ampelina_gca_001006365 Diaporthe_helianthi_gca_001702395 Diaporthe_helianthi_gca_001702395 Diaporthe_helianthi_gca_001702395 -dlabrax2021.110 Dicentrarchus_labrax dlabrax2021.110 Dichelobacter_nodosus Dichelobacter_nodosus Dichelobacter_nodosus Dichelobacter_nodosus_vcs1703a Dichelobacter_nodosus_vcs1703a Dichelobacter_nodosus_vcs1703a Dichelobacter_nodosus_vcs1703a_gca_000015345 Dichelobacter_nodosus_vcs1703a_gca_000015345 Dichelobacter_nodosus_vcs1703a_gca_000015345 @@ -17066,7 +16976,6 @@ Diplocarpon_rosae_gca_002317995 Diplocarpon_rosae_gca_002317995 Diplocarpon_ Diplodia_corticola_gca_001883845 Diplodia_corticola_gca_001883845 Diplodia_corticola_gca_001883845 Diplodia_seriata_gca_001006355 Diplodia_seriata_gca_001006355 Diplodia_seriata_gca_001006355 Diplodia_seriata_gca_001975905 Diplodia_seriata_gca_001975905 Diplodia_seriata_gca_001975905 -Dord_2.0.110 Dipodomys_ordii Dord_2.0.110 Dord_2.0.99 Dipodomys_ordii Dord_2.0.99 dipOrd1.75 Dipodomys_ordii dipOrd1.75 Dissulfuribacter_thermophilus Dissulfuribacter_thermophilus Dissulfuribacter_thermophilus @@ -17168,14 +17077,12 @@ Drancourtella_sp_an210_gca_002159995 Drancourtella_sp_an210_gca_002159995 Dr Drancourtella_sp_an57_gca_002161525 Drancourtella_sp_an57_gca_002161525 Drancourtella_sp_an57_gca_002161525 Drechmeria_coniospora_gca_001625195 Drechmeria_coniospora_gca_001625195 Drechmeria_coniospora_gca_001625195 Drechslerella_stenobrocha_248_gca_000525045 Drechslerella_stenobrocha_248_gca_000525045 Drechslerella_stenobrocha_248_gca_000525045 -droNov1.110 Dromaius_novaehollandiae droNov1.110 droNov1.99 Dromaius_novaehollandiae droNov1.99 Drosophila_ananassae Drosophila_ananassae Drosophila_ananassae Drosophila_erecta Drosophila_erecta Drosophila_erecta Drosophila_grimshawi Drosophila_grimshawi Drosophila_grimshawi BDGP5.75 Drosophila_melanogaster BDGP5.75 BDGP6.28.99 Drosophila_melanogaster BDGP6.28.99 -BDGP6.46.110 Drosophila_melanogaster BDGP6.46.110 Drosophila_melanogaster Drosophila_melanogaster Drosophila_melanogaster Drosophila_mojavensis Drosophila_mojavensis Drosophila_mojavensis Drosophila_persimilis Drosophila_persimilis Drosophila_persimilis @@ -17261,14 +17168,12 @@ Dysgonomonas_mossii_dsm_22836_gca_000213575 Dysgonomonas_mossii_dsm_22836_gca_ Dysgonomonas_sp_37_18_gca_001899125 Dysgonomonas_sp_37_18_gca_001899125 Dysgonomonas_sp_37_18_gca_001899125 Dysosmobacter_welbionis_gca_005121165 Dysosmobacter_welbionis_gca_005121165 Dysosmobacter_welbionis_gca_005121165 ebola_zaire Ebola ebola_zaire -fEcheNa1.1.110 Echeneis_naucrates fEcheNa1.1.110 fEcheNa1.1.99 Echeneis_naucrates fEcheNa1.1.99 Echinicola_strongylocentroti_gca_003260975 Echinicola_strongylocentroti_gca_003260975 Echinicola_strongylocentroti_gca_003260975 Echinicola_vietnamensis_dsm_17526 Echinicola_vietnamensis_dsm_17526 Echinicola_vietnamensis_dsm_17526 Echinicola_vietnamensis_dsm_17526_gca_000325705 Echinicola_vietnamensis_dsm_17526_gca_000325705 Echinicola_vietnamensis_dsm_17526_gca_000325705 Echinochloa_crusgalli Echinochloa_crusgalli Echinochloa_crusgalli Echinococcus_granulosus_gca000524195v1rs Echinococcus_granulosus_gca000524195v1rs Echinococcus_granulosus_gca000524195v1rs -TENREC.110 Echinops_telfairi TENREC.110 TENREC.75 Echinops_telfairi TENREC.75 TENREC.99 Echinops_telfairi TENREC.99 Ectocarpus_siliculosus_gca_000310025 Ectocarpus_siliculosus_gca_000310025 Ectocarpus_siliculosus_gca_000310025 @@ -17387,7 +17292,6 @@ Eisenbergiella_tayi_gca_001717135 Eisenbergiella_tayi_gca_001717135 Eisenber Eisenbergiella_tayi_gca_001722555 Eisenbergiella_tayi_gca_001722555 Eisenbergiella_tayi_gca_001722555 Ekhidna_lutea_gca_900188325 Ekhidna_lutea_gca_900188325 Ekhidna_lutea_gca_900188325 Elaphomyces_granulatus_gca_002240705 Elaphomyces_granulatus_gca_002240705 Elaphomyces_granulatus_gca_002240705 -Ee_SOAP_WITH_SSPACE.110 Electrophorus_electricus Ee_SOAP_WITH_SSPACE.110 Ee_SOAP_WITH_SSPACE.99 Electrophorus_electricus Ee_SOAP_WITH_SSPACE.99 Elizabethkingia_anophelis Elizabethkingia_anophelis Elizabethkingia_anophelis Elizabethkingia_anophelis_502 Elizabethkingia_anophelis_502 Elizabethkingia_anophelis_502 @@ -19412,16 +19316,13 @@ Epilithonimonas_xixisoli_gca_004365655 Epilithonimonas_xixisoli_gca_004365655 Epilithonimonas_zeae_gca_900141765 Epilithonimonas_zeae_gca_900141765 Epilithonimonas_zeae_gca_900141765 Epsilonproteobacteria_bacterium_ex_lamellibrachia_satsuma__gca_003934925 Epsilonproteobacteria_bacterium_ex_lamellibrachia_satsuma__gca_003934925 Epsilonproteobacteria_bacterium_ex_lamellibrachia_satsuma__gca_003934925 Epsilonproteobacteria_bacterium_gca_003643835 Epsilonproteobacteria_bacterium_gca_003643835 Epsilonproteobacteria_bacterium_gca_003643835 -Eburgeri_3.2.110 Eptatretus_burgeri Eburgeri_3.2.110 Eburgeri_3.2.99 Eptatretus_burgeri Eburgeri_3.2.99 Epulopiscium_sp_as2m_bin001_gca_002007295 Epulopiscium_sp_as2m_bin001_gca_002007295 Epulopiscium_sp_as2m_bin001_gca_002007295 Epulopiscium_sp_nuni2h_mbin001_gca_001994995 Epulopiscium_sp_nuni2h_mbin001_gca_001994995 Epulopiscium_sp_nuni2h_mbin001_gca_001994995 Epulopiscium_sp_scg_b11wga_epuloa1_gca_001983455 Epulopiscium_sp_scg_b11wga_epuloa1_gca_001983455 Epulopiscium_sp_scg_b11wga_epuloa1_gca_001983455 Epulopiscium_sp_scg_c07wga_epuloa2_gca_001983555 Epulopiscium_sp_scg_c07wga_epuloa2_gca_001983555 Epulopiscium_sp_scg_c07wga_epuloa2_gca_001983555 -ASM1607732v2.110 Equus_asinus ASM1607732v2.110 ASM303372v1.99 Equus_asinus_asinus ASM303372v1.99 EquCab2.75 Equus_caballus EquCab2.75 -EquCab3.0.110 Equus_caballus EquCab3.0.110 EquCab3.0.99 Equus_caballus EquCab3.0.99 Eragrostis_curvula Eragrostis_curvula Eragrostis_curvula Eragrostis_tef Eragrostis_tef Eragrostis_tef @@ -19431,10 +19332,8 @@ Eremococcus_coleocola_acs_139_v_col8_gca_000183205 Eremococcus_coleocola_acs_1 Eremomyces_bilateralis_cbs_781_70_gca_010015585 Eremomyces_bilateralis_cbs_781_70_gca_010015585 Eremomyces_bilateralis_cbs_781_70_gca_010015585 Eremothecium_cymbalariae_dbvpg_7215_gca_000235365 Eremothecium_cymbalariae_dbvpg_7215_gca_000235365 Eremothecium_cymbalariae_dbvpg_7215_gca_000235365 Eremothecium_gossypii_fdag1_gca_000968835 Eremothecium_gossypii_fdag1_gca_000968835 Eremothecium_gossypii_fdag1_gca_000968835 -HEDGEHOG.110 Erinaceus_europaeus HEDGEHOG.110 HEDGEHOG.75 Erinaceus_europaeus HEDGEHOG.75 HEDGEHOG.99 Erinaceus_europaeus HEDGEHOG.99 -fErpCal1.1.110 Erpetoichthys_calabaricus fErpCal1.1.110 fErpCal1.1.99 Erpetoichthys_calabaricus fErpCal1.1.99 Erwinia_amylovora_01sfr_bo Erwinia_amylovora_01sfr_bo Erwinia_amylovora_01sfr_bo Erwinia_amylovora_acw56400 Erwinia_amylovora_acw56400 Erwinia_amylovora_acw56400 @@ -19576,7 +19475,6 @@ Erythrobacter_sp_yt30_gca_001542875 Erythrobacter_sp_yt30_gca_001542875 Eryt Erythrobacteraceae_bacterium_cfh_75059_gca_004331795 Erythrobacteraceae_bacterium_cfh_75059_gca_004331795 Erythrobacteraceae_bacterium_cfh_75059_gca_004331795 Erythrobacteraceae_bacterium_hl_111 Erythrobacteraceae_bacterium_hl_111 Erythrobacteraceae_bacterium_hl_111 Erythrobacteraceae_bacterium_hl_111_gca_001314765 Erythrobacteraceae_bacterium_hl_111_gca_001314765 Erythrobacteraceae_bacterium_hl_111_gca_001314765 -GouldianFinch.110 Erythrura_gouldiae GouldianFinch.110 GouldianFinch.99 Erythrura_gouldiae GouldianFinch.99 Escherichia_albertii Escherichia_albertii Escherichia_albertii Escherichia_albertii_b156_gca_002109845 Escherichia_albertii_b156_gca_002109845 Escherichia_albertii_b156_gca_002109845 @@ -23521,7 +23419,6 @@ Escherichia_sp_mr_gca_005280595 Escherichia_sp_mr_gca_005280595 Escherichia_ Escherichia_vulneris_nbrc_102420 Escherichia_vulneris_nbrc_102420 Escherichia_vulneris_nbrc_102420 Escovopsis_weberi_gca_001278495 Escovopsis_weberi_gca_001278495 Escovopsis_weberi_gca_001278495 Eluc_V3.99 Esox_lucius Eluc_V3.99 -Eluc_v4.110 Esox_lucius Eluc_v4.110 Estrella_lausannensis_gca_900000175 Estrella_lausannensis_gca_900000175 Estrella_lausannensis_gca_900000175 Ethanoligenens_harbinense_gca_003612855 Ethanoligenens_harbinense_gca_003612855 Ethanoligenens_harbinense_gca_003612855 Ethanoligenens_harbinense_yuan_3 Ethanoligenens_harbinense_yuan_3 Ethanoligenens_harbinense_yuan_3 @@ -23788,7 +23685,6 @@ Faecalitalea_cylindroides_atcc_27803 Faecalitalea_cylindroides_atcc_27803 Fa Faecalitalea_cylindroides_atcc_27803_gca_000469305 Faecalitalea_cylindroides_atcc_27803_gca_000469305 Faecalitalea_cylindroides_atcc_27803_gca_000469305 Faecalitalea_cylindroides_gca_002160375 Faecalitalea_cylindroides_gca_002160375 Faecalitalea_cylindroides_gca_002160375 Faecalitalea_cylindroides_t2_87 Faecalitalea_cylindroides_t2_87 Faecalitalea_cylindroides_t2_87 -FalTin1.0.110 Falco_tinnunculus FalTin1.0.110 Falseniella_ignava_ccug_37419_gca_000301055 Falseniella_ignava_ccug_37419_gca_000301055 Falseniella_ignava_ccug_37419_gca_000301055 Falseniella_ignava_gca_002847645 Falseniella_ignava_gca_002847645 Falseniella_ignava_gca_002847645 Falsibacillus_albus_gca_003668575 Falsibacillus_albus_gca_003668575 Falsibacillus_albus_gca_003668575 @@ -23802,7 +23698,6 @@ Falsochrobactrum_ovis_gca_003259955 Falsochrobactrum_ovis_gca_003259955 Fals Falsochrobactrum_shanghaiense_gca_003149535 Falsochrobactrum_shanghaiense_gca_003149535 Falsochrobactrum_shanghaiense_gca_003149535 Felis_catus Felis_catus Felis_catus Felis_catus_6.2.75 Felis_catus Felis_catus_6.2.75 -Felis_catus_9.0.110 Felis_catus Felis_catus_9.0.110 Felis_catus_9.0.99 Felis_catus Felis_catus_9.0.99 Fermentimonas_caenicola Fermentimonas_caenicola Fermentimonas_caenicola Fermentimonas_caenicola_gca_000953535 Fermentimonas_caenicola_gca_000953535 Fermentimonas_caenicola_gca_000953535 @@ -23889,7 +23784,6 @@ Fibrobacter_succinogenes_subsp_succinogenes_s85 Fibrobacter_succinogenes_subsp Fibrobacter_succinogenes_subsp_succinogenes_s85_gca_000146505 Fibrobacter_succinogenes_subsp_succinogenes_s85_gca_000146505 Fibrobacter_succinogenes_subsp_succinogenes_s85_gca_000146505 Fibroporia_radiculosa_gca_000313525 Fibroporia_radiculosa_gca_000313525 Fibroporia_radiculosa_gca_000313525 Fibularhizoctonia_sp_cbs_109695_gca_001630335 Fibularhizoctonia_sp_cbs_109695_gca_001630335 Fibularhizoctonia_sp_cbs_109695_gca_001630335 -FicAlb1.5.110 Ficedula_albicollis FicAlb1.5.110 FicAlb_1.4.75 Ficedula_albicollis FicAlb_1.4.75 FicAlb_1.4.99 Ficedula_albicollis FicAlb_1.4.99 Fictibacillus_aquaticus_gca_002245695 Fictibacillus_aquaticus_gca_002245695 Fictibacillus_aquaticus_gca_002245695 @@ -24694,7 +24588,6 @@ Fructobacillus_sp_efb_n1 Fructobacillus_sp_efb_n1 Fructobacillus_sp_efb_n1 Fructobacillus_sp_efb_n1_gca_001038455 Fructobacillus_sp_efb_n1_gca_001038455 Fructobacillus_sp_efb_n1_gca_001038455 Fructobacillus_tropaeoli_gca_001047135 Fructobacillus_tropaeoli_gca_001047135 Fructobacillus_tropaeoli_gca_001047135 Fuerstiella_marisgermanici_gca_001983935 Fuerstiella_marisgermanici_gca_001983935 Fuerstiella_marisgermanici_gca_001983935 -DMR_v1.0.110 Fukomys_damarensis DMR_v1.0.110 DMR_v1.0.99 Fukomys_damarensis DMR_v1.0.99 Fulvimarina_endophytica_gca_003403015 Fulvimarina_endophytica_gca_003403015 Fulvimarina_endophytica_gca_003403015 Fulvimarina_manganoxydans_gca_900176465 Fulvimarina_manganoxydans_gca_900176465 Fulvimarina_manganoxydans_gca_900176465 @@ -24704,7 +24597,6 @@ Fulvimarina_sp__gca_002700095 Fulvimarina_sp__gca_002700095 Fulvimarina_sp__ Fulvimonas_soli_gca_003148905 Fulvimonas_soli_gca_003148905 Fulvimonas_soli_gca_003148905 Fulvivirga_imtechensis_ak7 Fulvivirga_imtechensis_ak7 Fulvivirga_imtechensis_ak7 Fulvivirga_imtechensis_ak7_gca_000331535 Fulvivirga_imtechensis_ak7_gca_000331535 Fulvivirga_imtechensis_ak7_gca_000331535 -Fundulus_heteroclitus-3.0.2.110 Fundulus_heteroclitus Fundulus_heteroclitus-3.0.2.110 Fundulus_heteroclitus-3.0.2.99 Fundulus_heteroclitus Fundulus_heteroclitus-3.0.2.99 Furfurilactobacillus_rossiae_dsm_15814_gca_001435135 Furfurilactobacillus_rossiae_dsm_15814_gca_001435135 Furfurilactobacillus_rossiae_dsm_15814_gca_001435135 Furfurilactobacillus_siliginis_gca_001437435 Furfurilactobacillus_siliginis_gca_001437435 Furfurilactobacillus_siliginis_gca_001437435 @@ -24952,7 +24844,6 @@ test_GRCh38.mane.1.0.refseq.chr21 GRCh38 test_GRCh38.mane.1.0.refseq.chr21 GRCh38.86 GRCh38.86 GRCh38.86 gadMor1.75 Gadus_morhua gadMor1.75 gadMor1.99 Gadus_morhua gadMor1.99 -gadMor3.0.110 Gadus_morhua gadMor3.0.110 Gaetbulibacter_sp_4g1_gca_002741945 Gaetbulibacter_sp_4g1_gca_002741945 Gaetbulibacter_sp_4g1_gca_002741945 Gaetbulibacter_sp_5u11_gca_002742325 Gaetbulibacter_sp_5u11_gca_002742325 Gaetbulibacter_sp_5u11_gca_002742325 Gaeumannomyces_graminis Gaeumannomyces_graminis Gaeumannomyces_graminis @@ -25016,10 +24907,6 @@ Gallionellales_bacterium_rifcsplowo2_02_full_57_47_gca_001801175 Gallionellale Gallionellales_bacterium_rifcsplowo2_12_full_59_22_gca_001801255 Gallionellales_bacterium_rifcsplowo2_12_full_59_22_gca_001801255 Gallionellales_bacterium_rifcsplowo2_12_full_59_22_gca_001801255 GRCg6a.99 Gallus_gallus GRCg6a.99 Galgal4.75 Gallus_gallus Galgal4.75 -bGalGal1.mat.broiler.GRCg7b.110 Gallus_gallus bGalGal1.mat.broiler.GRCg7b.110 -GRCg6a.110 Gallus_gallus_gca000002315v5 GRCg6a.110 -bGalGal1.pat.whiteleghornlayer.GRCg7w.110 Gallus_gallus_gca016700215v2 bGalGal1.pat.whiteleghornlayer.GRCg7w.110 -ASM309773v1.110 Gambusia_affinis ASM309773v1.110 ASM309773v1.99 Gambusia_affinis ASM309773v1.99 Gamma_proteobacterium_bdw918 Gamma_proteobacterium_bdw918 Gamma_proteobacterium_bdw918 Gamma_proteobacterium_bdw918_gca_000259575 Gamma_proteobacterium_bdw918_gca_000259575 Gamma_proteobacterium_bdw918_gca_000259575 @@ -25202,7 +25089,6 @@ Gardnerella_vaginalis_jcp8481a Gardnerella_vaginalis_jcp8481a Gardnerella_va Gardnerella_vaginalis_jcp8481b Gardnerella_vaginalis_jcp8481b Gardnerella_vaginalis_jcp8481b Gardnerella_vaginalis_jcp8522 Gardnerella_vaginalis_jcp8522 Gardnerella_vaginalis_jcp8522 Gardnerella_vaginalis_jcp8522_gca_000414425 Gardnerella_vaginalis_jcp8522_gca_000414425 Gardnerella_vaginalis_jcp8522_gca_000414425 -BROADS1.110 Gasterosteus_aculeatus BROADS1.110 BROADS1.75 Gasterosteus_aculeatus BROADS1.75 BROADS1.99 Gasterosteus_aculeatus BROADS1.99 Geitlerinema_sp_pcc_7407 Geitlerinema_sp_pcc_7407 Geitlerinema_sp_pcc_7407 @@ -25447,7 +25333,6 @@ Georgenia_satyanarayanai_gca_900116375 Georgenia_satyanarayanai_gca_900116375 Georgenia_soli_gca_002563695 Georgenia_soli_gca_002563695 Georgenia_soli_gca_002563695 Georgenia_sp_subg003 Georgenia_sp_subg003 Georgenia_sp_subg003 Georgenia_yuyongxinii_gca_006352065 Georgenia_yuyongxinii_gca_006352065 Georgenia_yuyongxinii_gca_006352065 -GeoFor_1.0.110 Geospiza_fortis GeoFor_1.0.110 Geosporobacter_ferrireducens Geosporobacter_ferrireducens Geosporobacter_ferrireducens Geosporobacter_ferrireducens_gca_001750685 Geosporobacter_ferrireducens_gca_001750685 Geosporobacter_ferrireducens_gca_001750685 Geosporobacter_subterraneus_dsm_17957_gca_900142145 Geosporobacter_subterraneus_dsm_17957_gca_900142145 Geosporobacter_subterraneus_dsm_17957_gca_900142145 @@ -25642,9 +25527,7 @@ Golovinomyces_cichoracearum_gca_003611215 Golovinomyces_cichoracearum_gca_0036 Golovinomyces_cichoracearum_gca_003611235 Golovinomyces_cichoracearum_gca_003611235 Golovinomyces_cichoracearum_gca_003611235 Golovinomyces_magnicellulatus_gca_006912115 Golovinomyces_magnicellulatus_gca_006912115 Golovinomyces_magnicellulatus_gca_006912115 Gonapodya_prolifera_jel478_gca_001574975 Gonapodya_prolifera_jel478_gca_001574975 Gonapodya_prolifera_jel478_gca_001574975 -ASM289641v1.110 Gopherus_agassizii ASM289641v1.110 ASM289641v1.99 Gopherus_agassizii ASM289641v1.99 -rGopEvg1_v1.p.110 Gopherus_evgoodei rGopEvg1_v1.p.110 Gordonia_aichiensis_nbrc_108223 Gordonia_aichiensis_nbrc_108223 Gordonia_aichiensis_nbrc_108223 Gordonia_aichiensis_nbrc_108223_gca_000332975 Gordonia_aichiensis_nbrc_108223_gca_000332975 Gordonia_aichiensis_nbrc_108223_gca_000332975 Gordonia_alkanivorans_cgmcc_6845 Gordonia_alkanivorans_cgmcc_6845 Gordonia_alkanivorans_cgmcc_6845 @@ -25726,13 +25609,11 @@ Gordonia_terrae_nbrc_100016_gca_000248035 Gordonia_terrae_nbrc_100016_gca_0002 Gordonia_westfalica_gca_900105725 Gordonia_westfalica_gca_900105725 Gordonia_westfalica_gca_900105725 Gordonibacter_pamelaeae_7_10_1_b Gordonibacter_pamelaeae_7_10_1_b Gordonibacter_pamelaeae_7_10_1_b gorGor3.1.75 Gorilla_gorilla gorGor3.1.75 -gorGor4.110 Gorilla_gorilla gorGor4.110 gorGor4.99 Gorilla_gorilla gorGor4.99 Gossypium_raimondii Gossypium_raimondii Gossypium_raimondii Gottfriedia_luciferensis_gca_001712755 Gottfriedia_luciferensis_gca_001712755 Gottfriedia_luciferensis_gca_001712755 Gottschalkia_acidurici_9a_gca_000299355 Gottschalkia_acidurici_9a_gca_000299355 Gottschalkia_acidurici_9a_gca_000299355 Gottschalkia_purinilytica_gca_001190785 Gottschalkia_purinilytica_gca_001190785 Gottschalkia_purinilytica_gca_001190785 -fGouWil2.1.110 Gouania_willdenowi fGouWil2.1.110 fGouWil2.1.99 Gouania_willdenowi fGouWil2.1.99 Gracilibacillus_boraciitolerans_jcm_21714 Gracilibacillus_boraciitolerans_jcm_21714 Gracilibacillus_boraciitolerans_jcm_21714 Gracilibacillus_boraciitolerans_jcm_21714_gca_000521485 Gracilibacillus_boraciitolerans_jcm_21714_gca_000521485 Gracilibacillus_boraciitolerans_jcm_21714_gca_000521485 @@ -26619,7 +26500,6 @@ Hanstruepera_neustonica_gca_002895005 Hanstruepera_neustonica_gca_002895005 Hapalosiphon_sp_mrb220 Hapalosiphon_sp_mrb220 Hapalosiphon_sp_mrb220 Hapalosiphon_sp_mrb220_gca_001275395 Hapalosiphon_sp_mrb220_gca_001275395 Hapalosiphon_sp_mrb220_gca_001275395 Hapalosiphonaceae_cyanobacterium_jju2_gca_003261315 Hapalosiphonaceae_cyanobacterium_jju2_gca_003261315 Hapalosiphonaceae_cyanobacterium_jju2_gca_003261315 -AstBur1.0.110 Haplochromis_burtoni AstBur1.0.110 AstBur1.0.99 Haplochromis_burtoni AstBur1.0.99 Harpegnathos_saltator_gca003227715v2rs Harpegnathos_saltator_gca003227715v2rs Harpegnathos_saltator_gca003227715v2rs Harryflintia_acetispora_gca_003433795 Harryflintia_acetispora_gca_003433795 Harryflintia_acetispora_gca_003433795 @@ -27692,15 +27572,12 @@ Hespellia_stercorisuis_dsm_15480_gca_900142165 Hespellia_stercorisuis_dsm_1548 Hesseltinella_vesiculosa_gca_002104935 Hesseltinella_vesiculosa_gca_002104935 Hesseltinella_vesiculosa_gca_002104935 Heterobasidion_irregulare_tc_32_1_gca_000320585 Heterobasidion_irregulare_tc_32_1_gca_000320585 Heterobasidion_irregulare_tc_32_1_gca_000320585 HetGla_female_1.0.99 Heterocephalus_glaber_female HetGla_female_1.0.99 -Naked_mole-rat_maternal.110 Heterocephalus_glaber_female Naked_mole-rat_maternal.110 HetGla_1.0.99 Heterocephalus_glaber_male HetGla_1.0.99 -Naked_mole-rat_paternal.110 Heterocephalus_glaber_male Naked_mole-rat_paternal.110 Heyndrickxia_sporothermodurans_gca_001587375 Heyndrickxia_sporothermodurans_gca_001587375 Heyndrickxia_sporothermodurans_gca_001587375 Heyndrickxia_sporothermodurans_gca_003055045 Heyndrickxia_sporothermodurans_gca_003055045 Heyndrickxia_sporothermodurans_gca_003055045 Heyndrickxia_sporothermodurans_gca_003055065 Heyndrickxia_sporothermodurans_gca_003055065 Heyndrickxia_sporothermodurans_gca_003055065 Hippea_maritima_dsm_10411 Hippea_maritima_dsm_10411 Hippea_maritima_dsm_10411 Hippea_maritima_dsm_10411_gca_000194135 Hippea_maritima_dsm_10411_gca_000194135 Hippea_maritima_dsm_10411_gca_000194135 -H_comes_QL1_v1.110 Hippocampus_comes H_comes_QL1_v1.110 H_comes_QL1_v1.99 Hippocampus_comes H_comes_QL1_v1.99 Hirschia_baltica_atcc_49814 Hirschia_baltica_atcc_49814 Hirschia_baltica_atcc_49814 Hirschia_baltica_atcc_49814_gca_000023785 Hirschia_baltica_atcc_49814_gca_000023785 Hirschia_baltica_atcc_49814_gca_000023785 @@ -27752,7 +27629,6 @@ Holzapfelia_floricola_dsm_23037_jcm_16512_gca_001436605 Holzapfelia_floricola_ Homalodisca_vitripennis_gca021130785v2rs Homalodisca_vitripennis_gca021130785v2rs Homalodisca_vitripennis_gca021130785v2rs Homarus_americanus_gca018991925v1 Homarus_americanus_gca018991925v1 Homarus_americanus_gca018991925v1 GRCh37.75 Homo_sapiens GRCh37.75 -GRCh38.110 Homo_sapiens GRCh38.110 GRCh38.99 Homo_sapiens GRCh38.99 hg19kg Homo_sapiens hg19kg hg38kg Homo_sapiens hg38kg @@ -27777,7 +27653,6 @@ Hortaea_werneckii_gca_003704675 Hortaea_werneckii_gca_003704675 Hortaea_wern Hortaea_werneckii_gca_003704685 Hortaea_werneckii_gca_003704685 Hortaea_werneckii_gca_003704685 Hoyosella_subflava_dqs3_9a1 Hoyosella_subflava_dqs3_9a1 Hoyosella_subflava_dqs3_9a1 Hoyosella_subflava_dqs3_9a1_gca_000214175 Hoyosella_subflava_dqs3_9a1_gca_000214175 Hoyosella_subflava_dqs3_9a1_gca_000214175 -ASM331708v1.110 Hucho_hucho ASM331708v1.110 ASM331708v1.99 Hucho_hucho ASM331708v1.99 GRCh37.87 Human GRCh37.87 GRCh37.p13 Human GRCh37.p13 @@ -28024,9 +27899,7 @@ Hyunsoonleella_jejuensis_gca_900111025 Hyunsoonleella_jejuensis_gca_900111025 Hyunsoonleella_pacifica_gca_004310335 Hyunsoonleella_pacifica_gca_004310335 Hyunsoonleella_pacifica_gca_004310335 Ichthyenterobacterium_magnum_gca_003610635 Ichthyenterobacterium_magnum_gca_003610635 Ichthyenterobacterium_magnum_gca_003610635 Ichthyophthirius_multifiliis_gca_000220395 Ichthyophthirius_multifiliis_gca_000220395 Ichthyophthirius_multifiliis_gca_000220395 -IpCoco_1.2.110 Ictalurus_punctatus IpCoco_1.2.110 IpCoco_1.2.99 Ictalurus_punctatus IpCoco_1.2.99 -SpeTri2.0.110 Ictidomys_tridecemlineatus SpeTri2.0.110 SpeTri2.0.99 Ictidomys_tridecemlineatus SpeTri2.0.99 spetri2.75 Ictidomys_tridecemlineatus spetri2.75 Ideonella_sakaiensis Ideonella_sakaiensis Ideonella_sakaiensis @@ -28166,7 +28039,6 @@ Ixodes_scapularis_ise6 Ixodes_scapularis_ise6 Ixodes_scapularis_ise6 Izhakiella_australiensis_gca_002006995 Izhakiella_australiensis_gca_002006995 Izhakiella_australiensis_gca_002006995 Izhakiella_capsodis_gca_900115045 Izhakiella_capsodis_gca_900115045 Izhakiella_capsodis_gca_900115045 Jaapia_argillacea_mucl_33604_gca_000697665 Jaapia_argillacea_mucl_33604_gca_000697665 Jaapia_argillacea_mucl_33604_gca_000697665 -JacJac1.0.110 Jaculus_jaculus JacJac1.0.110 JacJac1.0.99 Jaculus_jaculus JacJac1.0.99 Jaminaea_rosea_gca_003144245 Jaminaea_rosea_gca_003144245 Jaminaea_rosea_gca_003144245 Janibacter_hoylei_pvas_1 Janibacter_hoylei_pvas_1 Janibacter_hoylei_pvas_1 @@ -28302,7 +28174,6 @@ Jonquetella_sp_bv3c21 Jonquetella_sp_bv3c21 Jonquetella_sp_bv3c21 Joostella_marina_dsm_19592 Joostella_marina_dsm_19592 Joostella_marina_dsm_19592 Joostella_marina_dsm_19592_gca_000260115 Joostella_marina_dsm_19592_gca_000260115 Joostella_marina_dsm_19592_gca_000260115 Juglans_regia Juglans_regia Juglans_regia -ASM382977v1.110 Junco_hyemalis ASM382977v1.110 ASM382977v1.99 Junco_hyemalis ASM382977v1.99 Kaistella_antarctica_gca_900637895 Kaistella_antarctica_gca_900637895 Kaistella_antarctica_gca_900637895 Kaistella_carnis_gca_003860585 Kaistella_carnis_gca_003860585 Kaistella_carnis_gca_003860585 @@ -30765,7 +30636,6 @@ Kribbella_speibonae_gca_004331375 Kribbella_speibonae_gca_004331375 Kribbell Kribbella_turkmenica_gca_004348725 Kribbella_turkmenica_gca_004348725 Kribbella_turkmenica_gca_004348725 Kriegella_aquimaris_gca_900103215 Kriegella_aquimaris_gca_900103215 Kriegella_aquimaris_gca_900103215 Kroppenstedtia_eburnea_gca_900156615 Kroppenstedtia_eburnea_gca_900156615 Kroppenstedtia_eburnea_gca_900156615 -ASM164957v1.110 Kryptolebias_marmoratus ASM164957v1.110 ASM164957v1.99 Kryptolebias_marmoratus ASM164957v1.99 Ktedonobacter_racemifer_dsm_44963 Ktedonobacter_racemifer_dsm_44963 Ktedonobacter_racemifer_dsm_44963 Ktedonobacter_racemifer_dsm_44963_gca_000178855 Ktedonobacter_racemifer_dsm_44963_gca_000178855 Ktedonobacter_racemifer_dsm_44963_gca_000178855 @@ -30834,7 +30704,6 @@ Labrenzia_sp_ob1 Labrenzia_sp_ob1 Labrenzia_sp_ob1 Labrenzia_sp_ob1_gca_001624695 Labrenzia_sp_ob1_gca_001624695 Labrenzia_sp_ob1_gca_001624695 Labrenzia_sp_pt13c1_gca_004365135 Labrenzia_sp_pt13c1_gca_004365135 Labrenzia_sp_pt13c1_gca_004365135 Labrenzia_sp_vg12_gca_002237595 Labrenzia_sp_vg12_gca_002237595 Labrenzia_sp_vg12_gca_002237595 -BallGen_V1.110 Labrus_bergylta BallGen_V1.110 BallGen_V1.99 Labrus_bergylta BallGen_V1.99 Labrys_okinawensis_gca_002982075 Labrys_okinawensis_gca_002982075 Labrys_okinawensis_gca_002982075 Laccaria_amethystina_laam_08_1_gca_000827195 Laccaria_amethystina_laam_08_1_gca_000827195 Laccaria_amethystina_laam_08_1_gca_000827195 @@ -32051,7 +31920,6 @@ Lapidilactobacillus_dextrinicus_dsm_20335_gca_001436095 Lapidilactobacillus_de Laribacter_hongkongensis_gca_002215055 Laribacter_hongkongensis_gca_002215055 Laribacter_hongkongensis_gca_002215055 Laribacter_hongkongensis_hlhk9 Laribacter_hongkongensis_hlhk9 Laribacter_hongkongensis_hlhk9 Laribacter_hongkongensis_hlhk9_gca_000021025 Laribacter_hongkongensis_hlhk9_gca_000021025 Laribacter_hongkongensis_hlhk9_gca_000021025 -L_crocea_2.0.110 Larimichthys_crocea L_crocea_2.0.110 L_crocea_2.0.99 Larimichthys_crocea L_crocea_2.0.99 Larkinella_arboricola_gca_003259745 Larkinella_arboricola_gca_003259745 Larkinella_arboricola_gca_003259745 Larkinella_knui_gca_003858645 Larkinella_knui_gca_003858645 Larkinella_knui_gca_003858645 @@ -32061,10 +31929,8 @@ Larkinella_sp_bk230_gca_004366505 Larkinella_sp_bk230_gca_004366505 Larkinel Lasallia_pustulata_gca_008636195 Lasallia_pustulata_gca_008636195 Lasallia_pustulata_gca_008636195 Lasallia_pustulata_gca_900169345 Lasallia_pustulata_gca_900169345 Lasallia_pustulata_gca_900169345 Lasiodiplodia_theobromae_gca_008931885 Lasiodiplodia_theobromae_gca_008931885 Lasiodiplodia_theobromae_gca_008931885 -ASB_HGAPassembly_v1.110 Lates_calcarifer ASB_HGAPassembly_v1.110 ASB_HGAPassembly_v1.99 Lates_calcarifer ASB_HGAPassembly_v1.99 Latescibacteria_bacterium_dg_63_gca_001302905 Latescibacteria_bacterium_dg_63_gca_001302905 Latescibacteria_bacterium_dg_63_gca_001302905 -latLat_1.0.110 Laticauda_laticaudata latLat_1.0.110 Latilactobacillus_curvatus_gca_000805355 Latilactobacillus_curvatus_gca_000805355 Latilactobacillus_curvatus_gca_000805355 Latilactobacillus_curvatus_gca_001698165 Latilactobacillus_curvatus_gca_001698165 Latilactobacillus_curvatus_gca_001698165 Latilactobacillus_curvatus_gca_003410375 Latilactobacillus_curvatus_gca_003410375 Latilactobacillus_curvatus_gca_003410375 @@ -32083,7 +31949,6 @@ Latilactobacillus_sakei_gca_900234355 Latilactobacillus_sakei_gca_900234355 Latilactobacillus_sakei_gca_900408275 Latilactobacillus_sakei_gca_900408275 Latilactobacillus_sakei_gca_900408275 Latilactobacillus_sakei_subsp_sakei_23k_gca_000026065 Latilactobacillus_sakei_subsp_sakei_23k_gca_000026065 Latilactobacillus_sakei_subsp_sakei_23k_gca_000026065 Latilactobacillus_sakei_subsp_sakei_gca_004354475 Latilactobacillus_sakei_subsp_sakei_gca_004354475 Latilactobacillus_sakei_subsp_sakei_gca_004354475 -LatCha1.110 Latimeria_chalumnae LatCha1.110 LatCha1.75 Latimeria_chalumnae LatCha1.75 LatCha1.99 Latimeria_chalumnae LatCha1.99 Lautropia_dentalis_gca_003892345 Lautropia_dentalis_gca_003892345 Lautropia_dentalis_gca_003892345 @@ -32555,13 +32420,10 @@ Lentzea_xinjiangensis_gca_900110955 Lentzea_xinjiangensis_gca_900110955 Lent Lepeophtheirus_salmonis Lepeophtheirus_salmonis Lepeophtheirus_salmonis Lepeophtheirus_salmonis_gca016086655v3rs Lepeophtheirus_salmonis_gca016086655v3rs Lepeophtheirus_salmonis_gca016086655v3rs Lepidopterella_palustris_cbs_459_81_gca_001692735 Lepidopterella_palustris_cbs_459_81_gca_001692735 Lepidopterella_palustris_cbs_459_81_gca_001692735 -Lepidothrix_coronata-1.0.110 Lepidothrix_coronata Lepidothrix_coronata-1.0.110 Lepidothrix_coronata-1.0.99 Lepidothrix_coronata Lepidothrix_coronata-1.0.99 -LepOcu1.110 Lepisosteus_oculatus LepOcu1.110 LepOcu1.75 Lepisosteus_oculatus LepOcu1.75 LepOcu1.99 Lepisosteus_oculatus LepOcu1.99 Leptinotarsa_decemlineata_gca000500325v2 Leptinotarsa_decemlineata_gca000500325v2 Leptinotarsa_decemlineata_gca000500325v2 -ASM966780v1.110 Leptobrachium_leishanense ASM966780v1.110 Leptolinea_tardivitalis Leptolinea_tardivitalis Leptolinea_tardivitalis Leptolinea_tardivitalis_gca_001306095 Leptolinea_tardivitalis_gca_001306095 Leptolinea_tardivitalis_gca_001306095 Leptolyngbya_boryana_nies_2135_gca_002368255 Leptolyngbya_boryana_nies_2135_gca_002368255 Leptolyngbya_boryana_nies_2135_gca_002368255 @@ -33715,7 +33577,6 @@ Loktanella_sp_s4079_gca_000967725 Loktanella_sp_s4079_gca_000967725 Loktanel Loktanella_vestfoldensis_ska53 Loktanella_vestfoldensis_ska53 Loktanella_vestfoldensis_ska53 Lolium_perenne Lolium_perenne Lolium_perenne Lomentospora_prolificans_gca_002276285 Lomentospora_prolificans_gca_002276285 Lomentospora_prolificans_gca_002276285 -LonStrDom1.110 Lonchura_striata_domestica LonStrDom1.110 LonStrDom1.99 Lonchura_striata_domestica LonStrDom1.99 Lonepinella_koalarum_gca_004339625 Lonepinella_koalarum_gca_004339625 Lonepinella_koalarum_gca_004339625 Longibacter_salinarum_gca_002554795 Longibacter_salinarum_gca_002554795 Longibacter_salinarum_gca_002554795 @@ -33732,7 +33593,6 @@ Lophiostoma_macrostomum_cbs_122681_gca_010405375 Lophiostoma_macrostomum_cbs_1 Lophiotrema_nucula_gca_010015825 Lophiotrema_nucula_gca_010015825 Lophiotrema_nucula_gca_010015825 Lophium_mytilinum_gca_010093605 Lophium_mytilinum_gca_010093605 Lophium_mytilinum_gca_010093605 Lottia_gigantea Lottia_gigantea Lottia_gigantea -loxAfr3.110 Loxodonta_africana loxAfr3.110 loxAfr3.75 Loxodonta_africana loxAfr3.75 loxAfr3.99 Loxodonta_africana loxAfr3.99 Lucifera_butyrica_gca_900476375 Lucifera_butyrica_gca_900476375 Lucifera_butyrica_gca_900476375 @@ -33792,7 +33652,6 @@ Lyngbya_aestuarii_bl_j_gca_000478195 Lyngbya_aestuarii_bl_j_gca_000478195 Ly Lyngbya_confervoides_bdu141951 Lyngbya_confervoides_bdu141951 Lyngbya_confervoides_bdu141951 Lyngbya_confervoides_bdu141951_gca_000817775 Lyngbya_confervoides_bdu141951_gca_000817775 Lyngbya_confervoides_bdu141951_gca_000817775 Lyngbya_sp_pcc_8106 Lyngbya_sp_pcc_8106 Lyngbya_sp_pcc_8106 -mLynCan4_v1.p.110 Lynx_canadensis mLynCan4_v1.p.110 mLynCan4_v1.p.99 Lynx_canadensis mLynCan4_v1.p.99 Lysinibacillus_antri_gca_003977595 Lysinibacillus_antri_gca_003977595 Lysinibacillus_antri_gca_003977595 Lysinibacillus_boronitolerans_jcm_21713_10a_nbrc_103108 Lysinibacillus_boronitolerans_jcm_21713_10a_nbrc_103108 Lysinibacillus_boronitolerans_jcm_21713_10a_nbrc_103108 @@ -33920,11 +33779,8 @@ Lysobacter_spongiicola_dsm_21749_gca_900167055 Lysobacter_spongiicola_dsm_2174 Lysobacter_tolerans_gca_900155935 Lysobacter_tolerans_gca_900155935 Lysobacter_tolerans_gca_900155935 Lytechinus_variegatus_gca018143015v1 Lytechinus_variegatus_gca018143015v1 Lytechinus_variegatus_gca018143015v1 Macaca_fascicularis_5.0.99 Macaca_fascicularis Macaca_fascicularis_5.0.99 -Macaca_fascicularis_6.0.110 Macaca_fascicularis Macaca_fascicularis_6.0.110 MMUL_1.75 Macaca_mulatta MMUL_1.75 -Mmul_10.110 Macaca_mulatta Mmul_10.110 Mmul_10.99 Macaca_mulatta Mmul_10.99 -Mnem_1.0.110 Macaca_nemestrina Mnem_1.0.110 Mnem_1.0.99 Macaca_nemestrina Mnem_1.0.99 Macellibacteroides_sp_hh_zs Macellibacteroides_sp_hh_zs Macellibacteroides_sp_hh_zs Macellibacteroides_sp_hh_zs_gca_001704385 Macellibacteroides_sp_hh_zs_gca_001704385 Macellibacteroides_sp_hh_zs_gca_001704385 @@ -34005,7 +33861,6 @@ Malikia_granosa_gca_002980595 Malikia_granosa_gca_002980595 Malikia_granosa_ Malikia_spinosa_gca_002980625 Malikia_spinosa_gca_002980625 Malikia_spinosa_gca_002980625 Maliponia_aquimaris_gca_900184945 Maliponia_aquimaris_gca_900184945 Maliponia_aquimaris_gca_900184945 Malonomonas_rubra_dsm_5091_gca_900142125 Malonomonas_rubra_dsm_5091_gca_900142125 Malonomonas_rubra_dsm_5091_gca_900142125 -mCya_1.0.110 Malurus_cyaneus_samueli mCya_1.0.110 Malus_domestica_golden Malus_domestica_golden Malus_domestica_golden Mameliella_alba Mameliella_alba Mameliella_alba Mameliella_alba_gca_000807715 Mameliella_alba_gca_000807715 Mameliella_alba_gca_000807715 @@ -34019,9 +33874,7 @@ Mammaliicoccus_sciuri_gca_003580455 Mammaliicoccus_sciuri_gca_003580455 Mamm Mammaliicoccus_sciuri_gca_003970475 Mammaliicoccus_sciuri_gca_003970475 Mammaliicoccus_sciuri_gca_003970475 Mammaliicoccus_stepanovicii_gca_900187075 Mammaliicoccus_stepanovicii_gca_900187075 Mammaliicoccus_stepanovicii_gca_900187075 Mammaliicoccus_vitulinus_gca_003043315 Mammaliicoccus_vitulinus_gca_003043315 Mammaliicoccus_vitulinus_gca_003043315 -ASM171598v2.110 Manacus_vitellinus ASM171598v2.110 ASM171598v2.99 Manacus_vitellinus ASM171598v2.99 -Mleu.le_1.0.110 Mandrillus_leucophaeus Mleu.le_1.0.110 Mleu.le_1.0.99 Mandrillus_leucophaeus Mleu.le_1.0.99 Manduca_sexta_gca014839805v1rs Manduca_sexta_gca014839805v1rs Manduca_sexta_gca014839805v1rs Mangrovibacter_phragmitis_gca_001655675 Mangrovibacter_phragmitis_gca_001655675 Mangrovibacter_phragmitis_gca_001655675 @@ -34372,7 +34225,6 @@ Marmoricola_scoriae_gca_900104965 Marmoricola_scoriae_gca_900104965 Marmoric Marmoricola_solisilvae_gca_003725775 Marmoricola_solisilvae_gca_003725775 Marmoricola_solisilvae_gca_003725775 Marmoricola_sp_leaf446 Marmoricola_sp_leaf446 Marmoricola_sp_leaf446 Marmoricola_sp_leaf446_gca_001424755 Marmoricola_sp_leaf446_gca_001424755 Marmoricola_sp_leaf446_gca_001424755 -marMar2.1.110 Marmota_marmota_marmota marMar2.1.110 marMar2.1.99 Marmota_marmota_marmota marMar2.1.99 Marortus_luteolus_gca_002915595 Marortus_luteolus_gca_002915595 Marortus_luteolus_gca_002915595 Marssonina_brunnea_f_sp_multigermtubi_mb_m1_gca_000298775 Marssonina_brunnea_f_sp_multigermtubi_mb_m1_gca_000298775 Marssonina_brunnea_f_sp_multigermtubi_mb_m1_gca_000298775 @@ -34435,12 +34287,10 @@ Massilimicrobiota_sp_an142_gca_002160725 Massilimicrobiota_sp_an142_gca_002160 Massilimicrobiota_sp_an80_gca_002159255 Massilimicrobiota_sp_an80_gca_002159255 Massilimicrobiota_sp_an80_gca_002159255 Massilimicrobiota_timonensis_gca_002160865 Massilimicrobiota_timonensis_gca_002160865 Massilimicrobiota_timonensis_gca_002160865 fMasArm1.1.99 Mastacembelus_armatus fMasArm1.1.99 -fMasArm1.2.110 Mastacembelus_armatus fMasArm1.2.110 Mastigocladus_laminosus_uu774 Mastigocladus_laminosus_uu774 Mastigocladus_laminosus_uu774 Mastigocoleus_testarum_bc008 Mastigocoleus_testarum_bc008 Mastigocoleus_testarum_bc008 Mastigocoleus_testarum_bc008_gca_001456025 Mastigocoleus_testarum_bc008_gca_001456025 Mastigocoleus_testarum_bc008_gca_001456025 Mayetiola_destructor Mayetiola_destructor Mayetiola_destructor -M_zebra_UMD2a.110 Maylandia_zebra M_zebra_UMD2a.110 M_zebra_UMD2a.99 Maylandia_zebra M_zebra_UMD2a.99 Medicago_truncatula Medicago_truncatula Medicago_truncatula Mediterranea_sp_an20_gca_002160055 Mediterranea_sp_an20_gca_002160055 Mediterranea_sp_an20_gca_002160055 @@ -34514,7 +34364,6 @@ Melaminivora_sp_sc2_9_gca_003008575 Melaminivora_sp_sc2_9_gca_003008575 Mela Melampsora_laricipopulina Melampsora_laricipopulina Melampsora_laricipopulina Melanomma_pulvis_pyrius_cbs_109_77_gca_010093585 Melanomma_pulvis_pyrius_cbs_109_77_gca_010093585 Melanomma_pulvis_pyrius_cbs_109_77_gca_010093585 Turkey_2.01.99 Meleagris_gallopavo Turkey_2.01.99 -Turkey_5.1.110 Meleagris_gallopavo Turkey_5.1.110 UMD2.75 Meleagris_gallopavo UMD2.75 Melghiribacillus_thermohalophilus_gca_004342905 Melghiribacillus_thermohalophilus_gca_004342905 Melghiribacillus_thermohalophilus_gca_004342905 Melghirimyces_profundicolus_gca_003054245 Melghirimyces_profundicolus_gca_003054245 Melghirimyces_profundicolus_gca_003054245 @@ -34545,11 +34394,9 @@ Melitaea_cinxia Melitaea_cinxia Melitaea_cinxia Melitaea_cinxia_gca905220565v1 Melitaea_cinxia_gca905220565v1 Melitaea_cinxia_gca905220565v1 Melittangium_boletus_dsm_14713_gca_002305855 Melittangium_boletus_dsm_14713_gca_002305855 Melittangium_boletus_dsm_14713_gca_002305855 Melopsittacus_undulatus_6.3.99 Melopsittacus_undulatus Melopsittacus_undulatus_6.3.99 -bMelUnd1.mat.Z.110 Melopsittacus_undulatus bMelUnd1.mat.Z.110 Mercenaria_mercenaria_gca014805675v2 Mercenaria_mercenaria_gca014805675v2 Mercenaria_mercenaria_gca014805675v2 Meridianimaribacter_sp_cl38_gca_004328055 Meridianimaribacter_sp_cl38_gca_004328055 Meridianimaribacter_sp_cl38_gca_004328055 Meridianimarinicoccus_roseus_gca_003172915 Meridianimarinicoccus_roseus_gca_003172915 Meridianimarinicoccus_roseus_gca_003172915 -MunDraft-v1.0.110 Meriones_unguiculatus MunDraft-v1.0.110 MunDraft-v1.0.99 Meriones_unguiculatus MunDraft-v1.0.99 Merismopedia_glauca_ccap_1448_3_gca_003003775 Merismopedia_glauca_ccap_1448_3_gca_003003775 Merismopedia_glauca_ccap_1448_3_gca_003003775 Mesoaciditoga_sp__gca_002878315 Mesoaciditoga_sp__gca_002878315 Mesoaciditoga_sp__gca_002878315 @@ -34563,7 +34410,6 @@ Mesobacillus_subterraneus_gca_003937825 Mesobacillus_subterraneus_gca_00393782 Mesobacillus_zeae_gca_003570705 Mesobacillus_zeae_gca_003570705 Mesobacillus_zeae_gca_003570705 Mesobaculum_littorinae_gca_004011175 Mesobaculum_littorinae_gca_004011175 Mesobaculum_littorinae_gca_004011175 Mesocricetibacter_intestinalis_gca_004363295 Mesocricetibacter_intestinalis_gca_004363295 Mesocricetibacter_intestinalis_gca_004363295 -MesAur1.0.110 Mesocricetus_auratus MesAur1.0.110 MesAur1.0.99 Mesocricetus_auratus MesAur1.0.99 Mesoflavibacter_sp_hg96_gca_003008415 Mesoflavibacter_sp_hg96_gca_003008415 Mesoflavibacter_sp_hg96_gca_003008415 Mesoflavibacter_zeaxanthinifaciens_subsp_sabulilitoris_gca_003008435 Mesoflavibacter_zeaxanthinifaciens_subsp_sabulilitoris_gca_003008435 Mesoflavibacter_zeaxanthinifaciens_subsp_sabulilitoris_gca_003008435 @@ -36108,7 +35954,6 @@ Microbulbifer_thermotolerans Microbulbifer_thermotolerans Microbulbifer_ther Microbulbifer_thermotolerans_gca_001617625 Microbulbifer_thermotolerans_gca_001617625 Microbulbifer_thermotolerans_gca_001617625 Microbulbifer_thermotolerans_gca_900112305 Microbulbifer_thermotolerans_gca_900112305 Microbulbifer_thermotolerans_gca_900112305 Microbulbifer_yueqingensis_gca_900100355 Microbulbifer_yueqingensis_gca_900100355 Microbulbifer_yueqingensis_gca_900100355 -Mmur_3.0.110 Microcebus_murinus Mmur_3.0.110 Mmur_3.0.99 Microcebus_murinus Mmur_3.0.99 micMur1.75 Microcebus_murinus micMur1.75 Microcella_alkaliphila_gca_002355395 Microcella_alkaliphila_gca_002355395 Microcella_alkaliphila_gca_002355395 @@ -36396,7 +36241,6 @@ Microterricola_viridarii Microterricola_viridarii Microterricola_viridarii Microterricola_viridarii_gca_001542775 Microterricola_viridarii_gca_001542775 Microterricola_viridarii_gca_001542775 Microterricola_viridarii_gca_900104895 Microterricola_viridarii_gca_900104895 Microterricola_viridarii_gca_900104895 Microthyrium_microscopicum_gca_010405405 Microthyrium_microscopicum_gca_010405405 Microthyrium_microscopicum_gca_010405405 -MicOch1.0.110 Microtus_ochrogaster MicOch1.0.110 MicOch1.0.99 Microtus_ochrogaster MicOch1.0.99 Microvirga_guangxiensis_gca_900102135 Microvirga_guangxiensis_gca_900102135 Microvirga_guangxiensis_gca_900102135 Microvirga_lotononidis Microvirga_lotononidis Microvirga_lotononidis @@ -36489,7 +36333,6 @@ Mogibacterium_sp_cm50_gca_000293155 Mogibacterium_sp_cm50_gca_000293155 Mogi Mogibacterium_timidum_atcc_33093 Mogibacterium_timidum_atcc_33093 Mogibacterium_timidum_atcc_33093 Mogibacterium_timidum_atcc_33093_gca_000525775 Mogibacterium_timidum_atcc_33093_gca_000525775 Mogibacterium_timidum_atcc_33093_gca_000525775 Moheibacter_sediminis_gca_900176425 Moheibacter_sediminis_gca_900176425 Moheibacter_sediminis_gca_900176425 -ASM169857v1.110 Mola_mola ASM169857v1.110 ASM169857v1.99 Mola_mola ASM169857v1.99 Monaibacterium_marinum_gca_900231835 Monaibacterium_marinum_gca_900231835 Monaibacterium_marinum_gca_900231835 Monascus_purpureus_gca_006542485 Monascus_purpureus_gca_006542485 Monascus_purpureus_gca_006542485 @@ -36500,13 +36343,10 @@ Monilinia_laxa_gca_009299455 Monilinia_laxa_gca_009299455 Monilinia_laxa_gca Moniliophthora_perniciosa_fa553_gca_000183025 Moniliophthora_perniciosa_fa553_gca_000183025 Moniliophthora_perniciosa_fa553_gca_000183025 Moniliophthora_roreri_gca_001466705 Moniliophthora_roreri_gca_001466705 Moniliophthora_roreri_gca_001466705 Moniliophthora_roreri_mca_2997_gca_000488995 Moniliophthora_roreri_mca_2997_gca_000488995 Moniliophthora_roreri_mca_2997_gca_000488995 -ASM229v1.110 Monodelphis_domestica ASM229v1.110 ASM229v1.99 Monodelphis_domestica ASM229v1.99 BROADO5.75 Monodelphis_domestica BROADO5.75 -NGI_Narwhal_1.110 Monodon_monoceros NGI_Narwhal_1.110 Monoglobus_pectinilyticus_gca_002874775 Monoglobus_pectinilyticus_gca_002874775 Monoglobus_pectinilyticus_gca_002874775 Monomorium_pharaonis_gca013373865v2 Monomorium_pharaonis_gca013373865v2 Monomorium_pharaonis_gca013373865v2 -M_albus_1.0.110 Monopterus_albus M_albus_1.0.110 M_albus_1.0.99 Monopterus_albus M_albus_1.0.99 Monosiga_brevicollis_mx1_gca_000002865 Monosiga_brevicollis_mx1_gca_000002865 Monosiga_brevicollis_mx1_gca_000002865 Monosporascus_cannonballus_gca_004154925 Monosporascus_cannonballus_gca_004154925 Monosporascus_cannonballus_gca_004154925 @@ -36656,7 +36496,6 @@ Morococcus_cerebrosus Morococcus_cerebrosus Morococcus_cerebrosus Morococcus_cerebrosus_gca_000813705 Morococcus_cerebrosus_gca_000813705 Morococcus_cerebrosus_gca_000813705 Mortierella_elongata_ag_77_gca_001651415 Mortierella_elongata_ag_77_gca_001651415 Mortierella_elongata_ag_77_gca_001651415 Mortierella_verticillata_nrrl_6337_gca_000739165 Mortierella_verticillata_nrrl_6337_gca_000739165 Mortierella_verticillata_nrrl_6337_gca_000739165 -MosMos_v2_BIUU_UCD.110 Moschus_moschiferus MosMos_v2_BIUU_UCD.110 MosMos_v2_BIUU_UCD.99 Moschus_moschiferus MosMos_v2_BIUU_UCD.99 Motilibacter_peucedani_gca_003634695 Motilibacter_peucedani_gca_003634695 Motilibacter_peucedani_gca_003634695 Motilibacter_rhizosphaerae_gca_004216915 Motilibacter_rhizosphaerae_gca_004216915 Motilibacter_rhizosphaerae_gca_004216915 @@ -36771,52 +36610,31 @@ Muricomes_intestini_gca_004346165 Muricomes_intestini_gca_004346165 Muricome Muriicola_soli_gca_004139715 Muriicola_soli_gca_004139715 Muriicola_soli_gca_004139715 Murimonas_intestini_gca_003148945 Murimonas_intestini_gca_003148945 Murimonas_intestini_gca_003148945 Murinocardiopsis_flavida_gca_003014485 Murinocardiopsis_flavida_gca_003014485 Murinocardiopsis_flavida_gca_003014485 -CAROLI_EIJ_v1.1.110 Mus_caroli CAROLI_EIJ_v1.1.110 CAROLI_EIJ_v1.1.99 Mus_caroli CAROLI_EIJ_v1.1.99 GRCm38.75 Mus_musculus GRCm38.75 GRCm38.99 Mus_musculus GRCm38.99 -GRCm39.110 Mus_musculus GRCm39.110 testMm37.61 Mus_musculus testMm37.61 -129S1_SvImJ_v1.110 Mus_musculus_129s1svimj 129S1_SvImJ_v1.110 129S1_SvImJ_v1.99 Mus_musculus_129s1svimj 129S1_SvImJ_v1.99 -A_J_v1.110 Mus_musculus_aj A_J_v1.110 A_J_v1.99 Mus_musculus_aj A_J_v1.99 -AKR_J_v1.110 Mus_musculus_akrj AKR_J_v1.110 AKR_J_v1.99 Mus_musculus_akrj AKR_J_v1.99 -BALB_cJ_v1.110 Mus_musculus_balbcj BALB_cJ_v1.110 BALB_cJ_v1.99 Mus_musculus_balbcj BALB_cJ_v1.99 -C3H_HeJ_v1.110 Mus_musculus_c3hhej C3H_HeJ_v1.110 C3H_HeJ_v1.99 Mus_musculus_c3hhej C3H_HeJ_v1.99 -C57BL_6NJ_v1.110 Mus_musculus_c57bl6nj C57BL_6NJ_v1.110 C57BL_6NJ_v1.99 Mus_musculus_c57bl6nj C57BL_6NJ_v1.99 -CAST_EiJ_v1.110 Mus_musculus_casteij CAST_EiJ_v1.110 CAST_EiJ_v1.99 Mus_musculus_casteij CAST_EiJ_v1.99 -CBA_J_v1.110 Mus_musculus_cbaj CBA_J_v1.110 CBA_J_v1.99 Mus_musculus_cbaj CBA_J_v1.99 -DBA_2J_v1.110 Mus_musculus_dba2j DBA_2J_v1.110 DBA_2J_v1.99 Mus_musculus_dba2j DBA_2J_v1.99 -FVB_NJ_v1.110 Mus_musculus_fvbnj FVB_NJ_v1.110 FVB_NJ_v1.99 Mus_musculus_fvbnj FVB_NJ_v1.99 -LP_J_v1.110 Mus_musculus_lpj LP_J_v1.110 LP_J_v1.99 Mus_musculus_lpj LP_J_v1.99 -NOD_ShiLtJ_v1.110 Mus_musculus_nodshiltj NOD_ShiLtJ_v1.110 NOD_ShiLtJ_v1.99 Mus_musculus_nodshiltj NOD_ShiLtJ_v1.99 -NZO_HlLtJ_v1.110 Mus_musculus_nzohlltj NZO_HlLtJ_v1.110 NZO_HlLtJ_v1.99 Mus_musculus_nzohlltj NZO_HlLtJ_v1.99 -PWK_PhJ_v1.110 Mus_musculus_pwkphj PWK_PhJ_v1.110 PWK_PhJ_v1.99 Mus_musculus_pwkphj PWK_PhJ_v1.99 -WSB_EiJ_v1.110 Mus_musculus_wsbeij WSB_EiJ_v1.110 WSB_EiJ_v1.99 Mus_musculus_wsbeij WSB_EiJ_v1.99 -PAHARI_EIJ_v1.1.110 Mus_pahari PAHARI_EIJ_v1.1.110 PAHARI_EIJ_v1.1.99 Mus_pahari PAHARI_EIJ_v1.1.99 -MUSP714.110 Mus_spicilegus MUSP714.110 MUSP714.99 Mus_spicilegus MUSP714.99 -SPRET_EiJ_v1.110 Mus_spretus SPRET_EiJ_v1.110 SPRET_EiJ_v1.99 Mus_spretus SPRET_EiJ_v1.99 Musa_acuminata Musa_acuminata Musa_acuminata Musca_domestica Musca_domestica Musca_domestica Musicola_paradisiaca_ech703_gca_000023545 Musicola_paradisiaca_ech703_gca_000023545 Musicola_paradisiaca_ech703_gca_000023545 -MusPutFur1.0.110 Mustela_putorius_furo MusPutFur1.0.110 MusPutFur1.0.75 Mustela_putorius_furo MusPutFur1.0.75 MusPutFur1.0.99 Mustela_putorius_furo MusPutFur1.0.99 Myceligenerans_xiligouense_gca_003814695 Myceligenerans_xiligouense_gca_003814695 Myceligenerans_xiligouense_gca_003814695 @@ -41523,10 +41341,8 @@ Mycoplasmopsis_synoviae_gca_003147565 Mycoplasmopsis_synoviae_gca_003147565 Mycoplasmopsis_synoviae_gca_003586085 Mycoplasmopsis_synoviae_gca_003586085 Mycoplasmopsis_synoviae_gca_003586085 Mycoplasmopsis_verecunda_gca_900167035 Mycoplasmopsis_verecunda_gca_900167035 Mycoplasmopsis_verecunda_gca_900167035 Mycosphaerella_eumusae_gca_001578235 Mycosphaerella_eumusae_gca_001578235 Mycosphaerella_eumusae_gca_001578235 -Myoluc2.0.110 Myotis_lucifugus Myoluc2.0.110 Myoluc2.0.75 Myotis_lucifugus Myoluc2.0.75 Myoluc2.0.99 Myotis_lucifugus Myoluc2.0.99 -fMyrMur1.1.110 Myripristis_murdjan fMyrMur1.1.110 fMyrMur1.1.99 Myripristis_murdjan fMyrMur1.1.99 Myroides_aquimaris_gca_900108395 Myroides_aquimaris_gca_900108395 Myroides_aquimaris_gca_900108395 Myroides_guanonis_gca_900114085 Myroides_guanonis_gca_900114085 Myroides_guanonis_gca_900114085 @@ -41572,7 +41388,6 @@ Naasia_lichenicola_gca_004801885 Naasia_lichenicola_gca_004801885 Naasia_lic Nadsonia_fulvescens_var_elongata_dsm_6958_gca_001661315 Nadsonia_fulvescens_var_elongata_dsm_6958_gca_001661315 Nadsonia_fulvescens_var_elongata_dsm_6958_gca_001661315 Naegleria_gruberi_gca_000004985 Naegleria_gruberi_gca_000004985 Naegleria_gruberi_gca_000004985 Naematelia_encephala_gca_002105065 Naematelia_encephala_gca_002105065 Naematelia_encephala_gca_002105065 -Nana_v5.110 Naja_naja Nana_v5.110 Nakamurella_antarctica_gca_003860405 Nakamurella_antarctica_gca_003860405 Nakamurella_antarctica_gca_003860405 Nakamurella_flava_gca_005298075 Nakamurella_flava_gca_005298075 Nakamurella_flava_gca_005298075 Nakamurella_multipartita_dsm_44233 Nakamurella_multipartita_dsm_44233 Nakamurella_multipartita_dsm_44233 @@ -41583,7 +41398,6 @@ Nannizzia_gypsea_cbs_118893_gca_000150975 Nannizzia_gypsea_cbs_118893_gca_0001 Nannochloropsis_gaditana_ccmp526_gca_000240725 Nannochloropsis_gaditana_ccmp526_gca_000240725 Nannochloropsis_gaditana_ccmp526_gca_000240725 Nannochloropsis_gaditana_gca_000569095 Nannochloropsis_gaditana_gca_000569095 Nannochloropsis_gaditana_gca_000569095 Nannocystis_exedens_gca_900112715 Nannocystis_exedens_gca_900112715 Nannocystis_exedens_gca_900112715 -S.galili_v1.0.110 Nannospalax_galili S.galili_v1.0.110 S.galili_v1.0.99 Nannospalax_galili S.galili_v1.0.99 Nanoarchaeota_archaeon_gca_002687775 Nanoarchaeota_archaeon_gca_002687775 Nanoarchaeota_archaeon_gca_002687775 Nanoarchaeota_archaeon_gca_002687825 Nanoarchaeota_archaeon_gca_002687825 Nanoarchaeota_archaeon_gca_002687825 @@ -42551,10 +42365,8 @@ Neochlamydia_sp_tume1_gca_000813645 Neochlamydia_sp_tume1_gca_000813645 Neoc Neodiprion_lecontei_gca021901455v1rs Neodiprion_lecontei_gca021901455v1rs Neodiprion_lecontei_gca021901455v1rs Neodiprion_pinetum_gca021155775v1rs Neodiprion_pinetum_gca021155775v1rs Neodiprion_pinetum_gca021155775v1rs Neofusicoccum_parvum_ucrnp2_gca_000385595 Neofusicoccum_parvum_ucrnp2_gca_000385595 Neofusicoccum_parvum_ucrnp2_gca_000385595 -RGoby_Basel_V2.110 Neogobius_melanostomus RGoby_Basel_V2.110 RGoby_Basel_V2.99 Neogobius_melanostomus RGoby_Basel_V2.99 Neohortaea_acidophila_gca_010093505 Neohortaea_acidophila_gca_010093505 Neohortaea_acidophila_gca_010093505 -NeoBri1.0.110 Neolamprologus_brichardi NeoBri1.0.110 NeoBri1.0.99 Neolamprologus_brichardi NeoBri1.0.99 Neolecta_irregularis_dah_3_gca_001929475 Neolecta_irregularis_dah_3_gca_001929475 Neolecta_irregularis_dah_3_gca_001929475 Neolentinus_lepideus_hhb14362_ss_1_gca_001632425 Neolentinus_lepideus_hhb14362_ss_1_gca_001632425 Neolentinus_lepideus_hhb14362_ss_1_gca_001632425 @@ -42584,7 +42396,6 @@ Neorickettsia_sennetsu_str_miyayama Neorickettsia_sennetsu_str_miyayama Neor Neorickettsia_sennetsu_str_miyayama_gca_000013165 Neorickettsia_sennetsu_str_miyayama_gca_000013165 Neorickettsia_sennetsu_str_miyayama_gca_000013165 Neosartorya_fischeri Neosartorya_fischeri Neosartorya_fischeri Neosynechococcus_sphagnicola_sy1 Neosynechococcus_sphagnicola_sy1 Neosynechococcus_sphagnicola_sy1 -NNQGG.v01.110 Neovison_vison NNQGG.v01.110 NNQGG.v01.99 Neovison_vison NNQGG.v01.99 Neptuniibacter_caesariensis Neptuniibacter_caesariensis Neptuniibacter_caesariensis Neptunomonas_antarctica_gca_900156635 Neptunomonas_antarctica_gca_900156635 Neptunomonas_antarctica_gca_900156635 @@ -42984,7 +42795,6 @@ Nodularia_spumigena_ccy9414_gca_000340565 Nodularia_spumigena_ccy9414_gca_0003 Nodularia_spumigena_cena596 Nodularia_spumigena_cena596 Nodularia_spumigena_cena596 Nodularia_spumigena_cena596_gca_001623485 Nodularia_spumigena_cena596_gca_001623485 Nodularia_spumigena_cena596_gca_001623485 Nleu1.0.75 Nomascus_leucogenys Nleu1.0.75 -Nleu_3.0.110 Nomascus_leucogenys Nleu_3.0.110 Nleu_3.0.99 Nomascus_leucogenys Nleu_3.0.99 Nonlabens_agnitus_gca_002994045 Nonlabens_agnitus_gca_002994045 Nonlabens_agnitus_gca_002994045 Nonlabens_arenilitoris_gca_002954765 Nonlabens_arenilitoris_gca_002954765 Nonlabens_arenilitoris_gca_002954765 @@ -43069,13 +42879,9 @@ Nostoc_sp_peltigera_membranacea_cyanobiont_n6_gca_002949735 Nostoc_sp_peltiger Nostoc_sp_rf31ymg_gca_002155185 Nostoc_sp_rf31ymg_gca_002155185 Nostoc_sp_rf31ymg_gca_002155185 Nostoc_sp_t09_gca_002154695 Nostoc_sp_t09_gca_002154695 Nostoc_sp_t09_gca_002154695 Nostocales_cyanobacterium_ht_58_2_gca_002163975 Nostocales_cyanobacterium_ht_58_2_gca_002163975 Nostocales_cyanobacterium_ht_58_2_gca_002163975 -Meug_1.0.110 Notamacropus_eugenii Meug_1.0.110 Meug_1.0.99 Notamacropus_eugenii Meug_1.0.99 -TS10Xv2-PRI.110 Notechis_scutatus TS10Xv2-PRI.110 TS10Xv2-PRI.99 Notechis_scutatus TS10Xv2-PRI.99 -Nfu_20140520.110 Nothobranchius_furzeri Nfu_20140520.110 Nothophytophthora_sp_chile5_gca_001712635 Nothophytophthora_sp_chile5_gca_001712635 Nothophytophthora_sp_chile5_gca_001712635 -notPer1.110 Nothoprocta_perdicaria notPer1.110 notPer1.99 Nothoprocta_perdicaria notPer1.99 Notoacmeibacter_marinus_gca_002238045 Notoacmeibacter_marinus_gca_002238045 Notoacmeibacter_marinus_gca_002238045 Novacetimonas_cocois_gca_003311635 Novacetimonas_cocois_gca_003311635 Novacetimonas_cocois_gca_003311635 @@ -43165,7 +42971,6 @@ Novosphingobium_subterraneum Novosphingobium_subterraneum Novosphingobium_su Novosphingobium_subterraneum_gca_000807925 Novosphingobium_subterraneum_gca_000807925 Novosphingobium_subterraneum_gca_000807925 Novosphingobium_tardaugens_nbrc_16725 Novosphingobium_tardaugens_nbrc_16725 Novosphingobium_tardaugens_nbrc_16725 Novosphingobium_umbonatum_gca_004005905 Novosphingobium_umbonatum_gca_004005905 Novosphingobium_umbonatum_gca_004005905 -NumMel1.0.110 Numida_meleagris NumMel1.0.110 NumMel1.0.99 Numida_meleagris NumMel1.0.99 Nymphaea_colorata Nymphaea_colorata Nymphaea_colorata Obba_rivulosa_gca_001687445 Obba_rivulosa_gca_001687445 Obba_rivulosa_gca_001687445 @@ -43243,7 +43048,6 @@ Oceanospirillum_linum_gca_001995095 Oceanospirillum_linum_gca_001995095 Ocea Oceanospirillum_multiglobuliferum_gca_002059185 Oceanospirillum_multiglobuliferum_gca_002059185 Oceanospirillum_multiglobuliferum_gca_002059185 Oceanospirillum_sp__gca_002684995 Oceanospirillum_sp__gca_002684995 Oceanospirillum_sp__gca_002684995 Oceanotoga_teriensis_gca_003148465 Oceanotoga_teriensis_gca_003148465 Oceanotoga_teriensis_gca_003148465 -OchPri2.0-Ens.110 Ochotona_princeps OchPri2.0-Ens.110 OchPri2.0-Ens.99 Ochotona_princeps OchPri2.0-Ens.99 pika.75 Ochotona_princeps pika.75 Ochrobactrum_anthropi Ochrobactrum_anthropi Ochrobactrum_anthropi @@ -43278,7 +43082,6 @@ Octadecabacter_arcticus_238_gca_000155735 Octadecabacter_arcticus_238_gca_0001 Octadecabacter_ascidiaceicola_gca_900185015 Octadecabacter_ascidiaceicola_gca_900185015 Octadecabacter_ascidiaceicola_gca_900185015 Octadecabacter_temperatus Octadecabacter_temperatus Octadecabacter_temperatus Octadecabacter_temperatus_gca_001187845 Octadecabacter_temperatus_gca_001187845 Octadecabacter_temperatus_gca_001187845 -OctDeg1.0.110 Octodon_degus OctDeg1.0.110 OctDeg1.0.99 Octodon_degus OctDeg1.0.99 Octopus_bimaculoides Octopus_bimaculoides Octopus_bimaculoides Octopus_bimaculoides_gca001194135v1 Octopus_bimaculoides_gca001194135v1 Octopus_bimaculoides_gca001194135v1 @@ -43439,9 +43242,6 @@ Omnitrophica_wor_2_bacterium_rifcsplowo2_12_full_63_16_gca_001805925 Omnitroph Omnitrophica_wor_2_bacterium_rifoxya2_full_38_17_gca_001805965 Omnitrophica_wor_2_bacterium_rifoxya2_full_38_17_gca_001805965 Omnitrophica_wor_2_bacterium_rifoxya2_full_38_17_gca_001805965 Omnitrophica_wor_2_bacterium_sm23_72_gca_001304135 Omnitrophica_wor_2_bacterium_sm23_72_gca_001304135 Omnitrophica_wor_2_bacterium_sm23_72_gca_001304135 Onchocerca_volvulus Onchocerca_volvulus Onchocerca_volvulus -Okis_V2.110 Oncorhynchus_kisutch Okis_V2.110 -USDA_OmykA_1.1.110 Oncorhynchus_mykiss USDA_OmykA_1.1.110 -Otsh_v1.0.110 Oncorhynchus_tshawytscha Otsh_v1.0.110 Onion_yellows_phytoplasma_oy_m Onion_yellows_phytoplasma_oy_m Onion_yellows_phytoplasma_oy_m Onion_yellows_phytoplasma_oy_m_gca_000009845 Onion_yellows_phytoplasma_oy_m_gca_000009845 Onion_yellows_phytoplasma_oy_m_gca_000009845 Onthophagus_taurus_gca000648695v2 Onthophagus_taurus_gca000648695v2 Onthophagus_taurus_gca000648695v2 @@ -43483,9 +43283,7 @@ Ordospora_colligata_oc4_gca_000803265 Ordospora_colligata_oc4_gca_000803265 Orenia_marismortui_gca_004365685 Orenia_marismortui_gca_004365685 Orenia_marismortui_gca_004365685 Orenia_metallireducens Orenia_metallireducens Orenia_metallireducens Orenia_metallireducens_gca_900215265 Orenia_metallireducens_gca_900215265 Orenia_metallireducens_gca_900215265 -ASM587006v1.110 Oreochromis_aureus ASM587006v1.110 ASM587006v1.99 Oreochromis_aureus ASM587006v1.99 -O_niloticus_UMD_NMBU.110 Oreochromis_niloticus O_niloticus_UMD_NMBU.110 O_niloticus_UMD_NMBU.99 Oreochromis_niloticus O_niloticus_UMD_NMBU.99 Orenil1.0.75 Oreochromis_niloticus Orenil1.0.75 Oribacterium_asaccharolyticum_acb7 Oribacterium_asaccharolyticum_acb7 Oribacterium_asaccharolyticum_acb7 @@ -43532,12 +43330,10 @@ Ornithobacterium_rhinotracheale_h06_030791 Ornithobacterium_rhinotracheale_h06 Ornithobacterium_rhinotracheale_ort_umn_88 Ornithobacterium_rhinotracheale_ort_umn_88 Ornithobacterium_rhinotracheale_ort_umn_88 OANA5.75 Ornithorhynchus_anatinus OANA5.75 OANA5.99 Ornithorhynchus_anatinus OANA5.99 -mOrnAna1.p.v1.110 Ornithorhynchus_anatinus mOrnAna1.p.v1.110 Orrella_dioscoreae Orrella_dioscoreae Orrella_dioscoreae Orrella_dioscoreae_gca_900089455 Orrella_dioscoreae_gca_900089455 Orrella_dioscoreae_gca_900089455 Orrella_marina_gca_003058465 Orrella_marina_gca_003058465 Orrella_marina_gca_003058465 Orussus_abietinus_gca000612105v2 Orussus_abietinus_gca000612105v2 Orussus_abietinus_gca000612105v2 -OryCun2.0.110 Oryctolagus_cuniculus OryCun2.0.110 OryCun2.0.75 Oryctolagus_cuniculus OryCun2.0.75 OryCun2.0.99 Oryctolagus_cuniculus OryCun2.0.99 Oryza_barthii Oryza_barthii Oryza_barthii @@ -43566,17 +43362,11 @@ Oryza_sativa_n22 Oryza_sativa_n22 Oryza_sativa_n22 Oryza_sativa_natelboro Oryza_sativa_natelboro Oryza_sativa_natelboro Oryza_sativa_pr106 Oryza_sativa_pr106 Oryza_sativa_pr106 Oryza_sativa_zs97 Oryza_sativa_zs97 Oryza_sativa_zs97 -OJAV_1.1.110 Oryzias_javanicus OJAV_1.1.110 -ASM223467v1.110 Oryzias_latipes ASM223467v1.110 ASM223467v1.99 Oryzias_latipes ASM223467v1.99 MEDAKA1.75 Oryzias_latipes MEDAKA1.75 -ASM223471v1.110 Oryzias_latipes_hni ASM223471v1.110 ASM223471v1.99 Oryzias_latipes_hni ASM223471v1.99 -ASM223469v1.110 Oryzias_latipes_hsok ASM223469v1.110 ASM223469v1.99 Oryzias_latipes_hsok ASM223469v1.99 -Om_v0.7.RACA.110 Oryzias_melastigma Om_v0.7.RACA.110 Om_v0.7.RACA.99 Oryzias_melastigma Om_v0.7.RACA.99 -ASM858656v1.110 Oryzias_sinensis ASM858656v1.110 Oryzisolibacter_propanilivorax_gca_900103645 Oryzisolibacter_propanilivorax_gca_900103645 Oryzisolibacter_propanilivorax_gca_900103645 Oscillatoria_acuminata_pcc_6304 Oscillatoria_acuminata_pcc_6304 Oscillatoria_acuminata_pcc_6304 Oscillatoria_acuminata_pcc_6304_gca_000317105 Oscillatoria_acuminata_pcc_6304_gca_000317105 Oscillatoria_acuminata_pcc_6304_gca_000317105 @@ -43623,17 +43413,13 @@ Osedax_symbiont_rs1_gca_000416275 Osedax_symbiont_rs1_gca_000416275 Osedax_s Osedax_symbiont_rs2_gca_000416315 Osedax_symbiont_rs2_gca_000416315 Osedax_symbiont_rs2_gca_000416315 Ostreococcus_lucimarinus Ostreococcus_lucimarinus Ostreococcus_lucimarinus Otariodibacter_oris_gca_003634665 Otariodibacter_oris_gca_003634665 Otariodibacter_oris_gca_003634665 -OtoGar3.110 Otolemur_garnettii OtoGar3.110 OtoGar3.75 Otolemur_garnettii OtoGar3.75 OtoGar3.99 Otolemur_garnettii OtoGar3.99 Ottowia_oryzae_gca_003008535 Ottowia_oryzae_gca_003008535 Ottowia_oryzae_gca_003008535 Ottowia_sp_oral_taxon_894 Ottowia_sp_oral_taxon_894 Ottowia_sp_oral_taxon_894 Ottowia_sp_oral_taxon_894_gca_001262075 Ottowia_sp_oral_taxon_894_gca_001262075 Ottowia_sp_oral_taxon_894_gca_001262075 -OtuSun1.0.110 Otus_sunia OtuSun1.0.110 -Oar_v3.1.110 Ovis_aries Oar_v3.1.110 Oar_v3.1.75 Ovis_aries Oar_v3.1.75 Oar_v3.1.99 Ovis_aries Oar_v3.1.99 -Oar_rambouillet_v1.0.110 Ovis_aries_rambouillet Oar_rambouillet_v1.0.110 Owenia_fusiformis_gca903813345v1 Owenia_fusiformis_gca903813345v1 Owenia_fusiformis_gca903813345v1 Owenweeksia_hongkongensis_dsm_17368 Owenweeksia_hongkongensis_dsm_17368 Owenweeksia_hongkongensis_dsm_17368 Owenweeksia_hongkongensis_dsm_17368_gca_000236705 Owenweeksia_hongkongensis_dsm_17368_gca_000236705 Owenweeksia_hongkongensis_dsm_17368_gca_000236705 @@ -44061,10 +43847,8 @@ Paludibacter_sp_47_17_gca_001898935 Paludibacter_sp_47_17_gca_001898935 Palu Paludibacterium_purpuratum_gca_004363805 Paludibacterium_purpuratum_gca_004363805 Paludibacterium_purpuratum_gca_004363805 Paludifilum_halophilum_gca_002245355 Paludifilum_halophilum_gca_002245355 Paludifilum_halophilum_gca_002245355 Paludisphaera_borealis_gca_001956985 Paludisphaera_borealis_gca_001956985 Paludisphaera_borealis_gca_001956985 -panpan1.1.110 Pan_paniscus panpan1.1.110 panpan1.1.99 Pan_paniscus panpan1.1.99 CHIMP2.1.4.75 Pan_troglodytes CHIMP2.1.4.75 -Pan_tro_3.0.110 Pan_troglodytes Pan_tro_3.0.110 Pan_tro_3.0.99 Pan_troglodytes Pan_tro_3.0.99 Panacagrimonas_perspica_gca_004364935 Panacagrimonas_perspica_gca_004364935 Panacagrimonas_perspica_gca_004364935 Panacagrimonas_perspica_gca_004799025 Panacagrimonas_perspica_gca_004799025 Panacagrimonas_perspica_gca_004799025 @@ -44107,10 +43891,7 @@ Pannonibacter_indicus_gca_001517385 Pannonibacter_indicus_gca_001517385 Pann Pannonibacter_phragmitetus Pannonibacter_phragmitetus Pannonibacter_phragmitetus Pannonibacter_phragmitetus_gca_001484065 Pannonibacter_phragmitetus_gca_001484065 Pannonibacter_phragmitetus_gca_001484065 Pannonibacter_phragmitetus_gca_900454465 Pannonibacter_phragmitetus_gca_900454465 Pannonibacter_phragmitetus_gca_900454465 -PanLeo1.0.110 Panthera_leo PanLeo1.0.110 -PanPar1.0.110 Panthera_pardus PanPar1.0.110 PanPar1.0.99 Panthera_pardus PanPar1.0.99 -PanTig1.0.110 Panthera_tigris_altaica PanTig1.0.110 PanTig1.0.99 Panthera_tigris_altaica PanTig1.0.99 Pantoea_agglomerans Pantoea_agglomerans Pantoea_agglomerans Pantoea_agglomerans_299r Pantoea_agglomerans_299r Pantoea_agglomerans_299r @@ -44217,7 +43998,6 @@ Pantoea_wallisii_gca_002095485 Pantoea_wallisii_gca_002095485 Pantoea_wallis Papaver_somniferum Papaver_somniferum Papaver_somniferum Papillibacter_cinnamivorans_dsm_12816_gca_900176335 Papillibacter_cinnamivorans_dsm_12816_gca_900176335 Papillibacter_cinnamivorans_dsm_12816_gca_900176335 Panu_3.0.99 Papio_anubis Panu_3.0.99 -Panubis1.0.110 Papio_anubis Panubis1.0.110 Parabacteroides_acidifaciens_gca_003363715 Parabacteroides_acidifaciens_gca_003363715 Parabacteroides_acidifaciens_gca_003363715 Parabacteroides_chartae_gca_900168155 Parabacteroides_chartae_gca_900168155 Parabacteroides_chartae_gca_900168155 Parabacteroides_chinchillae_gca_900108035 Parabacteroides_chinchillae_gca_900108035 Parabacteroides_chinchillae_gca_900108035 @@ -44550,13 +44330,11 @@ Paraliobacillus_ryukyuensis_gca_003315295 Paraliobacillus_ryukyuensis_gca_0033 Paraliobacillus_sp_pm_2 Paraliobacillus_sp_pm_2 Paraliobacillus_sp_pm_2 Paraliobacillus_sp_pm_2_gca_001368815 Paraliobacillus_sp_pm_2_gca_001368815 Paraliobacillus_sp_pm_2_gca_001368815 Paramaledivibacter_caminithermalis_dsm_15212_gca_900142245 Paramaledivibacter_caminithermalis_dsm_15212_gca_900142245 Paramaledivibacter_caminithermalis_dsm_15212_gca_900142245 -fParRan2.1.110 Parambassis_ranga fParRan2.1.110 fParRan2.1.99 Parambassis_ranga fParRan2.1.99 Paramecium_tetraurelia Paramecium_tetraurelia Paramecium_tetraurelia Paramesorhizobium_deserti Paramesorhizobium_deserti Paramesorhizobium_deserti Paramesorhizobium_deserti_gca_001558695 Paramesorhizobium_deserti_gca_001558695 Paramesorhizobium_deserti_gca_001558695 Paramicrosporidium_saccamoebae_gca_002794465 Paramicrosporidium_saccamoebae_gca_002794465 Paramicrosporidium_saccamoebae_gca_002794465 -PKINGS_0.1.110 Paramormyrops_kingsleyae PKINGS_0.1.110 PKINGS_0.1.99 Paramormyrops_kingsleyae PKINGS_0.1.99 Paramuribaculum_intestinale_gca_003024815 Paramuribaculum_intestinale_gca_003024815 Paramuribaculum_intestinale_gca_003024815 Paraoerskovia_marina_gca_900105445 Paraoerskovia_marina_gca_900105445 Paraoerskovia_marina_gca_900105445 @@ -44818,7 +44596,6 @@ Parendozoicomonas_haliclonae_gca_900174585 Parendozoicomonas_haliclonae_gca_90 Parenemella_sanctibonifatiensis_gca_002250475 Parenemella_sanctibonifatiensis_gca_002250475 Parenemella_sanctibonifatiensis_gca_002250475 Parenemella_sanctibonifatiensis_gca_002250565 Parenemella_sanctibonifatiensis_gca_002250565 Parenemella_sanctibonifatiensis_gca_002250565 Paroceanicella_profunda_gca_005887635 Paroceanicella_profunda_gca_005887635 Paroceanicella_profunda_gca_005887635 -Parus_major1.1.110 Parus_major Parus_major1.1.110 Parus_major1.1.99 Parus_major Parus_major1.1.99 Parvibacter_caecicola_gca_005046025 Parvibacter_caecicola_gca_005046025 Parvibacter_caecicola_gca_005046025 Parvibaculum_lavamentivorans_ds_1 Parvibaculum_lavamentivorans_ds_1 Parvibaculum_lavamentivorans_ds_1 @@ -44940,7 +44717,6 @@ Paucilactobacillus_vaccinostercus_dsm_20634_gca_001436295 Paucilactobacillus_v Paucilactobacillus_wasatchensis_gca_000876205 Paucilactobacillus_wasatchensis_gca_000876205 Paucilactobacillus_wasatchensis_gca_000876205 Paucimonas_lemoignei_gca_004342585 Paucimonas_lemoignei_gca_004342585 Paucimonas_lemoignei_gca_004342585 Paucimonas_lemoignei_gca_900475325 Paucimonas_lemoignei_gca_900475325 Paucimonas_lemoignei_gca_900475325 -AIIM_Pcri_1.0.110 Pavo_cristatus AIIM_Pcri_1.0.110 AIIM_Pcri_1.0.99 Pavo_cristatus AIIM_Pcri_1.0.99 Paxillus_involutus_atcc_200175_gca_000827475 Paxillus_involutus_atcc_200175_gca_000827475 Paxillus_involutus_atcc_200175_gca_000827475 Paxillus_rubicundulus_ve08_2h10_gca_000827395 Paxillus_rubicundulus_ve08_2h10_gca_000827395 Paxillus_rubicundulus_ve08_2h10_gca_000827395 @@ -45196,7 +44972,6 @@ Pelodictyon_luteolum_dsm_273_gca_000012485 Pelodictyon_luteolum_dsm_273_gca_00 Pelodictyon_luteolum_gca_001622165 Pelodictyon_luteolum_gca_001622165 Pelodictyon_luteolum_gca_001622165 Pelodictyon_phaeoclathratiforme_bu_1 Pelodictyon_phaeoclathratiforme_bu_1 Pelodictyon_phaeoclathratiforme_bu_1 Pelodictyon_phaeoclathratiforme_bu_1_gca_000020645 Pelodictyon_phaeoclathratiforme_bu_1_gca_000020645 Pelodictyon_phaeoclathratiforme_bu_1_gca_000020645 -PelSin_1.0.110 Pelodiscus_sinensis PelSin_1.0.110 PelSin_1.0.75 Pelodiscus_sinensis PelSin_1.0.75 PelSin_1.0.99 Pelodiscus_sinensis PelSin_1.0.99 Pelolinea_submarina_gca_003385075 Pelolinea_submarina_gca_003385075 Pelolinea_submarina_gca_003385075 @@ -45229,7 +45004,6 @@ Pelotomaculum_sp_ptau1_bin065_gca_002067395 Pelotomaculum_sp_ptau1_bin065_gca_ Pelotomaculum_thermopropionicum_si Pelotomaculum_thermopropionicum_si Pelotomaculum_thermopropionicum_si Pelotomaculum_thermopropionicum_si_gca_000010565 Pelotomaculum_thermopropionicum_si_gca_000010565 Pelotomaculum_thermopropionicum_si_gca_000010565 Peltaster_fructicola_gca_001592805 Peltaster_fructicola_gca_001592805 Peltaster_fructicola_gca_001592805 -Pelusios_castaneus-1.0.110 Pelusios_castaneus Pelusios_castaneus-1.0.110 Penaeus_chinensis_gca019202785v2rs Penaeus_chinensis_gca019202785v2rs Penaeus_chinensis_gca019202785v2rs Penaeus_japonicus_gca017312705v1 Penaeus_japonicus_gca017312705v1 Penaeus_japonicus_gca017312705v1 Penaeus_monodon_gca015228065v1 Penaeus_monodon_gca015228065v1 Penaeus_monodon_gca015228065v1 @@ -45371,13 +45145,11 @@ Peribacillus_simplex_gca_900000145 Peribacillus_simplex_gca_900000145 Periba Peribacillus_simplex_gca_900156045 Peribacillus_simplex_gca_900156045 Peribacillus_simplex_gca_900156045 Peribacillus_simplex_nbrc_15720_dsm_1321_gca_002243645 Peribacillus_simplex_nbrc_15720_dsm_1321_gca_002243645 Peribacillus_simplex_nbrc_15720_dsm_1321_gca_002243645 Periconia_macrospinosa_gca_003073855 Periconia_macrospinosa_gca_003073855 Periconia_macrospinosa_gca_003073855 -PM.fa.110 Periophthalmus_magnuspinnatus PM.fa.110 PM.fa.99 Periophthalmus_magnuspinnatus PM.fa.99 Periweissella_cryptocerci_gca_004358325 Periweissella_cryptocerci_gca_004358325 Periweissella_cryptocerci_gca_004358325 Perkinsela_sp_ccap_1560_4_gca_001235845 Perkinsela_sp_ccap_1560_4_gca_001235845 Perkinsela_sp_ccap_1560_4_gca_001235845 Perkinsus_marinus_atcc_50983_gca_000006405 Perkinsus_marinus_atcc_50983_gca_000006405 Perkinsus_marinus_atcc_50983_gca_000006405 Permianibacter_aggregans_gca_004363125 Permianibacter_aggregans_gca_004363125 Permianibacter_aggregans_gca_004363125 -HU_Pman_2.1.110 Peromyscus_maniculatus_bairdii HU_Pman_2.1.110 HU_Pman_2.1.99 Peromyscus_maniculatus_bairdii HU_Pman_2.1.99 Peronospora_effusa_gca_003704535 Peronospora_effusa_gca_003704535 Peronospora_effusa_gca_003704535 Peronospora_effusa_gca_003843895 Peronospora_effusa_gca_003843895 Peronospora_effusa_gca_003843895 @@ -45388,7 +45160,6 @@ Pestalotiopsis_fici_w106_1_gca_000516985 Pestalotiopsis_fici_w106_1_gca_000516 Petrimonas_mucosa_gca_900095795 Petrimonas_mucosa_gca_900095795 Petrimonas_mucosa_gca_900095795 Petrimonas_sp_ibaraki_gca_002356435 Petrimonas_sp_ibaraki_gca_002356435 Petrimonas_sp_ibaraki_gca_002356435 Petrocella_atlantisensis_gca_900538275 Petrocella_atlantisensis_gca_900538275 Petrocella_atlantisensis_gca_900538275 -Pmarinus_7.0.110 Petromyzon_marinus Pmarinus_7.0.110 Pmarinus_7.0.75 Petromyzon_marinus Pmarinus_7.0.75 Pmarinus_7.0.99 Petromyzon_marinus Pmarinus_7.0.99 Petrotoga_halophila_dsm_16923_gca_002924615 Petrotoga_halophila_dsm_16923_gca_002924615 Petrotoga_halophila_dsm_16923_gca_002924615 @@ -45453,10 +45224,8 @@ Phascolarctobacterium_succinatutens_gca_001916865 Phascolarctobacterium_succin Phascolarctobacterium_succinatutens_gca_003452535 Phascolarctobacterium_succinatutens_gca_003452535 Phascolarctobacterium_succinatutens_gca_003452535 Phascolarctobacterium_succinatutens_yit_12067 Phascolarctobacterium_succinatutens_yit_12067 Phascolarctobacterium_succinatutens_yit_12067 Phascolarctobacterium_succinatutens_yit_12067_gca_000188175 Phascolarctobacterium_succinatutens_yit_12067_gca_000188175 Phascolarctobacterium_succinatutens_yit_12067_gca_000188175 -phaCin_unsw_v4.1.110 Phascolarctos_cinereus phaCin_unsw_v4.1.110 phaCin_unsw_v4.1.99 Phascolarctos_cinereus phaCin_unsw_v4.1.99 Phaseolus_vulgaris Phaseolus_vulgaris Phaseolus_vulgaris -ASM414374v1.110 Phasianus_colchicus ASM414374v1.110 ASM414374v1.99 Phasianus_colchicus ASM414374v1.99 Phellinidium_pouzarii_gca_004802695 Phellinidium_pouzarii_gca_004802695 Phellinidium_pouzarii_gca_004802695 Phellinus_noxius_gca_002287475 Phellinus_noxius_gca_002287475 Phellinus_noxius_gca_002287475 @@ -45560,7 +45329,6 @@ Phocaeicola_vulgatus_gca_900109635 Phocaeicola_vulgatus_gca_900109635 Phocae Phocaeicola_vulgatus_gca_900445545 Phocaeicola_vulgatus_gca_900445545 Phocaeicola_vulgatus_gca_900445545 Phocaeicola_vulgatus_pc510_gca_000178195 Phocaeicola_vulgatus_pc510_gca_000178195 Phocaeicola_vulgatus_pc510_gca_000178195 Phocaeicola_vulgatus_str_3975_rp4_gca_000699865 Phocaeicola_vulgatus_str_3975_rp4_gca_000699865 Phocaeicola_vulgatus_str_3975_rp4_gca_000699865 -mPhoSin1.pri.110 Phocoena_sinus mPhoSin1.pri.110 Phocoenobacter_uteri_gca_900454895 Phocoenobacter_uteri_gca_900454895 Phocoenobacter_uteri_gca_900454895 Phorcysia_thermohydrogeniphila_gca_004339575 Phorcysia_thermohydrogeniphila_gca_004339575 Phorcysia_thermohydrogeniphila_gca_004339575 Phormidesmis_priestleyi_ana Phormidesmis_priestleyi_ana Phormidesmis_priestleyi_ana @@ -45767,7 +45535,6 @@ Phyllobacterium_sp_yr620_gca_900104165 Phyllobacterium_sp_yr620_gca_900104165 Phyllobacterium_zundukense_gca_002763465 Phyllobacterium_zundukense_gca_002763465 Phyllobacterium_zundukense_gca_002763465 Physcomitrella_patens Physcomitrella_patens Physcomitrella_patens Physcomitrium_patens Physcomitrium_patens Physcomitrium_patens -ASM283717v2.110 Physeter_catodon ASM283717v2.110 ASM283717v2.99 Physeter_catodon ASM283717v2.99 Phytoactinopolyspora_halophila_gca_003287285 Phytoactinopolyspora_halophila_gca_003287285 Phytoactinopolyspora_halophila_gca_003287285 Phytobacter_diazotrophicus_gca_004346725 Phytobacter_diazotrophicus_gca_004346725 Phytobacter_diazotrophicus_gca_004346725 @@ -45813,7 +45580,6 @@ Pigmentiphaga_sp_h8_gca_003854895 Pigmentiphaga_sp_h8_gca_003854895 Pigmenti Pigmentiphaga_sp_nml030171_gca_002188635 Pigmentiphaga_sp_nml030171_gca_002188635 Pigmentiphaga_sp_nml030171_gca_002188635 Pigmentiphaga_sp_nml080357_gca_002188465 Pigmentiphaga_sp_nml080357_gca_002188465 Pigmentiphaga_sp_nml080357_gca_002188465 Pilibacter_termitis_gca_900167335 Pilibacter_termitis_gca_900167335 Pilibacter_termitis_gca_900167335 -ASM277652v2.110 Piliocolobus_tephrosceles ASM277652v2.110 ASM277652v2.99 Piliocolobus_tephrosceles ASM277652v2.99 Piloderma_croceum_f_1598_gca_000827315 Piloderma_croceum_f_1598_gca_000827315 Piloderma_croceum_f_1598_gca_000827315 Pimelobacter_simplex Pimelobacter_simplex Pimelobacter_simplex @@ -46040,19 +45806,13 @@ Pneumocystis_murina_b123_gca_000349005 Pneumocystis_murina_b123_gca_000349005 Pochonia_chlamydosporia_123_gca_000411695 Pochonia_chlamydosporia_123_gca_000411695 Pochonia_chlamydosporia_123_gca_000411695 Pochonia_chlamydosporia_170_gca_001653235 Pochonia_chlamydosporia_170_gca_001653235 Pochonia_chlamydosporia_170_gca_001653235 Pocillopora_damicornis_gca003704095v1 Pocillopora_damicornis_gca003704095v1 Pocillopora_damicornis_gca003704095v1 -PodMur_1.0.110 Podarcis_muralis PodMur_1.0.110 PodMur_1.0.99 Podarcis_muralis PodMur_1.0.99 Podospora_anserina_s_mat__gca_000226545 Podospora_anserina_s_mat__gca_000226545 Podospora_anserina_s_mat__gca_000226545 Podospora_anserina_s_mat_gca_000226545 Podospora_anserina_s_mat_gca_000226545 Podospora_anserina_s_mat_gca_000226545 -PoeFor_5.1.2.110 Poecilia_formosa PoeFor_5.1.2.110 PoeFor_5.1.2.99 Poecilia_formosa PoeFor_5.1.2.99 -P_latipinna-1.0.110 Poecilia_latipinna P_latipinna-1.0.110 P_latipinna-1.0.99 Poecilia_latipinna P_latipinna-1.0.99 -P_mexicana-1.0.110 Poecilia_mexicana P_mexicana-1.0.110 P_mexicana-1.0.99 Poecilia_mexicana P_mexicana-1.0.99 -Guppy_female_1.0_MT.110 Poecilia_reticulata Guppy_female_1.0_MT.110 Guppy_female_1.0_MT.99 Poecilia_reticulata Guppy_female_1.0_MT.99 -pvi1.1.110 Pogona_vitticeps pvi1.1.110 pvi1.1.99 Pogona_vitticeps pvi1.1.99 Pogonomyrmex_barbatus_gca000187915v1rs Pogonomyrmex_barbatus_gca000187915v1rs Pogonomyrmex_barbatus_gca000187915v1rs Pokkaliibacter_plantistimulans_gca_003194385 Pokkaliibacter_plantistimulans_gca_003194385 Pokkaliibacter_plantistimulans_gca_003194385 @@ -46139,7 +45899,6 @@ Pomacea_canaliculata_gca003073045v1 Pomacea_canaliculata_gca003073045v1 Poma Pomphorhynchus_laevis_gca012934845v2gb Pomphorhynchus_laevis_gca012934845v2gb Pomphorhynchus_laevis_gca012934845v2gb PPYG2.75 Pongo_abelii PPYG2.75 PPYG2.99 Pongo_abelii PPYG2.99 -Susie_PABv2.110 Pongo_abelii Susie_PABv2.110 Pontibaca_methylaminivorans_gca_900156525 Pontibaca_methylaminivorans_gca_900156525 Pontibaca_methylaminivorans_gca_900156525 Pontibacillus_chungwhensis_bh030062 Pontibacillus_chungwhensis_bh030062 Pontibacillus_chungwhensis_bh030062 Pontibacillus_chungwhensis_bh030062_gca_000770675 Pontibacillus_chungwhensis_bh030062_gca_000770675 Pontibacillus_chungwhensis_bh030062_gca_000770675 @@ -46645,7 +46404,6 @@ Primorskyibacter_flagellatus_gca_900176485 Primorskyibacter_flagellatus_gca_90 Primorskyibacter_sedentarius_gca_004342065 Primorskyibacter_sedentarius_gca_004342065 Primorskyibacter_sedentarius_gca_004342065 Pristionchus_pacificus Pristionchus_pacificus Pristionchus_pacificus Procambarus_clarkii_gca020424385v2 Procambarus_clarkii_gca020424385v2 Procambarus_clarkii_gca020424385v2 -proCap1.110 Procavia_capensis proCap1.110 proCap1.75 Procavia_capensis proCap1.75 proCap1.99 Procavia_capensis proCap1.99 Prochlorococcus_marinus_str_as9601 Prochlorococcus_marinus_str_as9601 Prochlorococcus_marinus_str_as9601 @@ -46733,7 +46491,6 @@ Prochlorococcus_sp_rs01_gca_001989435 Prochlorococcus_sp_rs01_gca_001989435 Prochlorococcus_sp_ss52 Prochlorococcus_sp_ss52 Prochlorococcus_sp_ss52 Prochlorothrix_hollandica_pcc_9006_gca_000341585 Prochlorothrix_hollandica_pcc_9006_gca_000341585 Prochlorothrix_hollandica_pcc_9006_gca_000341585 Profundibacter_amoris_gca_003544895 Profundibacter_amoris_gca_003544895 Profundibacter_amoris_gca_003544895 -Prosim_1.0.110 Prolemur_simus Prosim_1.0.110 Prosim_1.0.99 Prolemur_simus Prosim_1.0.99 Prolinoborus_fasciculus_gca_900322255 Prolinoborus_fasciculus_gca_900322255 Prolinoborus_fasciculus_gca_900322255 Prolixibacter_denitrificans_gca_003014495 Prolixibacter_denitrificans_gca_003014495 Prolixibacter_denitrificans_gca_003014495 @@ -46926,7 +46683,6 @@ Propionispora_sp_2_2_37 Propionispora_sp_2_2_37 Propionispora_sp_2_2_37 Propionispora_sp_2_2_37_gca_001298735 Propionispora_sp_2_2_37_gca_001298735 Propionispora_sp_2_2_37_gca_001298735 Propionispora_vibrioides_gca_900110485 Propionispora_vibrioides_gca_900110485 Propionispora_vibrioides_gca_900110485 Propionivibrio_dicarboxylicus_gca_900099695 Propionivibrio_dicarboxylicus_gca_900099695 Propionivibrio_dicarboxylicus_gca_900099695 -Pcoq_1.0.110 Propithecus_coquereli Pcoq_1.0.110 Pcoq_1.0.99 Propithecus_coquereli Pcoq_1.0.99 Prosthecobacter_debontii_gca_900167535 Prosthecobacter_debontii_gca_900167535 Prosthecobacter_debontii_gca_900167535 Prosthecobacter_fusiformis_gca_004364345 Prosthecobacter_fusiformis_gca_004364345 Prosthecobacter_fusiformis_gca_004364345 @@ -49748,7 +49504,6 @@ Pseudomonas_yangmingensis_gca_900114825 Pseudomonas_yangmingensis_gca_90011482 Pseudomonas_zeshuii_gca_900141925 Pseudomonas_zeshuii_gca_900141925 Pseudomonas_zeshuii_gca_900141925 Pseudomonas_zhaodongensis_gca_003293815 Pseudomonas_zhaodongensis_gca_003293815 Pseudomonas_zhaodongensis_gca_003293815 Pseudomonas_zhaodongensis_gca_003696365 Pseudomonas_zhaodongensis_gca_003696365 Pseudomonas_zhaodongensis_gca_003696365 -EBS10Xv2-PRI.110 Pseudonaja_textilis EBS10Xv2-PRI.110 EBS10Xv2-PRI.99 Pseudonaja_textilis EBS10Xv2-PRI.99 Pseudonitzschia_multistriata Pseudonitzschia_multistriata Pseudonitzschia_multistriata Pseudonocardia_alni_gca_002813375 Pseudonocardia_alni_gca_002813375 Pseudonocardia_alni_gca_002813375 @@ -49970,7 +49725,6 @@ Psychromonas_sp_psych_6c06_gca_002835465 Psychromonas_sp_psych_6c06_gca_002835 Psychromonas_sp_urea_02u_13_gca_002835995 Psychromonas_sp_urea_02u_13_gca_002835995 Psychromonas_sp_urea_02u_13_gca_002835995 Psychroserpens_sp_njdz02_gca_004843725 Psychroserpens_sp_njdz02_gca_004843725 Psychroserpens_sp_njdz02_gca_004843725 Psychrosphaera_saromensis_gca_002954545 Psychrosphaera_saromensis_gca_002954545 Psychrosphaera_saromensis_gca_002954545 -pteVam1.110 Pteropus_vampyrus pteVam1.110 pteVam1.75 Pteropus_vampyrus pteVam1.75 pteVam1.99 Pteropus_vampyrus pteVam1.99 Pterula_gracilis_gca_004369125 Pterula_gracilis_gca_004369125 Pterula_gracilis_gca_004369125 @@ -49990,7 +49744,6 @@ Pueribacillus_theae_gca_003097615 Pueribacillus_theae_gca_003097615 Pueribac Pukyongia_salina_gca_002966125 Pukyongia_salina_gca_002966125 Pukyongia_salina_gca_002966125 Pukyongiella_litopenaei_gca_003008555 Pukyongiella_litopenaei_gca_003008555 Pukyongiella_litopenaei_gca_003008555 Punctularia_strigosozonata_hhb_11173_ss5_gca_000264995 Punctularia_strigosozonata_hhb_11173_ss5_gca_000264995 Punctularia_strigosozonata_hhb_11173_ss5_gca_000264995 -PunNye1.0.110 Pundamilia_nyererei PunNye1.0.110 PunNye1.0.99 Pundamilia_nyererei PunNye1.0.99 Puniceibacterium_antarcticum_gca_002760615 Puniceibacterium_antarcticum_gca_002760615 Puniceibacterium_antarcticum_gca_002760615 Puniceibacterium_sediminis_gca_900188035 Puniceibacterium_sediminis_gca_900188035 Puniceibacterium_sediminis_gca_900188035 @@ -50019,7 +49772,6 @@ Pustulibacterium_marinum_gca_900116665 Pustulibacterium_marinum_gca_900116665 Puteibacter_caeruleilacunae_gca_005217565 Puteibacter_caeruleilacunae_gca_005217565 Puteibacter_caeruleilacunae_gca_005217565 Putridiphycobacter_roseus_gca_003234935 Putridiphycobacter_roseus_gca_003234935 Putridiphycobacter_roseus_gca_003234935 Pvc_group_bacterium_ex_bugula_neritina_ab1__gca_001730085 Pvc_group_bacterium_ex_bugula_neritina_ab1__gca_001730085 Pvc_group_bacterium_ex_bugula_neritina_ab1__gca_001730085 -Pygocentrus_nattereri-1.0.2.110 Pygocentrus_nattereri Pygocentrus_nattereri-1.0.2.110 Pygocentrus_nattereri-1.0.2.99 Pygocentrus_nattereri Pygocentrus_nattereri-1.0.2.99 Pyramidobacter_piscolens_w5455 Pyramidobacter_piscolens_w5455 Pyramidobacter_piscolens_w5455 Pyramidobacter_piscolens_w5455_gca_000177335 Pyramidobacter_piscolens_w5455_gca_000177335 Pyramidobacter_piscolens_w5455_gca_000177335 @@ -50262,10 +50014,6 @@ Rathayibacter_tritici_gca_001641005 Rathayibacter_tritici_gca_001641005 Rath Rathayibacter_tritici_gca_002931485 Rathayibacter_tritici_gca_002931485 Rathayibacter_tritici_gca_002931485 Rnor_5.0.75 Rattus_norvegicus Rnor_5.0.75 Rnor_6.0.99 Rattus_norvegicus Rnor_6.0.99 -mRatBN7.2.110 Rattus_norvegicus mRatBN7.2.110 -UTH_Rnor_SHRSP_BbbUtx_1.0.110 Rattus_norvegicus_shrspbbbutx UTH_Rnor_SHRSP_BbbUtx_1.0.110 -UTH_Rnor_SHR_Utx.110 Rattus_norvegicus_shrutx UTH_Rnor_SHR_Utx.110 -UTH_Rnor_WKY_Bbb_1.0.110 Rattus_norvegicus_wkybbb UTH_Rnor_WKY_Bbb_1.0.110 Reichenbachiella_agariperforans_gca_900142205 Reichenbachiella_agariperforans_gca_900142205 Reichenbachiella_agariperforans_gca_900142205 Reichenbachiella_faecimaris_gca_900176375 Reichenbachiella_faecimaris_gca_900176375 Reichenbachiella_faecimaris_gca_900176375 Reichenbachiella_sp_5m10_gca_002742335 Reichenbachiella_sp_5m10_gca_002742335 Reichenbachiella_sp_5m10_gca_002742335 @@ -50301,11 +50049,8 @@ Rheinheimera_sp_sa_1_gca_001669775 Rheinheimera_sp_sa_1_gca_001669775 Rheinh Rheinheimera_sp_yqf_1_gca_004005375 Rheinheimera_sp_yqf_1_gca_004005375 Rheinheimera_sp_yqf_1_gca_004005375 Rhinocladiella_mackenziei_cbs_650_93_gca_000835555 Rhinocladiella_mackenziei_cbs_650_93_gca_000835555 Rhinocladiella_mackenziei_cbs_650_93_gca_000835555 KF569996.1 Rhinolophus KF569996.1 -mRhiFer1_v1.p.110 Rhinolophus_ferrumequinum mRhiFer1_v1.p.110 mRhiFer1_v1.p.99 Rhinolophus_ferrumequinum mRhiFer1_v1.p.99 -ASM169854v1.110 Rhinopithecus_bieti ASM169854v1.110 ASM169854v1.99 Rhinopithecus_bieti ASM169854v1.99 -Rrox_v1.110 Rhinopithecus_roxellana Rrox_v1.110 Rrox_v1.99 Rhinopithecus_roxellana Rrox_v1.99 Rhipicephalus_microplus_gca013339725v1 Rhipicephalus_microplus_gca013339725v1 Rhipicephalus_microplus_gca013339725v1 Rhipicephalus_sanguineus_gca013339695v1 Rhipicephalus_sanguineus_gca013339695v1 Rhipicephalus_sanguineus_gca013339695v1 @@ -52028,7 +51773,6 @@ Saccharomonospora_xinjiangensis_xj_54_gca_000258175 Saccharomonospora_xinjiang Saccharomyces_arboricola_h_6_gca_000292725 Saccharomyces_arboricola_h_6_gca_000292725 Saccharomyces_arboricola_h_6_gca_000292725 Saccharomyces_boulardii_nom_inval_gca_001298375 Saccharomyces_boulardii_nom_inval_gca_001298375 Saccharomyces_boulardii_nom_inval_gca_001298375 Saccharomyces_boulardii_nom_inval_gca_001413975 Saccharomyces_boulardii_nom_inval_gca_001413975 Saccharomyces_boulardii_nom_inval_gca_001413975 -R64-1-1.110 Saccharomyces_cerevisiae R64-1-1.110 R64-1-1.75 Saccharomyces_cerevisiae R64-1-1.75 R64-1-1.99 Saccharomyces_cerevisiae R64-1-1.99 Saccharomyces_cerevisiae Saccharomyces_cerevisiae Saccharomyces_cerevisiae @@ -52195,14 +51939,12 @@ Saccoglossus_kowalevskii_gca000003605v1 Saccoglossus_kowalevskii_gca000003605v Saezia_sanguinis_gca_003991585 Saezia_sanguinis_gca_003991585 Saezia_sanguinis_gca_003991585 Sagittula_sp_p11_gca_002814095 Sagittula_sp_p11_gca_002814095 Sagittula_sp_p11_gca_002814095 Sagittula_stellata_e_37 Sagittula_stellata_e_37 Sagittula_stellata_e_37 -SaiBol1.0.110 Saimiri_boliviensis_boliviensis SaiBol1.0.110 SaiBol1.0.99 Saimiri_boliviensis_boliviensis SaiBol1.0.99 Saitoella_complicata_nrrl_y_17804_gca_000227095 Saitoella_complicata_nrrl_y_17804_gca_000227095 Saitoella_complicata_nrrl_y_17804_gca_000227095 Saitoella_complicata_nrrl_y_17804_gca_001661265 Saitoella_complicata_nrrl_y_17804_gca_001661265 Saitoella_complicata_nrrl_y_17804_gca_001661265 Saitozyma_podzolica_gca_003942215 Saitozyma_podzolica_gca_003942215 Saitozyma_podzolica_gca_003942215 Sala_cibi_gca_003722095 Sala_cibi_gca_003722095 Sala_cibi_gca_003722095 Salana_multivorans_gca_003751805 Salana_multivorans_gca_003751805 Salana_multivorans_gca_003751805 -fSalaFa1.1.110 Salarias_fasciatus fSalaFa1.1.110 fSalaFa1.1.99 Salarias_fasciatus fSalaFa1.1.99 Salegentibacter_agarivorans_gca_900113135 Salegentibacter_agarivorans_gca_900113135 Salegentibacter_agarivorans_gca_900113135 Salegentibacter_echinorum_gca_900129445 Salegentibacter_echinorum_gca_900129445 Salegentibacter_echinorum_gca_900129445 @@ -52313,8 +52055,6 @@ Salisediminibacterium_beveridgei_gca_001721685 Salisediminibacterium_beveridge Salisediminibacterium_haloalkalitolerans_gca_900111285 Salisediminibacterium_haloalkalitolerans_gca_900111285 Salisediminibacterium_haloalkalitolerans_gca_900111285 Saliterribacillus_persicus_gca_003337485 Saliterribacillus_persicus_gca_003337485 Saliterribacillus_persicus_gca_003337485 ICSASG_v2.99 Salmo_salar ICSASG_v2.99 -Ssal_v3.1.110 Salmo_salar Ssal_v3.1.110 -fSalTru1.1.110 Salmo_trutta fSalTru1.1.110 fSalTru1.1.99 Salmo_trutta fSalTru1.1.99 Salmonella_bongori_gca_900635485 Salmonella_bongori_gca_900635485 Salmonella_bongori_gca_900635485 Salmonella_bongori_n268_08 Salmonella_bongori_n268_08 Salmonella_bongori_n268_08 @@ -56662,7 +56402,6 @@ Salmonella_enterica_subsp_salamae_serovar_58_l_z13_z28_z6_str_00_0163 Salmonel Salmonella_sp_hmsc13b08_gca_001808015 Salmonella_sp_hmsc13b08_gca_001808015 Salmonella_sp_hmsc13b08_gca_001808015 Salpingoeca_rosetta_gca_000188695 Salpingoeca_rosetta_gca_000188695 Salpingoeca_rosetta_gca_000188695 Salsuginibacillus_halophilus_gca_003014715 Salsuginibacillus_halophilus_gca_003014715 Salsuginibacillus_halophilus_gca_003014715 -HLtupMer3.110 Salvator_merianae HLtupMer3.110 HLtupMer3.99 Salvator_merianae HLtupMer3.99 Samsonia_erythrinae_gca_004342665 Samsonia_erythrinae_gca_004342665 Samsonia_erythrinae_gca_004342665 Sandaracinomonas_limnophila_gca_004005965 Sandaracinomonas_limnophila_gca_004005965 Sandaracinomonas_limnophila_gca_004005965 @@ -56671,7 +56410,6 @@ Sandaracinus_amylolyticus_gca_000737325 Sandaracinus_amylolyticus_gca_00073732 Sandaracinus_sp__gca_002699025 Sandaracinus_sp__gca_002699025 Sandaracinus_sp__gca_002699025 Sandaracinus_sp__gca_002703625 Sandaracinus_sp__gca_002703625 Sandaracinus_sp__gca_002703625 Sandarakinorhabdus_cyanobacteriorum_gca_002251755 Sandarakinorhabdus_cyanobacteriorum_gca_002251755 Sandarakinorhabdus_cyanobacteriorum_gca_002251755 -SLUC_FBN_1.110 Sander_lucioperca SLUC_FBN_1.110 Sanguibacter_antarcticus_gca_002564005 Sanguibacter_antarcticus_gca_002564005 Sanguibacter_antarcticus_gca_002564005 Sanguibacter_gelidistatuariae_gca_900096585 Sanguibacter_gelidistatuariae_gca_900096585 Sanguibacter_gelidistatuariae_gca_900096585 Sanguibacter_keddieii_dsm_10542 Sanguibacter_keddieii_dsm_10542 Sanguibacter_keddieii_dsm_10542 @@ -56713,7 +56451,6 @@ Sarcina_sp_dsm_11001_gca_900101015 Sarcina_sp_dsm_11001_gca_900101015 Sarcin Sarcina_ventriculi_gca_001404895 Sarcina_ventriculi_gca_001404895 Sarcina_ventriculi_gca_001404895 DEVIL7.0.75 Sarcophilus_harrisii DEVIL7.0.75 DEVIL7.0.99 Sarcophilus_harrisii DEVIL7.0.99 -mSarHar1.11.110 Sarcophilus_harrisii mSarHar1.11.110 Sarcoptes_scabiei Sarcoptes_scabiei Sarcoptes_scabiei Scandinavium_goeteborgense_gca_003208195 Scandinavium_goeteborgense_gca_003208195 Scandinavium_goeteborgense_gca_003208195 Scandinavium_goeteborgense_gca_003935895 Scandinavium_goeteborgense_gca_003935895 Scandinavium_goeteborgense_gca_003935895 @@ -56766,14 +56503,11 @@ Schleiferilactobacillus_shenzhenensis_ly_73_gca_000469325 Schleiferilactobacil Schleiferilactobacillus_silagei_jcm_19001_gca_002217945 Schleiferilactobacillus_silagei_jcm_19001_gca_002217945 Schleiferilactobacillus_silagei_jcm_19001_gca_002217945 Schleiferilactobacillus_similis_dsm_23365_jcm_2765_gca_001436595 Schleiferilactobacillus_similis_dsm_23365_jcm_2765_gca_001436595 Schleiferilactobacillus_similis_dsm_23365_jcm_2765_gca_001436595 Schwartzia_succinivorans_dsm_10502_gca_900129225 Schwartzia_succinivorans_dsm_10502_gca_900129225 Schwartzia_succinivorans_dsm_10502_gca_900129225 -mSciVul1.1.110 Sciurus_vulgaris mSciVul1.1.110 Scleroderma_citrinum_foug_a_gca_000827425 Scleroderma_citrinum_foug_a_gca_000827425 Scleroderma_citrinum_foug_a_gca_000827425 -fSclFor1.1.110 Scleropages_formosus fSclFor1.1.110 fSclFor1.1.99 Scleropages_formosus fSclFor1.1.99 Sclerotinia_borealis_f_4128_gca_000503235 Sclerotinia_borealis_f_4128_gca_000503235 Sclerotinia_borealis_f_4128_gca_000503235 Sclerotinia_sclerotiorum Sclerotinia_sclerotiorum Sclerotinia_sclerotiorum Sclerotinia_sclerotiorum_1980_uf_70_gca_001857865 Sclerotinia_sclerotiorum_1980_uf_70_gca_001857865 Sclerotinia_sclerotiorum_1980_uf_70_gca_001857865 -ASM1334776v1.110 Scophthalmus_maximus ASM1334776v1.110 ASM318616v1.99 Scophthalmus_maximus ASM318616v1.99 Scopulibacillus_darangshiensis_gca_004341035 Scopulibacillus_darangshiensis_gca_004341035 Scopulibacillus_darangshiensis_gca_004341035 Scytalidium_lignicola_gca_002812745 Scytalidium_lignicola_gca_002812745 Scytalidium_lignicola_gca_002812745 @@ -56890,11 +56624,8 @@ Serinicoccus_hydrothermalis_gca_001685415 Serinicoccus_hydrothermalis_gca_0016 Serinicoccus_sp_cnj_927_gca_001942435 Serinicoccus_sp_cnj_927_gca_001942435 Serinicoccus_sp_cnj_927_gca_001942435 Serinicoccus_sp_cua_874_gca_001942225 Serinicoccus_sp_cua_874_gca_001942225 Serinicoccus_sp_cua_874_gca_001942225 Serinicoccus_sp_jlt9 Serinicoccus_sp_jlt9 Serinicoccus_sp_jlt9 -SCA1.110 Serinus_canaria SCA1.110 SCA1.99 Serinus_canaria SCA1.99 -Sdu_1.0.110 Seriola_dumerili Sdu_1.0.110 Sdu_1.0.99 Seriola_dumerili Sdu_1.0.99 -Sedor1.110 Seriola_lalandi_dorsalis Sedor1.110 Sedor1.99 Seriola_lalandi_dorsalis Sedor1.99 Serpentinicella_alkaliphila_gca_004345905 Serpentinicella_alkaliphila_gca_004345905 Serpentinicella_alkaliphila_gca_004345905 Serpentinimonas_maccroryi_gca_000828915 Serpentinimonas_maccroryi_gca_000828915 Serpentinimonas_maccroryi_gca_000828915 @@ -57885,11 +57616,8 @@ Sinirhodobacter_populi_gca_004022585 Sinirhodobacter_populi_gca_004022585 Si Sinobaca_qinghaiensis_gca_003610495 Sinobaca_qinghaiensis_gca_003610495 Sinobaca_qinghaiensis_gca_003610495 Sinobacteraceae_bacterium_gca_003730135 Sinobacteraceae_bacterium_gca_003730135 Sinobacteraceae_bacterium_gca_003730135 Sinobacterium_caligoides_gca_003752585 Sinobacterium_caligoides_gca_003752585 Sinobacterium_caligoides_gca_003752585 -SAMN03320099.WGS_v1.1.110 Sinocyclocheilus_anshuiensis SAMN03320099.WGS_v1.1.110 SAMN03320099.WGS_v1.1.99 Sinocyclocheilus_anshuiensis SAMN03320099.WGS_v1.1.99 -SAMN03320097.WGS_v1.1.110 Sinocyclocheilus_grahami SAMN03320097.WGS_v1.1.110 SAMN03320097.WGS_v1.1.99 Sinocyclocheilus_grahami SAMN03320097.WGS_v1.1.99 -SAMN03320098_v1.1.110 Sinocyclocheilus_rhinocerous SAMN03320098_v1.1.110 SAMN03320098_v1.1.99 Sinocyclocheilus_rhinocerous SAMN03320098_v1.1.99 Sinomicrobium_oceani_gca_900119185 Sinomicrobium_oceani_gca_900119185 Sinomicrobium_oceani_gca_900119185 Sinomicrobium_pectinilyticum_gca_003725735 Sinomicrobium_pectinilyticum_gca_003725735 Sinomicrobium_pectinilyticum_gca_003725735 @@ -58069,20 +57797,16 @@ Sorangium_cellulosum_so_ce56 Sorangium_cellulosum_so_ce56 Sorangium_cellulos Sorangium_cellulosum_so_ce56_gca_000067165 Sorangium_cellulosum_so_ce56_gca_000067165 Sorangium_cellulosum_so_ce56_gca_000067165 Sordaria_macrospora_gca_008692325 Sordaria_macrospora_gca_008692325 Sordaria_macrospora_gca_008692325 Sordaria_macrospora_k_hell_gca_000182805 Sordaria_macrospora_k_hell_gca_000182805 Sordaria_macrospora_k_hell_gca_000182805 -COMMON_SHREW1.110 Sorex_araneus COMMON_SHREW1.110 COMMON_SHREW1.75 Sorex_araneus COMMON_SHREW1.75 COMMON_SHREW1.99 Sorex_araneus COMMON_SHREW1.99 Sorghum_bicolor Sorghum_bicolor Sorghum_bicolor Sparassis_crispa_gca_003851025 Sparassis_crispa_gca_003851025 Sparassis_crispa_gca_003851025 Spartobacteria_bacterium_lr76_gca_003054655 Spartobacteria_bacterium_lr76_gca_003054655 Spartobacteria_bacterium_lr76_gca_003054655 -fSpaAur1.1.110 Sparus_aurata fSpaAur1.1.110 fSpaAur1.1.99 Sparus_aurata fSpaAur1.1.99 Spathaspora_passalidarum_nrrl_y_27907_gca_000223485 Spathaspora_passalidarum_nrrl_y_27907_gca_000223485 Spathaspora_passalidarum_nrrl_y_27907_gca_000223485 Spathaspora_sp_ja1_gca_003676035 Spathaspora_sp_ja1_gca_003676035 Spathaspora_sp_ja1_gca_003676035 -ASM240643v1.110 Spermophilus_dauricus ASM240643v1.110 ASM240643v1.99 Spermophilus_dauricus ASM240643v1.99 Sphaceloma_murrayae_gca_002895985 Sphaceloma_murrayae_gca_002895985 Sphaceloma_murrayae_gca_002895985 -fSphaOr1.1.110 Sphaeramia_orbicularis fSphaOr1.1.110 fSphaOr1.1.99 Sphaeramia_orbicularis fSphaOr1.1.99 Sphaerisporangium_album_gca_003323745 Sphaerisporangium_album_gca_003323745 Sphaerisporangium_album_gca_003323745 Sphaerisporangium_cinnabarinum_gca_003052455 Sphaerisporangium_cinnabarinum_gca_003052455 Sphaerisporangium_cinnabarinum_gca_003052455 @@ -58103,7 +57827,6 @@ Sphaerotilus_hippei_gca_003201595 Sphaerotilus_hippei_gca_003201595 Sphaerot Sphaerotilus_natans_subsp_natans_dsm_6575 Sphaerotilus_natans_subsp_natans_dsm_6575 Sphaerotilus_natans_subsp_natans_dsm_6575 Sphaerotilus_natans_subsp_natans_dsm_6575_gca_000689195 Sphaerotilus_natans_subsp_natans_dsm_6575_gca_000689195 Sphaerotilus_natans_subsp_natans_dsm_6575_gca_000689195 Sphaerulina_musiva_so2202_gca_000320565 Sphaerulina_musiva_so2202_gca_000320565 Sphaerulina_musiva_so2202_gca_000320565 -ASM311381v1.110 Sphenodon_punctatus ASM311381v1.110 ASM311381v1.99 Sphenodon_punctatus ASM311381v1.99 Sphingobacteriaceae_bacterium_gca_002319075 Sphingobacteriaceae_bacterium_gca_002319075 Sphingobacteriaceae_bacterium_gca_002319075 Sphingobacteriaceae_bacterium_gca_004176105 Sphingobacteriaceae_bacterium_gca_004176105 Sphingobacteriaceae_bacterium_gca_004176105 @@ -58755,7 +58478,6 @@ Stachybotrys_chartarum_ibt_40288_gca_000732765 Stachybotrys_chartarum_ibt_4028 Stachybotrys_chartarum_ibt_40293_gca_000732565 Stachybotrys_chartarum_ibt_40293_gca_000732565 Stachybotrys_chartarum_ibt_40293_gca_000732565 Stachybotrys_chartarum_ibt_7711_gca_000730325 Stachybotrys_chartarum_ibt_7711_gca_000730325 Stachybotrys_chartarum_ibt_7711_gca_000730325 Stachybotrys_chlorohalonata_ibt_40285_gca_000732775 Stachybotrys_chlorohalonata_ibt_40285_gca_000732775 Stachybotrys_chlorohalonata_ibt_40285_gca_000732775 -ASM869450v1.110 Stachyris_ruficeps ASM869450v1.110 Stackebrandtia_nassauensis_dsm_44728 Stackebrandtia_nassauensis_dsm_44728 Stackebrandtia_nassauensis_dsm_44728 Stackebrandtia_nassauensis_dsm_44728_gca_000024545 Stackebrandtia_nassauensis_dsm_44728_gca_000024545 Stackebrandtia_nassauensis_dsm_44728_gca_000024545 Stagonospora_sp_src1lsm3a_gca_001644525 Stagonospora_sp_src1lsm3a_gca_001644525 Stagonospora_sp_src1lsm3a_gca_001644525 @@ -64312,7 +64034,6 @@ Starkeya_novella_dsm_506_gca_000092925 Starkeya_novella_dsm_506_gca_000092925 Starkeya_novella_gca_003241485 Starkeya_novella_gca_003241485 Starkeya_novella_gca_003241485 Starkeya_novella_gca_003241695 Starkeya_novella_gca_003241695 Starkeya_novella_gca_003241695 Steccherinum_ochraceum_gca_004332605 Steccherinum_ochraceum_gca_004332605 Steccherinum_ochraceum_gca_004332605 -Stegastes_partitus-1.0.2.110 Stegastes_partitus Stegastes_partitus-1.0.2.110 Stegastes_partitus-1.0.2.99 Stegastes_partitus Stegastes_partitus-1.0.2.99 Stegodyphus_dumicola_gca010614865v2rs Stegodyphus_dumicola_gca010614865v2rs Stegodyphus_dumicola_gca010614865v2rs Stegodyphus_mimosarum Stegodyphus_mimosarum Stegodyphus_mimosarum @@ -72530,12 +72251,9 @@ Streptosporangium_sp_caverna__gca_003203775 Streptosporangium_sp_caverna__gca_ Streptosporangium_subroseum_gca_900188345 Streptosporangium_subroseum_gca_900188345 Streptosporangium_subroseum_gca_900188345 Strigamia_maritima Strigamia_maritima Strigamia_maritima Strigomonas_culicis_gca_000442495 Strigomonas_culicis_gca_000442495 Strigomonas_culicis_gca_000442495 -bStrHab1_v1.p.110 Strigops_habroptila bStrHab1_v1.p.110 bStrHab1_v1.p.99 Strigops_habroptila bStrHab1_v1.p.99 -Soccid_v01.110 Strix_occidentalis_caurina Soccid_v01.110 Strongylocentrotus_purpuratus Strongylocentrotus_purpuratus Strongylocentrotus_purpuratus Strongyloides_ratti Strongyloides_ratti Strongyloides_ratti -ASM69896v1.110 Struthio_camelus_australis ASM69896v1.110 ASM69896v1.99 Struthio_camelus_australis ASM69896v1.99 Stutzerimonas_balearica_dsm_6083_gca_900103375 Stutzerimonas_balearica_dsm_6083_gca_900103375 Stutzerimonas_balearica_dsm_6083_gca_900103375 Stutzerimonas_chloritidismutans_aw_1_gca_000495915 Stutzerimonas_chloritidismutans_aw_1_gca_000495915 Stutzerimonas_chloritidismutans_aw_1_gca_000495915 @@ -72770,34 +72488,20 @@ Sunxiuqinia_dokdonensis_gca_001270965 Sunxiuqinia_dokdonensis_gca_001270965 Sunxiuqinia_elliptica_gca_004361925 Sunxiuqinia_elliptica_gca_004361925 Sunxiuqinia_elliptica_gca_004361925 Sunxiuqinia_elliptica_gca_900113005 Sunxiuqinia_elliptica_gca_900113005 Sunxiuqinia_elliptica_gca_900113005 Superficieibacter_electus_gca_002915575 Superficieibacter_electus_gca_002915575 Superficieibacter_electus_gca_002915575 -meerkat_22Aug2017_6uvM2_HiC.110 Suricata_suricatta meerkat_22Aug2017_6uvM2_HiC.110 meerkat_22Aug2017_6uvM2_HiC.99 Suricata_suricatta meerkat_22Aug2017_6uvM2_HiC.99 Sscrofa10.2.75 Sus_scrofa Sscrofa10.2.75 -Sscrofa11.1.110 Sus_scrofa Sscrofa11.1.110 Sscrofa11.1.99 Sus_scrofa Sscrofa11.1.99 -Bamei_pig_v1.110 Sus_scrofa_bamei Bamei_pig_v1.110 Bamei_pig_v1.99 Sus_scrofa_bamei Bamei_pig_v1.99 -Berkshire_pig_v1.110 Sus_scrofa_berkshire Berkshire_pig_v1.110 Berkshire_pig_v1.99 Sus_scrofa_berkshire Berkshire_pig_v1.99 -Hampshire_pig_v1.110 Sus_scrofa_hampshire Hampshire_pig_v1.110 Hampshire_pig_v1.99 Sus_scrofa_hampshire Hampshire_pig_v1.99 -Jinhua_pig_v1.110 Sus_scrofa_jinhua Jinhua_pig_v1.110 Jinhua_pig_v1.99 Sus_scrofa_jinhua Jinhua_pig_v1.99 -Landrace_pig_v1.110 Sus_scrofa_landrace Landrace_pig_v1.110 Landrace_pig_v1.99 Sus_scrofa_landrace Landrace_pig_v1.99 -Large_White_v1.110 Sus_scrofa_largewhite Large_White_v1.110 Large_White_v1.99 Sus_scrofa_largewhite Large_White_v1.99 -Meishan_pig_v1.110 Sus_scrofa_meishan Meishan_pig_v1.110 Meishan_pig_v1.99 Sus_scrofa_meishan Meishan_pig_v1.99 -Pietrain_pig_v1.110 Sus_scrofa_pietrain Pietrain_pig_v1.110 Pietrain_pig_v1.99 Sus_scrofa_pietrain Pietrain_pig_v1.99 -Rongchang_pig_v1.110 Sus_scrofa_rongchang Rongchang_pig_v1.110 Rongchang_pig_v1.99 Sus_scrofa_rongchang Rongchang_pig_v1.99 -Tibetan_Pig_v2.110 Sus_scrofa_tibetan Tibetan_Pig_v2.110 Tibetan_Pig_v2.99 Sus_scrofa_tibetan Tibetan_Pig_v2.99 -USMARCv1.0.110 Sus_scrofa_usmarc USMARCv1.0.110 USMARCv1.0.99 Sus_scrofa_usmarc USMARCv1.0.99 -minipig_v1.0.110 Sus_scrofa_wuzhishan minipig_v1.0.110 minipig_v1.0.99 Sus_scrofa_wuzhishan minipig_v1.0.99 Sutcliffiella_cohnii_gca_002250055 Sutcliffiella_cohnii_gca_002250055 Sutcliffiella_cohnii_gca_002250055 Sutcliffiella_horikoshii_gca_002157855 Sutcliffiella_horikoshii_gca_002157855 Sutcliffiella_horikoshii_gca_002157855 @@ -72951,7 +72655,6 @@ test_t_urticae_p3 T. test_t_urticae_p3 Tabrizicola_alkalilacus_gca_003443995 Tabrizicola_alkalilacus_gca_003443995 Tabrizicola_alkalilacus_gca_003443995 Tabrizicola_piscis_gca_003940805 Tabrizicola_piscis_gca_003940805 Tabrizicola_piscis_gca_003940805 Tabrizicola_sp_th137_gca_002855575 Tabrizicola_sp_th137_gca_002855575 Tabrizicola_sp_th137_gca_002855575 -bTaeGut1_v1.p.110 Taeniopygia_guttata bTaeGut1_v1.p.110 bTaeGut1_v1.p.99 Taeniopygia_guttata bTaeGut1_v1.p.99 taeGut3.2.4.75 Taeniopygia_guttata taeGut3.2.4.75 Tahibacter_aquaticus_gca_004363655 Tahibacter_aquaticus_gca_004363655 Tahibacter_aquaticus_gca_004363655 @@ -72960,7 +72663,6 @@ Taibaiella_soli_gca_003236175 Taibaiella_soli_gca_003236175 Taibaiella_soli_ Taibaiella_sp_kbw10_gca_003852495 Taibaiella_sp_kbw10_gca_003852495 Taibaiella_sp_kbw10_gca_003852495 FUGU4.75 Takifugu_rubripes FUGU4.75 Takifugu_rubripes Takifugu_rubripes Takifugu_rubripes -fTakRub1.2.110 Takifugu_rubripes fTakRub1.2.110 fTakRub1.2.99 Takifugu_rubripes fTakRub1.2.99 Talaromyces_amestolkiae_gca_001896365 Talaromyces_amestolkiae_gca_001896365 Talaromyces_amestolkiae_gca_001896365 Talaromyces_atroroseus_gca_001907595 Talaromyces_atroroseus_gca_001907595 Talaromyces_atroroseus_gca_001907595 @@ -73112,7 +72814,6 @@ Terrabacter_sp_soil810_gca_001429645 Terrabacter_sp_soil810_gca_001429645 Te Terrabacter_sp_soil811 Terrabacter_sp_soil811 Terrabacter_sp_soil811 Terrabacter_sp_soil811_gca_001429655 Terrabacter_sp_soil811_gca_001429655 Terrabacter_sp_soil811_gca_001429655 Terracoccus_luteus_gca_003635045 Terracoccus_luteus_gca_003635045 Terracoccus_luteus_gca_003635045 -T_m_triunguis-2.0.110 Terrapene_carolina_triunguis T_m_triunguis-2.0.110 T_m_triunguis-2.0.99 Terrapene_carolina_triunguis T_m_triunguis-2.0.99 Terribacillus_aidingensis Terribacillus_aidingensis Terribacillus_aidingensis Terribacillus_aidingensis_gca_900215625 Terribacillus_aidingensis_gca_900215625 Terribacillus_aidingensis_gca_900215625 @@ -73216,7 +72917,6 @@ Tetragenococcus_muriaticus_pmc_11_5_gca_000747235 Tetragenococcus_muriaticus_p Tetragenococcus_osmophilus_gca_003795125 Tetragenococcus_osmophilus_gca_003795125 Tetragenococcus_osmophilus_gca_003795125 Tetrahymena_thermophila Tetrahymena_thermophila Tetrahymena_thermophila Tetranychus_urticae Tetranychus_urticae Tetranychus_urticae -TETRAODON8.110 Tetraodon_nigroviridis TETRAODON8.110 TETRAODON8.75 Tetraodon_nigroviridis TETRAODON8.75 TETRAODON8.99 Tetraodon_nigroviridis TETRAODON8.99 Tetrapisispora_blattae_cbs_6284_gca_000315915 Tetrapisispora_blattae_cbs_6284_gca_000315915 Tetrapisispora_blattae_cbs_6284_gca_000315915 @@ -73741,7 +73441,6 @@ Thermus_thermophilus_jl_18 Thermus_thermophilus_jl_18 Thermus_thermophilus_j Thermus_thermophilus_jl_18_gca_000258245 Thermus_thermophilus_jl_18_gca_000258245 Thermus_thermophilus_jl_18_gca_000258245 Thermus_thermophilus_sg0_5jp17_16 Thermus_thermophilus_sg0_5jp17_16 Thermus_thermophilus_sg0_5jp17_16 Thermus_thermophilus_sg0_5jp17_16_gca_000214845 Thermus_thermophilus_sg0_5jp17_16_gca_000214845 Thermus_thermophilus_sg0_5jp17_16_gca_000214845 -Tgel_1.0.110 Theropithecus_gelada Tgel_1.0.110 Tgel_1.0.99 Theropithecus_gelada Tgel_1.0.99 Thielavia_terrestris_nrrl_8126_gca_000226115 Thielavia_terrestris_nrrl_8126_gca_000226115 Thielavia_terrestris_nrrl_8126_gca_000226115 Thielaviopsis_punctulata_gca_000968615 Thielaviopsis_punctulata_gca_000968615 Thielaviopsis_punctulata_gca_000968615 @@ -74193,7 +73892,6 @@ Tumebacillus_flagellatus Tumebacillus_flagellatus Tumebacillus_flagellatus Tumebacillus_flagellatus_gca_000714935 Tumebacillus_flagellatus_gca_000714935 Tumebacillus_flagellatus_gca_000714935 Tumebacillus_permanentifrigoris_gca_003148565 Tumebacillus_permanentifrigoris_gca_003148565 Tumebacillus_permanentifrigoris_gca_003148565 Tumebacillus_sp_bk434_gca_004340785 Tumebacillus_sp_bk434_gca_004340785 Tumebacillus_sp_bk434_gca_004340785 -TREESHREW.110 Tupaia_belangeri TREESHREW.110 TREESHREW.75 Tupaia_belangeri TREESHREW.75 TREESHREW.99 Tupaia_belangeri TREESHREW.99 Turicella_otitidis Turicella_otitidis Turicella_otitidis @@ -74210,7 +73908,6 @@ Turicibacter_sp_hgf1 Turicibacter_sp_hgf1 Turicibacter_sp_hgf1 Turicimonas_muris_gca_002221595 Turicimonas_muris_gca_002221595 Turicimonas_muris_gca_002221595 Turneriella_parva_dsm_21527 Turneriella_parva_dsm_21527 Turneriella_parva_dsm_21527 Turneriella_parva_dsm_21527_gca_000266885 Turneriella_parva_dsm_21527_gca_000266885 Turneriella_parva_dsm_21527_gca_000266885 -turTru1.110 Tursiops_truncatus turTru1.110 turTru1.75 Tursiops_truncatus turTru1.75 turTru1.99 Tursiops_truncatus turTru1.99 Tychonema_bourrellyi_fem_gt703_gca_002412335 Tychonema_bourrellyi_fem_gt703_gca_002412335 Tychonema_bourrellyi_fem_gt703_gca_002412335 @@ -74277,14 +73974,10 @@ Ureibacillus_massiliensis_4400831_cip_108448_ccug_49529_gca_000772965 Ureibaci Ureibacillus_sinduriensis_blb_1_jcm_15800_gca_000772955 Ureibacillus_sinduriensis_blb_1_jcm_15800_gca_000772955 Ureibacillus_sinduriensis_blb_1_jcm_15800_gca_000772955 Ureibacillus_thermophilus_gca_004331915 Ureibacillus_thermophilus_gca_004331915 Ureibacillus_thermophilus_gca_004331915 Ureibacillus_xyleni_gca_900217795 Ureibacillus_xyleni_gca_900217795 Ureibacillus_xyleni_gca_900217795 -ASM342692v1.110 Urocitellus_parryii ASM342692v1.110 ASM342692v1.99 Urocitellus_parryii ASM342692v1.99 lekn01 Ursidibacter lekn01 -ASM334442v1.110 Ursus_americanus ASM334442v1.110 ASM334442v1.99 Ursus_americanus ASM334442v1.99 -UrsMar_1.0.110 Ursus_maritimus UrsMar_1.0.110 UrsMar_1.0.99 Ursus_maritimus UrsMar_1.0.99 -ASM966005v1.110 Ursus_thibetanus_thibetanus ASM966005v1.110 Uruburuella_suis_gca_004341385 Uruburuella_suis_gca_004341385 Uruburuella_suis_gca_004341385 Ustilaginoidea_virens_gca_000687475 Ustilaginoidea_virens_gca_000687475 Ustilaginoidea_virens_gca_000687475 Ustilaginoidea_virens_gca_000965225 Ustilaginoidea_virens_gca_000965225 Ustilaginoidea_virens_gca_000965225 @@ -74329,7 +74022,6 @@ Vandammella_animalimorsus_gca_003703375 Vandammella_animalimorsus_gca_00370337 Vanderwaltozyma_polyspora_dsm_70294_gca_000150035 Vanderwaltozyma_polyspora_dsm_70294_gca_000150035 Vanderwaltozyma_polyspora_dsm_70294_gca_000150035 Vannielia_litorea_gca_900142295 Vannielia_litorea_gca_900142295 Vannielia_litorea_gca_900142295 Vanrija_humicola_gca_008065275 Vanrija_humicola_gca_008065275 Vanrija_humicola_gca_008065275 -ASM479886v1.110 Varanus_komodoensis ASM479886v1.110 ASM479886v1.99 Varanus_komodoensis ASM479886v1.99 Varibaculum_cambriense Varibaculum_cambriense Varibaculum_cambriense Varibaculum_cambriense_dora_20_gca_000508625 Varibaculum_cambriense_dora_20_gca_000508625 Varibaculum_cambriense_dora_20_gca_000508625 @@ -75665,7 +75357,6 @@ Vibrionales_bacterium_c3r12_gca_003318175 Vibrionales_bacterium_c3r12_gca_0033 Vibrionales_bacterium_swat_3 Vibrionales_bacterium_swat_3 Vibrionales_bacterium_swat_3 Victivallales_bacterium_ccug_44730_gca_002998355 Victivallales_bacterium_ccug_44730_gca_002998355 Victivallales_bacterium_ccug_44730_gca_002998355 Victivallis_vadensis_gca_003096415 Victivallis_vadensis_gca_003096415 Victivallis_vadensis_gca_003096415 -vicPac1.110 Vicugna_pacos vicPac1.110 vicPac1.75 Vicugna_pacos vicPac1.75 vicPac1.99 Vicugna_pacos vicPac1.99 Vigna_angularis Vigna_angularis Vigna_angularis @@ -75710,7 +75401,6 @@ Vogesella_sp_eb Vogesella_sp_eb Vogesella_sp_eb Vogesella_sp_eb_gca_001037925 Vogesella_sp_eb_gca_001037925 Vogesella_sp_eb_gca_001037925 Vogesella_sp_lig4_gca_900090205 Vogesella_sp_lig4_gca_900090205 Vogesella_sp_lig4_gca_900090205 Volucribacter_psittacicida_gca_004339025 Volucribacter_psittacicida_gca_004339025 Volucribacter_psittacicida_gca_004339025 -bare-nosed_wombat_genome_assembly.110 Vombatus_ursinus bare-nosed_wombat_genome_assembly.110 bare-nosed_wombat_genome_assembly.99 Vombatus_ursinus bare-nosed_wombat_genome_assembly.99 Vulcaniibacterium_tengchongense_gca_003814555 Vulcaniibacterium_tengchongense_gca_003814555 Vulcaniibacterium_tengchongense_gca_003814555 Vulcanisaeta_distributa_dsm_14429 Vulcanisaeta_distributa_dsm_14429 Vulcanisaeta_distributa_dsm_14429 @@ -75724,7 +75414,6 @@ Vulcanisaeta_sp_mg_3 Vulcanisaeta_sp_mg_3 Vulcanisaeta_sp_mg_3 Vulcanisaeta_sp_osp_8 Vulcanisaeta_sp_osp_8 Vulcanisaeta_sp_osp_8 Vulgatibacter_incomptus Vulgatibacter_incomptus Vulgatibacter_incomptus Vulgatibacter_incomptus_gca_001263175 Vulgatibacter_incomptus_gca_001263175 Vulgatibacter_incomptus_gca_001263175 -VulVul2.2.110 Vulpes_vulpes VulVul2.2.110 VulVul2.2.99 Vulpes_vulpes VulVul2.2.99 Waddlia_chondrophila_wsu_86_1044 Waddlia_chondrophila_wsu_86_1044 Waddlia_chondrophila_wsu_86_1044 Waddlia_chondrophila_wsu_86_1044_gca_000092785 Waddlia_chondrophila_wsu_86_1044_gca_000092785 Waddlia_chondrophila_wsu_86_1044_gca_000092785 @@ -76379,7 +76068,6 @@ Xenococcus_sp_pcc_7305 Xenococcus_sp_pcc_7305 Xenococcus_sp_pcc_7305 Xenococcus_sp_pcc_7305_gca_000332055 Xenococcus_sp_pcc_7305_gca_000332055 Xenococcus_sp_pcc_7305_gca_000332055 Xenophilus_sp_ap218f_gca_002213445 Xenophilus_sp_ap218f_gca_002213445 Xenophilus_sp_ap218f_gca_002213445 JGI_4.2.75 Xenopus_tropicalis JGI_4.2.75 -UCB_Xtro_10.0.110 Xenopus_tropicalis UCB_Xtro_10.0.110 Xenopus_tropicalis_v9.1.99 Xenopus_tropicalis Xenopus_tropicalis_v9.1.99 Xenorhabdus_beddingii_gca_002127545 Xenorhabdus_beddingii_gca_002127545 Xenorhabdus_beddingii_gca_002127545 Xenorhabdus_bovienii Xenorhabdus_bovienii Xenorhabdus_bovienii @@ -76444,9 +76132,7 @@ Xenorhabdus_szentirmaii_dsm_16338_gca_000531455 Xenorhabdus_szentirmaii_dsm_16 Xenorhabdus_thuongxuanensis_gca_001908095 Xenorhabdus_thuongxuanensis_gca_001908095 Xenorhabdus_thuongxuanensis_gca_001908095 Xenorhabdus_vietnamensis_gca_002127535 Xenorhabdus_vietnamensis_gca_002127535 Xenorhabdus_vietnamensis_gca_002127535 Xinfangfangia_humi_gca_900609055 Xinfangfangia_humi_gca_900609055 Xinfangfangia_humi_gca_900609055 -Xiphophorus_couchianus-4.0.1.110 Xiphophorus_couchianus Xiphophorus_couchianus-4.0.1.110 Xiphophorus_couchianus-4.0.1.99 Xiphophorus_couchianus Xiphophorus_couchianus-4.0.1.99 -X_maculatus-5.0-male.110 Xiphophorus_maculatus X_maculatus-5.0-male.110 X_maculatus-5.0-male.99 Xiphophorus_maculatus X_maculatus-5.0-male.99 Xipmac4.4.2.75 Xiphophorus_maculatus Xipmac4.4.2.75 Xylanibacterium_ulmi_gca_004216535 Xylanibacterium_ulmi_gca_004216535 Xylanibacterium_ulmi_gca_004216535 @@ -76980,7 +76666,6 @@ Yoonia_vestfoldensis_gca_002158905 Yoonia_vestfoldensis_gca_002158905 Yoonia Youngiibacter_fragilis_232_1 Youngiibacter_fragilis_232_1 Youngiibacter_fragilis_232_1 Youngiibacter_fragilis_232_1_gca_000495435 Youngiibacter_fragilis_232_1_gca_000495435 Youngiibacter_fragilis_232_1_gca_000495435 Youngimonas_vesicularis_gca_004799325 Youngimonas_vesicularis_gca_004799325 Youngimonas_vesicularis_gca_004799325 -mZalCal1.pri.110 Zalophus_californianus mZalCal1.pri.110 Zasmidium_cellare_atcc_36951_gca_010093935 Zasmidium_cellare_atcc_36951_gca_010093935 Zasmidium_cellare_atcc_36951_gca_010093935 Zavarzinia_aquatilis_gca_003173035 Zavarzinia_aquatilis_gca_003173035 Zavarzinia_aquatilis_gca_003173035 Zavarzinia_compransoris_gca_003173055 Zavarzinia_compransoris_gca_003173055 Zavarzinia_compransoris_gca_003173055 @@ -77015,13 +76700,11 @@ Zobellia_galactanivorans Zobellia_galactanivorans Zobellia_galactanivorans Zobellia_galactanivorans_gca_000973105 Zobellia_galactanivorans_gca_000973105 Zobellia_galactanivorans_gca_000973105 Zobellia_uliginosa_gca_900156625 Zobellia_uliginosa_gca_900156625 Zobellia_uliginosa_gca_900156625 Zongyanglinia_marina_gca_005771405 Zongyanglinia_marina_gca_005771405 Zongyanglinia_marina_gca_005771405 -Zonotrichia_albicollis-1.0.1.110 Zonotrichia_albicollis Zonotrichia_albicollis-1.0.1.110 Zonotrichia_albicollis-1.0.1.99 Zonotrichia_albicollis Zonotrichia_albicollis-1.0.1.99 Zoogloeaceae_bacteirum_par_f_2_gca_003054515 Zoogloeaceae_bacteirum_par_f_2_gca_003054515 Zoogloeaceae_bacteirum_par_f_2_gca_003054515 Zooshikella_ganghwensis_gca_002261065 Zooshikella_ganghwensis_gca_002261065 Zooshikella_ganghwensis_gca_002261065 Zootermopsis_nevadensis Zootermopsis_nevadensis Zootermopsis_nevadensis Zopfia_rhizophila_cbs_207_26_gca_010093925 Zopfia_rhizophila_cbs_207_26_gca_010093925 Zopfia_rhizophila_cbs_207_26_gca_010093925 -ASM128173v1.110 Zosterops_lateralis_melanops ASM128173v1.110 Zunongwangia_atlantica_22ii14_10f7_gca_002094855 Zunongwangia_atlantica_22ii14_10f7_gca_002094855 Zunongwangia_atlantica_22ii14_10f7_gca_002094855 Zunongwangia_mangrovi_gca_900112105 Zunongwangia_mangrovi_gca_900112105 Zunongwangia_mangrovi_gca_900112105 Zunongwangia_profunda_gca_003541615 Zunongwangia_profunda_gca_003541615 Zunongwangia_profunda_gca_003541615 diff --git a/galaxy/tool-data/snpEff_genomes.loc.sample b/galaxy/tool-data/snpEff_genomes.loc.sample index bcc00d93..9f417ef7 100644 --- a/galaxy/tool-data/snpEff_genomes.loc.sample +++ b/galaxy/tool-data/snpEff_genomes.loc.sample @@ -15,13 +15,11 @@ Abyssibacter_profundi_gca_003151135 Abyssibacter_profundi_gca_003151135 Abys Abyssicoccus_albus_gca_003815035 Abyssicoccus_albus_gca_003815035 Abyssicoccus_albus_gca_003815035 Acanthamoeba_castellanii_str_neff_gca_000313135 Acanthamoeba_castellanii_str_neff_gca_000313135 Acanthamoeba_castellanii_str_neff_gca_000313135 Acanthaster_planci_gca001949145v1 Acanthaster_planci_gca001949145v1 Acanthaster_planci_gca001949145v1 -ASM210954v1.110 Acanthochromis_polyacanthus ASM210954v1.110 ASM210954v1.99 Acanthochromis_polyacanthus ASM210954v1.99 Acaromyces_ingoldii_gca_003144295 Acaromyces_ingoldii_gca_003144295 Acaromyces_ingoldii_gca_003144295 Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017 Acaryochloris_marina_mbic11017_gca_000018105 Acaryochloris_marina_mbic11017_gca_000018105 Acaryochloris_marina_mbic11017_gca_000018105 Acaryochloris_thomasi_rcc1774_gca_003231495 Acaryochloris_thomasi_rcc1774_gca_003231495 Acaryochloris_thomasi_rcc1774_gca_003231495 -Accipiter_nisus_ver1.0.110 Accipiter_nisus Accipiter_nisus_ver1.0.110 Accipiter_nisus_ver1.0.99 Accipiter_nisus Accipiter_nisus_ver1.0.99 Acetanaerobacterium_elongatum_gca_900103835 Acetanaerobacterium_elongatum_gca_900103835 Acetanaerobacterium_elongatum_gca_900103835 Acetatifactor_muris_gca_900248245 Acetatifactor_muris_gca_900248245 Acetatifactor_muris_gca_900248245 @@ -3205,7 +3203,6 @@ Ahrensia_sp__gca_002706335 Ahrensia_sp__gca_002706335 Ahrensia_sp__gca_00270 Ahrensia_sp_r2a130 Ahrensia_sp_r2a130 Ahrensia_sp_r2a130 Ahrensia_sp_r2a130_gca_000179775 Ahrensia_sp_r2a130_gca_000179775 Ahrensia_sp_r2a130_gca_000179775 Aidingimonas_halophila_gca_900106955 Aidingimonas_halophila_gca_900106955 Aidingimonas_halophila_gca_900106955 -ASM200744v2.110 Ailuropoda_melanoleuca ASM200744v2.110 ailMel1.75 Ailuropoda_melanoleuca ailMel1.75 ailMel1.99 Ailuropoda_melanoleuca ailMel1.99 Akanthomyces_lecanii_gca_001653215 Akanthomyces_lecanii_gca_001653215 Akanthomyces_lecanii_gca_001653215 @@ -3737,7 +3734,6 @@ Amanita_muscaria_koide_bx008_gca_000827485 Amanita_muscaria_koide_bx008_gca_00 Amanita_thiersii_skay4041_gca_002554575 Amanita_thiersii_skay4041_gca_002554575 Amanita_thiersii_skay4041_gca_002554575 Amantichitinum_ursilacus Amantichitinum_ursilacus Amantichitinum_ursilacus Amantichitinum_ursilacus_gca_001294205 Amantichitinum_ursilacus_gca_001294205 Amantichitinum_ursilacus_gca_001294205 -ASM394721v1.110 Amazona_collaria ASM394721v1.110 ASM394721v1.99 Amazona_collaria ASM394721v1.99 Amborella_trichopoda Amborella_trichopoda Amborella_trichopoda Amedibacillus_dolichus_dsm_3991_gca_000154285 Amedibacillus_dolichus_dsm_3991_gca_000154285 Amedibacillus_dolichus_dsm_3991_gca_000154285 @@ -3773,14 +3769,11 @@ Amphibacillus_marinus_gca_900110345 Amphibacillus_marinus_gca_900110345 Amph Amphibacillus_xylanus_nbrc_15112 Amphibacillus_xylanus_nbrc_15112 Amphibacillus_xylanus_nbrc_15112 Amphibacillus_xylanus_nbrc_15112_gca_000307165 Amphibacillus_xylanus_nbrc_15112_gca_000307165 Amphibacillus_xylanus_nbrc_15112_gca_000307165 Amphibalanus_amphitrite_gca019059575v1 Amphibalanus_amphitrite_gca019059575v1 Amphibalanus_amphitrite_gca019059575v1 -Midas_v5.110 Amphilophus_citrinellus Midas_v5.110 Midas_v5.99 Amphilophus_citrinellus Midas_v5.99 Amphimedon_queenslandica Amphimedon_queenslandica Amphimedon_queenslandica Amphimedon_queenslandica_gca000090795v2rs Amphimedon_queenslandica_gca000090795v2rs Amphimedon_queenslandica_gca000090795v2rs Amphiplicatus_metriothermophilus_gca_900199215 Amphiplicatus_metriothermophilus_gca_900199215 Amphiplicatus_metriothermophilus_gca_900199215 -AmpOce1.0.110 Amphiprion_ocellaris AmpOce1.0.110 AmpOce1.0.99 Amphiprion_ocellaris AmpOce1.0.99 -Nemo_v1.110 Amphiprion_percula Nemo_v1.110 Nemo_v1.99 Amphiprion_percula Nemo_v1.99 Amphritea_atlantica_gca_900111095 Amphritea_atlantica_gca_900111095 Amphritea_atlantica_gca_900111095 Amphritea_balenae_gca_003858655 Amphritea_balenae_gca_003858655 Amphritea_balenae_gca_003858655 @@ -3877,7 +3870,6 @@ Anabaena_sp_wa113_gca_001672155 Anabaena_sp_wa113_gca_001672155 Anabaena_sp_ Anabaena_variabilis_atcc_29413 Anabaena_variabilis_atcc_29413 Anabaena_variabilis_atcc_29413 Anabaenopsis_circularis_nies_21_gca_002367975 Anabaenopsis_circularis_nies_21_gca_002367975 Anabaenopsis_circularis_nies_21_gca_002367975 fAnaTes1.1.99 Anabas_testudineus fAnaTes1.1.99 -fAnaTes1.2.110 Anabas_testudineus fAnaTes1.2.110 Anaerobacillus_alkalidiazotrophicus_gca_001866055 Anaerobacillus_alkalidiazotrophicus_gca_001866055 Anaerobacillus_alkalidiazotrophicus_gca_001866055 Anaerobacillus_alkalilacustris_gca_001866005 Anaerobacillus_alkalilacustris_gca_001866005 Anaerobacillus_alkalilacustris_gca_001866005 Anaerobacillus_alkaliphilus_gca_004116265 Anaerobacillus_alkaliphilus_gca_004116265 Anaerobacillus_alkaliphilus_gca_004116265 @@ -4057,11 +4049,8 @@ Anaplasma_phagocytophilum_str_mrk Anaplasma_phagocytophilum_str_mrk Anaplasm Anaplasma_phagocytophilum_str_nch_1 Anaplasma_phagocytophilum_str_nch_1 Anaplasma_phagocytophilum_str_nch_1 Anaplasma_phagocytophilum_str_norway_variant2 Anaplasma_phagocytophilum_str_norway_variant2 Anaplasma_phagocytophilum_str_norway_variant2 Anaplasma_phagocytophilum_str_webster Anaplasma_phagocytophilum_str_webster Anaplasma_phagocytophilum_str_webster -ASM874695v1.110 Anas_platyrhynchos ASM874695v1.110 BGI_duck_1.0.75 Anas_platyrhynchos BGI_duck_1.0.75 -CAU_duck1.0.110 Anas_platyrhynchos_platyrhynchos CAU_duck1.0.110 CAU_duck1.0.99 Anas_platyrhynchos_platyrhynchos CAU_duck1.0.99 -ASM222487v1.110 Anas_zonorhyncha ASM222487v1.110 Ancrocorticia_populi_gca_003123745 Ancrocorticia_populi_gca_003123745 Ancrocorticia_populi_gca_003123745 Ancylobacter_aquaticus_gca_003963445 Ancylobacter_aquaticus_gca_003963445 Ancylobacter_aquaticus_gca_003963445 Ancylobacter_aquaticus_gca_004339465 Ancylobacter_aquaticus_gca_004339465 Ancylobacter_aquaticus_gca_004339465 @@ -4097,7 +4086,6 @@ Anncaliia_algerae_pra339_gca_000385875 Anncaliia_algerae_pra339_gca_000385875 Anneissia_japonica_gca011630105v1 Anneissia_japonica_gca011630105v1 Anneissia_japonica_gca011630105v1 AnoCar2.0.75 Anolis_carolinensis AnoCar2.0.75 AnoCar2.0.99 Anolis_carolinensis AnoCar2.0.99 -AnoCar2.0v2.110 Anolis_carolinensis AnoCar2.0v2.110 Anopheles_albimanus Anopheles_albimanus Anopheles_albimanus Anopheles_arabiensis Anopheles_arabiensis Anopheles_arabiensis Anopheles_atroparvus Anopheles_atroparvus Anopheles_atroparvus @@ -4162,9 +4150,7 @@ Anoxybacillus_thermarum_gca_000836725 Anoxybacillus_thermarum_gca_000836725 Anoxybacillus_vitaminiphilus_gca_003259935 Anoxybacillus_vitaminiphilus_gca_003259935 Anoxybacillus_vitaminiphilus_gca_003259935 Anoxybacter_fermentans_gca_003991135 Anoxybacter_fermentans_gca_003991135 Anoxybacter_fermentans_gca_003991135 Anseongella_ginsenosidimutans_gca_004346135 Anseongella_ginsenosidimutans_gca_004346135 Anseongella_ginsenosidimutans_gca_004346135 -ASM259213v1.110 Anser_brachyrhynchus ASM259213v1.110 ASM259213v1.99 Anser_brachyrhynchus ASM259213v1.99 -GooseV1.0.110 Anser_cygnoides GooseV1.0.110 GooseV1.0.99 Anser_cygnoides GooseV1.0.99 Antarcticibacterium_flavum_gca_006159205 Antarcticibacterium_flavum_gca_006159205 Antarcticibacterium_flavum_gca_006159205 Antarcticimicrobium_luteum_gca_004358185 Antarcticimicrobium_luteum_gca_004358185 Antarcticimicrobium_luteum_gca_004358185 @@ -4176,7 +4162,6 @@ Anthracocystis_flocculosa_gca_900322975 Anthracocystis_flocculosa_gca_90032297 Anthracocystis_flocculosa_pf_1_gca_000417875 Anthracocystis_flocculosa_pf_1_gca_000417875 Anthracocystis_flocculosa_pf_1_gca_000417875 Antricoccus_suffuscus_gca_003003235 Antricoccus_suffuscus_gca_003003235 Antricoccus_suffuscus_gca_003003235 Antrodiella_citrinella_gca_004802725 Antrodiella_citrinella_gca_004802725 Antrodiella_citrinella_gca_004802725 -Anan_2.0.110 Aotus_nancymaae Anan_2.0.110 Anan_2.0.99 Aotus_nancymaae Anan_2.0.99 Aphanizomenon_flos_aquae_2012_km1_d3 Aphanizomenon_flos_aquae_2012_km1_d3 Aphanizomenon_flos_aquae_2012_km1_d3 Aphanizomenon_flos_aquae_2012_km1_d3_gca_000789435 Aphanizomenon_flos_aquae_2012_km1_d3_gca_000789435 Aphanizomenon_flos_aquae_2012_km1_d3_gca_000789435 @@ -4231,11 +4216,8 @@ Apis_florea_gca000184785v2rs Apis_florea_gca000184785v2rs Apis_florea_gca000 Apis_mellifera Apis_mellifera Apis_mellifera Aplosporella_prunicola_cbs_121167_gca_010093885 Aplosporella_prunicola_cbs_121167_gca_010093885 Aplosporella_prunicola_cbs_121167_gca_010093885 Aplysia_californica_gca000002075v2 Aplysia_californica_gca000002075v2 Aplysia_californica_gca000002075v2 -aptHaa1.110 Apteryx_haastii aptHaa1.110 aptHaa1.99 Apteryx_haastii aptHaa1.99 -aptOwe1.110 Apteryx_owenii aptOwe1.110 aptOwe1.99 Apteryx_owenii aptOwe1.99 -aptRow1.110 Apteryx_rowi aptRow1.110 aptRow1.99 Apteryx_rowi aptRow1.99 Aquabacter_spiritensis_gca_004346185 Aquabacter_spiritensis_gca_004346185 Aquabacter_spiritensis_gca_004346185 Aquabacterium_commune_gca_004362855 Aquabacterium_commune_gca_004362855 Aquabacterium_commune_gca_004362855 @@ -4260,7 +4242,6 @@ Aquifex_aeolicus_vf5_gca_000008625 Aquifex_aeolicus_vf5_gca_000008625 Aquife Aquifex_sp__gca_003978875 Aquifex_sp__gca_003978875 Aquifex_sp__gca_003978875 Aquificae_bacterium_gca_003697005 Aquificae_bacterium_gca_003697005 Aquificae_bacterium_gca_003697005 Aquiflexum_balticum_dsm_16537_gca_900176595 Aquiflexum_balticum_dsm_16537_gca_900176595 Aquiflexum_balticum_dsm_16537_gca_900176595 -bAquChr1.2.110 Aquila_chrysaetos_chrysaetos bAquChr1.2.110 bAquChr1.2.99 Aquila_chrysaetos_chrysaetos bAquChr1.2.99 Aquimarina_aggregata_gca_001632745 Aquimarina_aggregata_gca_001632745 Aquimarina_aggregata_gca_001632745 Aquimarina_amphilecti_gca_900109375 Aquimarina_amphilecti_gca_900109375 Aquimarina_amphilecti_gca_900109375 @@ -4779,7 +4760,6 @@ Aspergillus_versicolor_cbs_583_65_gca_001890125 Aspergillus_versicolor_cbs_583 Aspergillus_violaceofuscus_cbs_115571_gca_003184705 Aspergillus_violaceofuscus_cbs_115571_gca_003184705 Aspergillus_violaceofuscus_cbs_115571_gca_003184705 Aspergillus_welwitschiae_gca_003344945 Aspergillus_welwitschiae_gca_003344945 Aspergillus_welwitschiae_gca_003344945 Aspergillus_wentii_dto_134e9_gca_001890725 Aspergillus_wentii_dto_134e9_gca_001890725 Aspergillus_wentii_dto_134e9_gca_001890725 -fAstCal1.2.110 Astatotilapia_calliptera fAstCal1.2.110 fAstCal1.2.99 Astatotilapia_calliptera fAstCal1.2.99 Aster_yellows_witches_broom_phytoplasma_aywb Aster_yellows_witches_broom_phytoplasma_aywb Aster_yellows_witches_broom_phytoplasma_aywb Aster_yellows_witches_broom_phytoplasma_aywb_gca_000012225 Aster_yellows_witches_broom_phytoplasma_aywb_gca_000012225 Aster_yellows_witches_broom_phytoplasma_aywb_gca_000012225 @@ -4802,13 +4782,10 @@ Asticcacaulis_sp_ybe204 Asticcacaulis_sp_ybe204 Asticcacaulis_sp_ybe204 Asticcacaulis_sp_ybe204_gca_000495855 Asticcacaulis_sp_ybe204_gca_000495855 Asticcacaulis_sp_ybe204_gca_000495855 Asticcacaulis_taihuensis_gca_900100255 Asticcacaulis_taihuensis_gca_900100255 Asticcacaulis_taihuensis_gca_900100255 AstMex102.75 Astyanax_mexicanus AstMex102.75 -Astyanax_mexicanus-2.0.110 Astyanax_mexicanus Astyanax_mexicanus-2.0.110 Astyanax_mexicanus-2.0.99 Astyanax_mexicanus Astyanax_mexicanus-2.0.99 -Astyanax_mexicanus-1.0.2.110 Astyanax_mexicanus_pachon Astyanax_mexicanus-1.0.2.110 Astyanax_mexicanus-1.0.2.99 Astyanax_mexicanus_pachon Astyanax_mexicanus-1.0.2.99 Athalia_rosae_gca000344095v2 Athalia_rosae_gca000344095v2 Athalia_rosae_gca000344095v2 Athalia_rosae_gca917208135v1 Athalia_rosae_gca917208135v1 Athalia_rosae_gca917208135v1 -athCun1.110 Athene_cunicularia athCun1.110 athCun1.99 Athene_cunicularia athCun1.99 Atlantibacter_hermannii_gca_900635495 Atlantibacter_hermannii_gca_900635495 Atlantibacter_hermannii_gca_900635495 Atlantibacter_hermannii_nbrc_105704 Atlantibacter_hermannii_nbrc_105704 Atlantibacter_hermannii_nbrc_105704 @@ -7303,7 +7280,6 @@ Bactrocera_latifrons_gca001853355v1 Bactrocera_latifrons_gca001853355v1 Bact Bactrocera_tryoni_gca016617805v2 Bactrocera_tryoni_gca016617805v2 Bactrocera_tryoni_gca016617805v2 Baia_soyae_gca_004341445 Baia_soyae_gca_004341445 Baia_soyae_gca_004341445 Bailinhaonella_thermotolerans_gca_003594875 Bailinhaonella_thermotolerans_gca_003594875 Bailinhaonella_thermotolerans_gca_003594875 -mBalMus1.v2.110 Balaenoptera_musculus mBalMus1.v2.110 Balneicella_halophila_gca_003096835 Balneicella_halophila_gca_003096835 Balneicella_halophila_gca_003096835 Balneola_sp__gca_002694685 Balneola_sp__gca_002694685 Balneola_sp__gca_002694685 Balneola_sp__gca_002696035 Balneola_sp__gca_002696035 Balneola_sp__gca_002696035 @@ -7568,7 +7544,6 @@ Betaproteobacteria_bacterium_scgc_ag_212_j23 Betaproteobacteria_bacterium_scgc Betaproteobacteria_bacterium_sg8_41_gca_001303585 Betaproteobacteria_bacterium_sg8_41_gca_001303585 Betaproteobacteria_bacterium_sg8_41_gca_001303585 Betaproteobacteria_bacterium_ukl13_2 Betaproteobacteria_bacterium_ukl13_2 Betaproteobacteria_bacterium_ukl13_2 Betaproteobacteria_bacterium_ukl13_2_gca_001602455 Betaproteobacteria_bacterium_ukl13_2_gca_001602455 Betaproteobacteria_bacterium_ukl13_2_gca_001602455 -fBetSpl5.2.110 Betta_splendens fBetSpl5.2.110 fBetSpl5.2.99 Betta_splendens fBetSpl5.2.99 Beutenbergia_cavernae_dsm_12333 Beutenbergia_cavernae_dsm_12333 Beutenbergia_cavernae_dsm_12333 Beutenbergia_cavernae_dsm_12333_gca_000023105 Beutenbergia_cavernae_dsm_12333_gca_000023105 Beutenbergia_cavernae_dsm_12333_gca_000023105 @@ -8077,7 +8052,6 @@ Bipolaris_sorokiniana_nd90pr_gca_000338995 Bipolaris_sorokiniana_nd90pr_gca_00 Bipolaris_victoriae_fi3_gca_000527765 Bipolaris_victoriae_fi3_gca_000527765 Bipolaris_victoriae_fi3_gca_000527765 Bipolaris_zeicola_26_r_13_gca_000523435 Bipolaris_zeicola_26_r_13_gca_000523435 Bipolaris_zeicola_26_r_13_gca_000523435 Bisgaardia_hudsonensis_gca_004345785 Bisgaardia_hudsonensis_gca_004345785 Bisgaardia_hudsonensis_gca_004345785 -Bison_UMD1.0.110 Bison_bison_bison Bison_UMD1.0.110 Bison_UMD1.0.99 Bison_bison_bison Bison_UMD1.0.99 Bizionia_argentinensis_jub59 Bizionia_argentinensis_jub59 Bizionia_argentinensis_jub59 Bizionia_echini_gca_900115185 Bizionia_echini_gca_900115185 Bizionia_echini_gca_900115185 @@ -8775,16 +8749,11 @@ Borreliella_spielmanii_a14s_gca_000181895 Borreliella_spielmanii_a14s_gca_0001 Borreliella_valaisiana_tom4006 Borreliella_valaisiana_tom4006 Borreliella_valaisiana_tom4006 Borreliella_valaisiana_vs116 Borreliella_valaisiana_vs116 Borreliella_valaisiana_vs116 Borreliella_valaisiana_vs116_gca_000170955 Borreliella_valaisiana_vs116_gca_000170955 Borreliella_valaisiana_vs116_gca_000170955 -LU_Bosgru_v3.0.110 Bos_grunniens LU_Bosgru_v3.0.110 LU_Bosgru_v3.0.99 Bos_grunniens LU_Bosgru_v3.0.99 -UOA_Brahman_1.110 Bos_indicus_hybrid UOA_Brahman_1.110 UOA_Brahman_1.99 Bos_indicus_hybrid UOA_Brahman_1.99 -BosGru_v2.0.110 Bos_mutus BosGru_v2.0.110 BosGru_v2.0.99 Bos_mutus BosGru_v2.0.99 -ARS-UCD1.2.110 Bos_taurus ARS-UCD1.2.110 ARS-UCD1.2.99 Bos_taurus ARS-UCD1.2.99 UMD3.1.75 Bos_taurus UMD3.1.75 -UOA_Angus_1.110 Bos_taurus_hybrid UOA_Angus_1.110 UOA_Angus_1.99 Bos_taurus_hybrid UOA_Angus_1.99 Bosea_caraganae_gca_003351325 Bosea_caraganae_gca_003351325 Bosea_caraganae_gca_003351325 Bosea_lathyri_gca_900108245 Bosea_lathyri_gca_900108245 Bosea_lathyri_gca_900108245 @@ -9667,7 +9636,6 @@ KJ473813.1 BtRf-BetaCoV/SX2013, KJ473813.1 KJ473815.1 BtRs-BetaCoV/GX2013, KJ473815.1 KJ473814.1 BtRs-BetaCoV/HuB2013, KJ473814.1 KJ473816.1 BtRs-BetaCoV/YN2013, KJ473816.1 -BubBub1.0.110 Bubo_bubo BubBub1.0.110 Buchananella_hordeovulneris_gca_001907235 Buchananella_hordeovulneris_gca_001907235 Buchananella_hordeovulneris_gca_001907235 Buchananella_hordeovulneris_gca_003858505 Buchananella_hordeovulneris_gca_003858505 Buchananella_hordeovulneris_gca_003858505 Buchnera_aphidicola_aphis_glycines_ Buchnera_aphidicola_aphis_glycines_ Buchnera_aphidicola_aphis_glycines_ @@ -10485,7 +10453,6 @@ Burkholderiales_bacterium_rifoxyc12_full_65_23_gca_001770995 Burkholderiales_b Burkholderiales_bacterium_rifoxyd12_full_59_19_gca_001771065 Burkholderiales_bacterium_rifoxyd12_full_59_19_gca_001771065 Burkholderiales_bacterium_rifoxyd12_full_59_19_gca_001771065 Burkholderiales_bacterium_yl45 Burkholderiales_bacterium_yl45 Burkholderiales_bacterium_yl45 Burkholderiales_bacterium_yl45_gca_001688905 Burkholderiales_bacterium_yl45_gca_001688905 Burkholderiales_bacterium_yl45_gca_001688905 -ButJap1.0.110 Buteo_japonicus ButJap1.0.110 Buttiauxella_agrestis_atcc_33320 Buttiauxella_agrestis_atcc_33320 Buttiauxella_agrestis_atcc_33320 Buttiauxella_agrestis_atcc_33320_gca_000735355 Buttiauxella_agrestis_atcc_33320_gca_000735355 Buttiauxella_agrestis_atcc_33320_gca_000735355 Buttiauxella_agrestis_gca_900446255 Buttiauxella_agrestis_gca_900446255 Buttiauxella_agrestis_gca_900446255 @@ -10599,12 +10566,10 @@ Caenispirillum_salinarum_ak4_gca_000315795 Caenispirillum_salinarum_ak4_gca_00 Caenorhabditis_brenneri Caenorhabditis_brenneri Caenorhabditis_brenneri Caenorhabditis_briggsae Caenorhabditis_briggsae Caenorhabditis_briggsae Caenorhabditis_elegans Caenorhabditis_elegans Caenorhabditis_elegans -WBcel235.110 Caenorhabditis_elegans WBcel235.110 WBcel235.75 Caenorhabditis_elegans WBcel235.75 WBcel235.99 Caenorhabditis_elegans WBcel235.99 Caenorhabditis_japonica Caenorhabditis_japonica Caenorhabditis_japonica Caenorhabditis_remanei Caenorhabditis_remanei Caenorhabditis_remanei -CaiMos1.0.110 Cairina_moschata_domestica CaiMos1.0.110 Cajanus_cajan Cajanus_cajan Cajanus_cajan Caldalkalibacillus_thermarum_ta2_a1 Caldalkalibacillus_thermarum_ta2_a1 Caldalkalibacillus_thermarum_ta2_a1 Caldalkalibacillus_thermarum_ta2_a1_gca_000218765 Caldalkalibacillus_thermarum_ta2_a1_gca_000218765 Caldalkalibacillus_thermarum_ta2_a1_gca_000218765 @@ -10681,14 +10646,10 @@ Caldivirga_sp_mg_3 Caldivirga_sp_mg_3 Caldivirga_sp_mg_3 Calidifontibacter_indicus_gca_003386865 Calidifontibacter_indicus_gca_003386865 Calidifontibacter_indicus_gca_003386865 Calidithermus_roseus_gca_003574095 Calidithermus_roseus_gca_003574095 Calidithermus_roseus_gca_003574095 Calidithermus_terrae_gca_003574345 Calidithermus_terrae_gca_003574345 Calidithermus_terrae_gca_003574345 -ASM143184v1.110 Calidris_pugnax ASM143184v1.110 ASM143184v1.99 Calidris_pugnax ASM143184v1.99 -ASM369795v1.110 Calidris_pygmaea ASM369795v1.110 ASM369795v1.99 Calidris_pygmaea ASM369795v1.99 ASM275486v1.99 Callithrix_jacchus ASM275486v1.99 C_jacchus3.2.1.75 Callithrix_jacchus C_jacchus3.2.1.75 -mCalJac1.pat.X.110 Callithrix_jacchus mCalJac1.pat.X.110 -Callorhinchus_milii-6.1.3.110 Callorhinchus_milii Callorhinchus_milii-6.1.3.110 Callorhinchus_milii-6.1.3.99 Callorhinchus_milii Callorhinchus_milii-6.1.3.99 Calocera_cornea_hhb12733_gca_001632435 Calocera_cornea_hhb12733_gca_001632435 Calocera_cornea_hhb12733_gca_001632435 Calocera_viscosa_tufc12733_gca_001630345 Calocera_viscosa_tufc12733_gca_001630345 Calocera_viscosa_tufc12733_gca_001630345 @@ -10720,10 +10681,8 @@ Calothrix_sp_pcc_6303 Calothrix_sp_pcc_6303 Calothrix_sp_pcc_6303 Calothrix_sp_pcc_6303_gca_000317435 Calothrix_sp_pcc_6303_gca_000317435 Calothrix_sp_pcc_6303_gca_000317435 Calothrix_sp_pcc_7507 Calothrix_sp_pcc_7507 Calothrix_sp_pcc_7507 Calothrix_sp_pcc_7507_gca_000316575 Calothrix_sp_pcc_7507_gca_000316575 Calothrix_sp_pcc_7507_gca_000316575 -Camarhynchus_parvulus_V1.1.110 Camarhynchus_parvulus Camarhynchus_parvulus_V1.1.110 Camelimonas_lactis_gca_004342915 Camelimonas_lactis_gca_004342915 Camelimonas_lactis_gca_004342915 Camelina_sativa Camelina_sativa Camelina_sativa -CamDro2.110 Camelus_dromedarius CamDro2.110 CamDro2.99 Camelus_dromedarius CamDro2.99 Caminibacter_mediatlanticus_tb_2 Caminibacter_mediatlanticus_tb_2 Caminibacter_mediatlanticus_tb_2 Caminibacter_mediatlanticus_tb_2_gca_005843985 Caminibacter_mediatlanticus_tb_2_gca_005843985 Caminibacter_mediatlanticus_tb_2_gca_005843985 @@ -12896,15 +12855,9 @@ Candidimonas_sp_syp_b2681_gca_003971065 Candidimonas_sp_syp_b2681_gca_00397106 Canicola_haemoglobinophilus_gca_900450725 Canicola_haemoglobinophilus_gca_900450725 Canicola_haemoglobinophilus_gca_900450725 CanFam3.1.75 Canis_familiaris CanFam3.1.75 CanFam3.1.99 Canis_familiaris CanFam3.1.99 -ASM325472v1.110 Canis_lupus_dingo ASM325472v1.110 ASM325472v1.99 Canis_lupus_dingo ASM325472v1.99 -ROS_Cfam_1.0.110 Canis_lupus_familiaris ROS_Cfam_1.0.110 -Basenji_breed-1.1.110 Canis_lupus_familiarisbasenji Basenji_breed-1.1.110 Basenji_breed-1.1.99 Canis_lupus_familiarisbasenji Basenji_breed-1.1.99 -Dog10K_Boxer_Tasha.110 Canis_lupus_familiarisboxer Dog10K_Boxer_Tasha.110 -UMICH_Zoey_3.1.110 Canis_lupus_familiarisgreatdane UMICH_Zoey_3.1.110 UMICH_Zoey_3.1.99 Canis_lupus_familiarisgreatdane UMICH_Zoey_3.1.99 -UU_Cfam_GSD_1.0.110 Canis_lupus_familiarisgsd UU_Cfam_GSD_1.0.110 Cannabis_sativa_female Cannabis_sativa_female Cannabis_sativa_female Capitella_teleta Capitella_teleta Capitella_teleta Capnocytophaga_canimorsus Capnocytophaga_canimorsus Capnocytophaga_canimorsus @@ -12973,16 +12926,13 @@ Capnocytophaga_sputigena_gca_002302595 Capnocytophaga_sputigena_gca_002302595 Capnocytophaga_sputigena_gca_002312885 Capnocytophaga_sputigena_gca_002312885 Capnocytophaga_sputigena_gca_002312885 Capnocytophaga_sputigena_gca_900638125 Capnocytophaga_sputigena_gca_900638125 Capnocytophaga_sputigena_gca_900638125 Capnocytophaga_stomatis_gca_002302635 Capnocytophaga_stomatis_gca_002302635 Capnocytophaga_stomatis_gca_002302635 -ARS1.110 Capra_hircus ARS1.110 ARS1.99 Capra_hircus ARS1.99 -CVASU_BBG_1.0.110 Capra_hircus_blackbengal CVASU_BBG_1.0.110 Caproiciproducens_sp_njn_50_gca_004103755 Caproiciproducens_sp_njn_50_gca_004103755 Caproiciproducens_sp_njn_50_gca_004103755 Capronia_coronata_cbs_617_96_gca_000585585 Capronia_coronata_cbs_617_96_gca_000585585 Capronia_coronata_cbs_617_96_gca_000585585 Capronia_epimyces_cbs_606_96_gca_000585565 Capronia_epimyces_cbs_606_96_gca_000585565 Capronia_epimyces_cbs_606_96_gca_000585565 Capsaspora_owczarzaki_atcc_30864_gca_000151315 Capsaspora_owczarzaki_atcc_30864_gca_000151315 Capsaspora_owczarzaki_atcc_30864_gca_000151315 Capsicum_annuum Capsicum_annuum Capsicum_annuum Capsulimonas_corticalis_gca_003574315 Capsulimonas_corticalis_gca_003574315 Capsulimonas_corticalis_gca_003574315 -ASM336829v1.110 Carassius_auratus ASM336829v1.110 Carbonactinospora_thermoautotrophica_gca_001543895 Carbonactinospora_thermoautotrophica_gca_001543895 Carbonactinospora_thermoautotrophica_gca_001543895 Carbonactinospora_thermoautotrophica_gca_001543925 Carbonactinospora_thermoautotrophica_gca_001543925 Carbonactinospora_thermoautotrophica_gca_001543925 Carboxydocella_sporoproducens_dsm_16521_gca_900167165 Carboxydocella_sporoproducens_dsm_16521_gca_900167165 Carboxydocella_sporoproducens_dsm_16521_gca_900167165 @@ -13000,7 +12950,6 @@ Cardiobacterium_valvarum_f0432 Cardiobacterium_valvarum_f0432 Cardiobacteriu Cardiobacterium_valvarum_f0432_gca_000239355 Cardiobacterium_valvarum_f0432_gca_000239355 Cardiobacterium_valvarum_f0432_gca_000239355 Cardiobacterium_valvarum_gca_900460955 Cardiobacterium_valvarum_gca_900460955 Cardiobacterium_valvarum_gca_900460955 Carideicomes_alvinocaridis_gca_005473895 Carideicomes_alvinocaridis_gca_005473895 Carideicomes_alvinocaridis_gca_005473895 -Tarsius_syrichta-2.0.1.110 Carlito_syrichta Tarsius_syrichta-2.0.1.110 Tarsius_syrichta-2.0.1.99 Carlito_syrichta Tarsius_syrichta-2.0.1.99 Carnobacterium_alterfunditum_gca_900143105 Carnobacterium_alterfunditum_gca_900143105 Carnobacterium_alterfunditum_gca_900143105 Carnobacterium_divergens_dsm_20623 Carnobacterium_divergens_dsm_20623 Carnobacterium_divergens_dsm_20623 @@ -13030,10 +12979,8 @@ Caryophanon_tenue Caryophanon_tenue Caryophanon_tenue Caryophanon_tenue_gca_001700315 Caryophanon_tenue_gca_001700315 Caryophanon_tenue_gca_001700315 Castellaniella_defragrans_65phen Castellaniella_defragrans_65phen Castellaniella_defragrans_65phen Castellaniella_defragrans_65phen_gca_000612685 Castellaniella_defragrans_65phen_gca_000612685 Castellaniella_defragrans_65phen_gca_000612685 -C.can_genome_v1.0.110 Castor_canadensis C.can_genome_v1.0.110 C.can_genome_v1.0.99 Castor_canadensis C.can_genome_v1.0.99 Catabacter_hongkongensis Catabacter_hongkongensis Catabacter_hongkongensis -CatWag_v2_BIUU_UCD.110 Catagonus_wagneri CatWag_v2_BIUU_UCD.110 CatWag_v2_BIUU_UCD.99 Catagonus_wagneri CatWag_v2_BIUU_UCD.99 Catalinimonas_alkaloidigena_gca_900100765 Catalinimonas_alkaloidigena_gca_900100765 Catalinimonas_alkaloidigena_gca_900100765 Catellatospora_citrea_gca_003610235 Catellatospora_citrea_gca_003610235 Catellatospora_citrea_gca_003610235 @@ -13051,7 +12998,6 @@ Catenovulum_agarivorans_ds_2_gca_000568405 Catenovulum_agarivorans_ds_2_gca_00 Catenovulum_maritimum_gca_001050375 Catenovulum_maritimum_gca_001050375 Catenovulum_maritimum_gca_001050375 Catenulispora_acidiphila_dsm_44928 Catenulispora_acidiphila_dsm_44928 Catenulispora_acidiphila_dsm_44928 Catenulispora_acidiphila_dsm_44928_gca_000024025 Catenulispora_acidiphila_dsm_44928_gca_000024025 Catenulispora_acidiphila_dsm_44928_gca_000024025 -bCatUst1.pri.110 Catharus_ustulatus bCatUst1.pri.110 Catonella_morbi_atcc_51271 Catonella_morbi_atcc_51271 Catonella_morbi_atcc_51271 Catonella_morbi_atcc_51271_gca_000160035 Catonella_morbi_atcc_51271_gca_000160035 Catonella_morbi_atcc_51271_gca_000160035 Caulobacter_crescentus_cb15 Caulobacter_crescentus_cb15 Caulobacter_crescentus_cb15 @@ -13109,14 +13055,11 @@ Caulobacterales_bacterium_rifcsphigho2_01_full_70_19_gca_001794825 Caulobacter Caulochytrium_protostelioides_gca_003615035 Caulochytrium_protostelioides_gca_003615035 Caulochytrium_protostelioides_gca_003615035 Caulochytrium_protostelioides_gca_003615045 Caulochytrium_protostelioides_gca_003615045 Caulochytrium_protostelioides_gca_003615045 Cavenderia_fasciculata_gca_000203815 Cavenderia_fasciculata_gca_000203815 Cavenderia_fasciculata_gca_000203815 -CavAp1.0.110 Cavia_aperea CavAp1.0.110 CavAp1.0.99 Cavia_aperea CavAp1.0.99 -Cavpor3.0.110 Cavia_porcellus Cavpor3.0.110 Cavpor3.0.99 Cavia_porcellus Cavpor3.0.99 cavPor3.75 Cavia_porcellus cavPor3.75 Caviibacterium_pharyngocola_gca_002795405 Caviibacterium_pharyngocola_gca_002795405 Caviibacterium_pharyngocola_gca_002795405 Cebus_imitator-1.0.99 Cebus_capucinus Cebus_imitator-1.0.99 -Cebus_imitator-1.0.110 Cebus_imitator Cebus_imitator-1.0.110 Cecembia_calidifontis_gca_004216715 Cecembia_calidifontis_gca_004216715 Cecembia_calidifontis_gca_004216715 Cecembia_lonarensis_lw9 Cecembia_lonarensis_lw9 Cecembia_lonarensis_lw9 Cecembia_lonarensis_lw9_gca_000298295 Cecembia_lonarensis_lw9_gca_000298295 Cecembia_lonarensis_lw9_gca_000298295 @@ -13244,7 +13187,6 @@ Ceraceosorus_guamensis_gca_003144195 Ceraceosorus_guamensis_gca_003144195 Ce Ceratitis_capitata_gca000347755v4 Ceratitis_capitata_gca000347755v4 Ceratitis_capitata_gca000347755v4 Ceratobasidium_theobromae_gca_009078325 Ceratobasidium_theobromae_gca_009078325 Ceratobasidium_theobromae_gca_009078325 Ceratocystis_platani_gca_000978885 Ceratocystis_platani_gca_000978885 Ceratocystis_platani_gca_000978885 -Caty_1.0.110 Cercocebus_atys Caty_1.0.110 Caty_1.0.99 Cercocebus_atys Caty_1.0.99 Cercospora_berteroae_gca_002933655 Cercospora_berteroae_gca_002933655 Cercospora_berteroae_gca_002933655 Cercospora_beticola_gca_002742065 Cercospora_beticola_gca_002742065 Cercospora_beticola_gca_002742065 @@ -13261,7 +13203,6 @@ Cereibacter_sphaeroides_f_sp_denitrificans_gca_003363065 Cereibacter_sphaeroid Cereibacter_sphaeroides_gca_003243455 Cereibacter_sphaeroides_gca_003243455 Cereibacter_sphaeroides_gca_003243455 Cereibacter_sphaeroides_gca_003846425 Cereibacter_sphaeroides_gca_003846425 Cereibacter_sphaeroides_gca_003846425 Cereibacter_sphaeroides_kd131_gca_000021005 Cereibacter_sphaeroides_kd131_gca_000021005 Cereibacter_sphaeroides_kd131_gca_000021005 -CEY_v1.110 Cervus_hanglu_yarkandensis CEY_v1.110 Cesiribacter_andamanensis_amv16 Cesiribacter_andamanensis_amv16 Cesiribacter_andamanensis_amv16 Cesiribacter_andamanensis_amv16_gca_000348925 Cesiribacter_andamanensis_amv16_gca_000348925 Cesiribacter_andamanensis_amv16_gca_000348925 Cetobacterium_ceti_gca_900167275 Cetobacterium_ceti_gca_900167275 Cetobacterium_ceti_gca_900167275 @@ -13290,15 +13231,12 @@ Chelatococcus_sp_co_6 Chelatococcus_sp_co_6 Chelatococcus_sp_co_6 Chelatococcus_sp_co_6_gca_001271345 Chelatococcus_sp_co_6_gca_001271345 Chelatococcus_sp_co_6_gca_001271345 Chelonobacter_oris Chelonobacter_oris Chelonobacter_oris Chelonobacter_oris_gca_000772535 Chelonobacter_oris_gca_000772535 Chelonobacter_oris_gca_000772535 -ASM359739v1.110 Chelonoidis_abingdonii ASM359739v1.110 ASM359739v1.99 Chelonoidis_abingdonii ASM359739v1.99 Chelonus_insularis_gca013357705v1rs Chelonus_insularis_gca013357705v1rs Chelonus_insularis_gca013357705v1rs -Chelydra_serpentina-1.0.110 Chelydra_serpentina Chelydra_serpentina-1.0.110 Chenopodium_quinoa Chenopodium_quinoa Chenopodium_quinoa Chimaeribacter_arupi_gca_002858825 Chimaeribacter_arupi_gca_002858825 Chimaeribacter_arupi_gca_002858825 Chimaeribacter_californicus_gca_002858675 Chimaeribacter_californicus_gca_002858675 Chimaeribacter_californicus_gca_002858675 Chimaeribacter_coloradensis_gca_002858715 Chimaeribacter_coloradensis_gca_002858715 Chimaeribacter_coloradensis_gca_002858715 -ChiLan1.0.110 Chinchilla_lanigera ChiLan1.0.110 ChiLan1.0.99 Chinchilla_lanigera ChiLan1.0.99 Chishuiella_changwenlii_gca_900142565 Chishuiella_changwenlii_gca_900142565 Chishuiella_changwenlii_gca_900142565 Chitinasiproducens_palmae_gca_900095735 Chitinasiproducens_palmae_gca_900095735 Chitinasiproducens_palmae_gca_900095735 @@ -13621,7 +13559,6 @@ Chlorobium_phaeovibrioides_gca_003968655 Chlorobium_phaeovibrioides_gca_003968 Chlorobium_sp_gbchlb Chlorobium_sp_gbchlb Chlorobium_sp_gbchlb Chlorobium_sp_n1_gca_004332115 Chlorobium_sp_n1_gca_004332115 Chlorobium_sp_n1_gca_004332115 Chlorobium_tepidum_tls Chlorobium_tepidum_tls Chlorobium_tepidum_tls -ChlSab1.1.110 Chlorocebus_sabaeus ChlSab1.1.110 ChlSab1.1.99 Chlorocebus_sabaeus ChlSab1.1.99 Chloroflexi_bacterium_13_1_40cm_65_17_gca_001917815 Chloroflexi_bacterium_13_1_40cm_65_17_gca_001917815 Chloroflexi_bacterium_13_1_40cm_65_17_gca_001917815 Chloroflexi_bacterium_44_23_gca_001899005 Chloroflexi_bacterium_44_23_gca_001899005 Chloroflexi_bacterium_44_23_gca_001899005 @@ -13735,7 +13672,6 @@ Chloroherpeton_thalassium_atcc_35110 Chloroherpeton_thalassium_atcc_35110 Ch Chloroherpeton_thalassium_atcc_35110_gca_000020525 Chloroherpeton_thalassium_atcc_35110_gca_000020525 Chloroherpeton_thalassium_atcc_35110_gca_000020525 Choanephora_cucurbitarum_gca_001683725 Choanephora_cucurbitarum_gca_001683725 Choanephora_cucurbitarum_gca_001683725 Choiromyces_venosus_120613_1_gca_003788595 Choiromyces_venosus_120613_1_gca_003788595 Choiromyces_venosus_120613_1_gca_003788595 -choHof1.110 Choloepus_hoffmanni choHof1.110 choHof1.75 Choloepus_hoffmanni choHof1.75 choHof1.99 Choloepus_hoffmanni choHof1.99 Chondrocystis_sp_nies_4102_gca_002368355 Chondrocystis_sp_nies_4102_gca_002368355 Chondrocystis_sp_nies_4102_gca_002368355 @@ -13800,7 +13736,6 @@ Chroococcidiopsis_thermalis_pcc_7203 Chroococcidiopsis_thermalis_pcc_7203 Ch Chroococcidiopsis_thermalis_pcc_7203_gca_000317125 Chroococcidiopsis_thermalis_pcc_7203_gca_000317125 Chroococcidiopsis_thermalis_pcc_7203_gca_000317125 Chroogloeocystis_siderophila_5_2_s_c_1_gca_001904655 Chroogloeocystis_siderophila_5_2_s_c_1_gca_001904655 Chroogloeocystis_siderophila_5_2_s_c_1_gca_001904655 Chroomonas_mesostigmatica_ccmp1168_gca_000286095 Chroomonas_mesostigmatica_ccmp1168_gca_000286095 Chroomonas_mesostigmatica_ccmp1168_gca_000286095 -Chrysemys_picta_bellii-3.0.3.110 Chrysemys_picta_bellii Chrysemys_picta_bellii-3.0.3.110 Chrysemys_picta_bellii-3.0.3.99 Chrysemys_picta_bellii Chrysemys_picta_bellii-3.0.3.99 Chryseobacterium_angstadtii Chryseobacterium_angstadtii Chryseobacterium_angstadtii Chryseobacterium_angstadtii_gca_001045465 Chryseobacterium_angstadtii_gca_001045465 Chryseobacterium_angstadtii_gca_001045465 @@ -13978,7 +13913,6 @@ Chryseolinea_serpens_gca_900129725 Chryseolinea_serpens_gca_900129725 Chryse Chryseolinea_soli_gca_003589925 Chryseolinea_soli_gca_003589925 Chryseolinea_soli_gca_003589925 Chryseomicrobium_excrementi_gca_002798305 Chryseomicrobium_excrementi_gca_002798305 Chryseomicrobium_excrementi_gca_002798305 Chryseotalea_sanaruensis_gca_003990915 Chryseotalea_sanaruensis_gca_003990915 Chryseotalea_sanaruensis_gca_003990915 -Chrysolophus_pictus_GenomeV1.0.110 Chrysolophus_pictus Chrysolophus_pictus_GenomeV1.0.110 Chrysolophus_pictus_GenomeV1.0.99 Chrysolophus_pictus Chrysolophus_pictus_GenomeV1.0.99 Chrysosporum_ovalisporum Chrysosporum_ovalisporum Chrysosporum_ovalisporum Chrysosporum_ovalisporum_gca_001458455 Chrysosporum_ovalisporum_gca_001458455 Chrysosporum_ovalisporum_gca_001458455 @@ -13995,10 +13929,8 @@ Ciceribacter_lividus_gca_003337715 Ciceribacter_lividus_gca_003337715 Ciceri Ciceribacter_naphthalenivorans_gca_900492205 Ciceribacter_naphthalenivorans_gca_900492205 Ciceribacter_naphthalenivorans_gca_900492205 Ciceribacter_selenitireducens_atcc_baa_1503_gca_900492185 Ciceribacter_selenitireducens_atcc_baa_1503_gca_900492185 Ciceribacter_selenitireducens_atcc_baa_1503_gca_900492185 Cimex_lectularius Cimex_lectularius Cimex_lectularius -KH.110 Ciona_intestinalis KH.110 KH.75 Ciona_intestinalis KH.75 KH.99 Ciona_intestinalis KH.99 -CSAV2.0.110 Ciona_savignyi CSAV2.0.110 CSAV2.0.75 Ciona_savignyi CSAV2.0.75 CSAV2.0.99 Ciona_savignyi CSAV2.0.99 Citreicella_sp_357 Citreicella_sp_357 Citreicella_sp_357 @@ -15107,7 +15039,6 @@ Clostridium_tyrobutyricum_divetgp_gca_000577845 Clostridium_tyrobutyricum_dive Clostridium_tyrobutyricum_gca_004924375 Clostridium_tyrobutyricum_gca_004924375 Clostridium_tyrobutyricum_gca_004924375 Clostridium_uliginosum_gca_900112485 Clostridium_uliginosum_gca_900112485 Clostridium_uliginosum_gca_900112485 Clostridium_vincentii_gca_002995745 Clostridium_vincentii_gca_002995745 Clostridium_vincentii_gca_002995745 -Ch_v2.0.2.110 Clupea_harengus Ch_v2.0.2.110 Ch_v2.0.2.99 Clupea_harengus Ch_v2.0.2.99 Clytia_hemisphaerica_gca902728285 Clytia_hemisphaerica_gca902728285 Clytia_hemisphaerica_gca902728285 Cnuella_takakiae_gca_900129015 Cnuella_takakiae_gca_900129015 Cnuella_takakiae_gca_900129015 @@ -15200,7 +15131,6 @@ Collinsella_intestinalis_dsm_13280 Collinsella_intestinalis_dsm_13280 Collin Collinsella_sp_4_8_47faa Collinsella_sp_4_8_47faa Collinsella_sp_4_8_47faa Collinsella_stercoris_dsm_13279 Collinsella_stercoris_dsm_13279 Collinsella_stercoris_dsm_13279 Collinsella_tanakaei_yit_12063 Collinsella_tanakaei_yit_12063 Collinsella_tanakaei_yit_12063 -Cang.pa_1.0.110 Colobus_angolensis_palliatus Cang.pa_1.0.110 Cang.pa_1.0.99 Colobus_angolensis_palliatus Cang.pa_1.0.99 Colwellia_chukchiensis_gca_900109795 Colwellia_chukchiensis_gca_900109795 Colwellia_chukchiensis_gca_900109795 Colwellia_marinimaniae_gca_002207865 Colwellia_marinimaniae_gca_002207865 Colwellia_marinimaniae_gca_002207865 @@ -15450,7 +15380,6 @@ Coriobacteriaceae_bacterium_gca_004793925 Coriobacteriaceae_bacterium_gca_0047 Coriobacteriales_bacterium_dnf00809 Coriobacteriales_bacterium_dnf00809 Coriobacteriales_bacterium_dnf00809 Coriobacterium_glomerans_pw2 Coriobacterium_glomerans_pw2 Coriobacterium_glomerans_pw2 Corticibacter_populi_gca_003703815 Corticibacter_populi_gca_003703815 Corticibacter_populi_gca_003703815 -bCorMon1.pri.110 Corvus_moneduloides bCorMon1.pri.110 Corylus_avellana Corylus_avellana Corylus_avellana Corymbia_citriodora Corymbia_citriodora Corymbia_citriodora Corynebacterium_accolens_atcc_49725 Corynebacterium_accolens_atcc_49725 Corynebacterium_accolens_atcc_49725 @@ -15820,9 +15749,7 @@ Corynebacterium_yudongzhengii_gca_003113335 Corynebacterium_yudongzhengii_gca_ Corynespora_cassiicola_philippines_gca_003016335 Corynespora_cassiicola_philippines_gca_003016335 Corynespora_cassiicola_philippines_gca_003016335 Cosenzaea_myxofaciens_atcc_19692 Cosenzaea_myxofaciens_atcc_19692 Cosenzaea_myxofaciens_atcc_19692 Cotesia_glomerata_gca020080835v1 Cotesia_glomerata_gca020080835v1 Cotesia_glomerata_gca020080835v1 -fCotGob3.1.110 Cottoperca_gobio fCotGob3.1.110 fCotGob3.1.99 Cottoperca_gobio fCotGob3.1.99 -Coturnix_japonica_2.0.110 Coturnix_japonica Coturnix_japonica_2.0.110 Coturnix_japonica_2.0.99 Coturnix_japonica Coturnix_japonica_2.0.99 Couchioplanes_caeruleus_gca_003751945 Couchioplanes_caeruleus_gca_003751945 Couchioplanes_caeruleus_gca_003751945 Couchioplanes_caeruleus_subsp_caeruleus_gca_001884705 Couchioplanes_caeruleus_subsp_caeruleus_gca_001884705 Couchioplanes_caeruleus_subsp_caeruleus_gca_001884705 @@ -15865,12 +15792,9 @@ Criblamydia_sequanensis_crib_18 Criblamydia_sequanensis_crib_18 Criblamydia_ Criblamydia_sequanensis_crib_18_gca_000750955 Criblamydia_sequanensis_crib_18_gca_000750955 Criblamydia_sequanensis_crib_18_gca_000750955 Cribrihabitans_marinus_gca_900109035 Cribrihabitans_marinus_gca_900109035 Cribrihabitans_marinus_gca_900109035 Cricetibacter_osteomyelitidis_gca_004340985 Cricetibacter_osteomyelitidis_gca_004340985 Cricetibacter_osteomyelitidis_gca_004340985 -CHOK1GS_HDv1.110 Cricetulus_griseus_chok1gshd CHOK1GS_HDv1.110 CHOK1GS_HDv1.99 Cricetulus_griseus_chok1gshd CHOK1GS_HDv1.99 -CriGri_1.0.110 Cricetulus_griseus_crigri CriGri_1.0.110 CriGri_1.0.99 Cricetulus_griseus_crigri CriGri_1.0.99 CriGri-PICR.99 Cricetulus_griseus_picr CriGri-PICR.99 -CriGri-PICRH-1.0.110 Cricetulus_griseus_picr CriGri-PICRH-1.0.110 Criibacterium_bergeronii_gca_001693775 Criibacterium_bergeronii_gca_001693775 Criibacterium_bergeronii_gca_001693775 Crinalium_epipsammum_pcc_9333 Crinalium_epipsammum_pcc_9333 Crinalium_epipsammum_pcc_9333 Crinalium_epipsammum_pcc_9333_gca_000317495 Crinalium_epipsammum_pcc_9333_gca_000317495 Crinalium_epipsammum_pcc_9333_gca_000317495 @@ -15895,7 +15819,6 @@ Crocinitomicaceae_bacterium_gca_002713215 Crocinitomicaceae_bacterium_gca_0027 Crocinitomicaceae_bacterium_gca_002723085 Crocinitomicaceae_bacterium_gca_002723085 Crocinitomicaceae_bacterium_gca_002723085 Crocinitomicaceae_bacterium_tmed16_gca_002167775 Crocinitomicaceae_bacterium_tmed16_gca_002167775 Crocinitomicaceae_bacterium_tmed16_gca_002167775 Crocinitomicaceae_bacterium_tmed209_gca_002170625 Crocinitomicaceae_bacterium_tmed209_gca_002170625 Crocinitomicaceae_bacterium_tmed209_gca_002170625 -CroPor_comp1.110 Crocodylus_porosus CroPor_comp1.110 CroPor_comp1.99 Crocodylus_porosus CroPor_comp1.99 Crocosphaera_subtropica_atcc_51142_gca_000017845 Crocosphaera_subtropica_atcc_51142_gca_000017845 Crocosphaera_subtropica_atcc_51142_gca_000017845 Crocosphaera_watsonii_wh_0003 Crocosphaera_watsonii_wh_0003 Crocosphaera_watsonii_wh_0003 @@ -16272,7 +16195,6 @@ Cutibacterium_granulosum_tm11 Cutibacterium_granulosum_tm11 Cutibacterium_gr Cutibacterium_modestum_hl044pa1_gca_000144085 Cutibacterium_modestum_hl044pa1_gca_000144085 Cutibacterium_modestum_hl044pa1_gca_000144085 Cutibacterium_modestum_p08_gca_000204235 Cutibacterium_modestum_p08_gca_000204235 Cutibacterium_modestum_p08_gca_000204235 Cyanidioschyzon_merolae Cyanidioschyzon_merolae Cyanidioschyzon_merolae -cyaCae2.110 Cyanistes_caeruleus cyaCae2.110 cyaCae2.99 Cyanistes_caeruleus cyaCae2.99 Cyanobacteria_bacterium_j003_gca_003696925 Cyanobacteria_bacterium_j003_gca_003696925 Cyanobacteria_bacterium_j003_gca_003696925 Cyanobacteria_bacterium_j007_gca_003695985 Cyanobacteria_bacterium_j007_gca_003695985 Cyanobacteria_bacterium_j007_gca_003695985 @@ -16335,7 +16257,6 @@ Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_m_gca_002101225 Cycloclasticu Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_n_gca_002101205 Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_n_gca_002101205 Cycloclasticus_sp_symbiont_of_poecilosclerida_sp_n_gca_002101205 Cycloclasticus_zancles_78_me Cycloclasticus_zancles_78_me Cycloclasticus_zancles_78_me Cycloclasticus_zancles_78_me_gca_000442595 Cycloclasticus_zancles_78_me_gca_000442595 Cycloclasticus_zancles_78_me_gca_000442595 -fCycLum1.pri.110 Cyclopterus_lumpus fCycLum1.pri.110 Cyclospora_cayetanensis_gca_000769155 Cyclospora_cayetanensis_gca_000769155 Cyclospora_cayetanensis_gca_000769155 Cylindrobasidium_torrendii_fp15055_ss_10_gca_000934385 Cylindrobasidium_torrendii_fp15055_ss_10_gca_000934385 Cylindrobasidium_torrendii_fp15055_ss_10_gca_000934385 Cylindrospermopsis_raciborskii_cena303_gca_002114155 Cylindrospermopsis_raciborskii_cena303_gca_002114155 Cylindrospermopsis_raciborskii_cena303_gca_002114155 @@ -16349,17 +16270,11 @@ Cylindrospermum_sp_nies_4074_gca_003994795 Cylindrospermum_sp_nies_4074_gca_00 Cylindrospermum_stagnale_pcc_7417 Cylindrospermum_stagnale_pcc_7417 Cylindrospermum_stagnale_pcc_7417 Cylindrospermum_stagnale_pcc_7417_gca_000317535 Cylindrospermum_stagnale_pcc_7417_gca_000317535 Cylindrospermum_stagnale_pcc_7417_gca_000317535 Cynara_cardunculus Cynara_cardunculus Cynara_cardunculus -Cse_v1.0.110 Cynoglossus_semilaevis Cse_v1.0.110 Cse_v1.0.99 Cynoglossus_semilaevis Cse_v1.0.99 Cyphellophora_europaea_cbs_101466_gca_000365145 Cyphellophora_europaea_cbs_101466_gca_000365145 Cyphellophora_europaea_cbs_101466_gca_000365145 -C_variegatus-1.0.110 Cyprinodon_variegatus C_variegatus-1.0.110 C_variegatus-1.0.99 Cyprinodon_variegatus C_variegatus-1.0.99 -Cypcar_WagV4.0.110 Cyprinus_carpio_carpio Cypcar_WagV4.0.110 -German_Mirror_carp_1.0.110 Cyprinus_carpio_germanmirror German_Mirror_carp_1.0.110 German_Mirror_carp_1.0.99 Cyprinus_carpio_germanmirror German_Mirror_carp_1.0.99 -Hebao_red_carp_1.0.110 Cyprinus_carpio_hebaored Hebao_red_carp_1.0.110 Hebao_red_carp_1.0.99 Cyprinus_carpio_hebaored Hebao_red_carp_1.0.99 -Hunaghe_carp_2.0.110 Cyprinus_carpio_huanghe Hunaghe_carp_2.0.110 Hunaghe_carp_2.0.99 Cyprinus_carpio_huanghe Hunaghe_carp_2.0.99 Cystobacter_ferrugineus_gca_001887355 Cystobacter_ferrugineus_gca_001887355 Cystobacter_ferrugineus_gca_001887355 Cystobacter_fuscus_dsm_2262 Cystobacter_fuscus_dsm_2262 Cystobacter_fuscus_dsm_2262 @@ -16398,7 +16313,6 @@ Daejeonella_lutea_gca_900168015 Daejeonella_lutea_gca_900168015 Daejeonella_ Daejeonella_rubra_gca_900103545 Daejeonella_rubra_gca_900103545 Daejeonella_rubra_gca_900103545 Daldinia_sp_ec12_gca_002120325 Daldinia_sp_ec12_gca_002120325 Daldinia_sp_ec12_gca_002120325 Danaus_plexippus Danaus_plexippus Danaus_plexippus -GRCz11.110 Danio_rerio GRCz11.110 GRCz11.99 Danio_rerio GRCz11.99 Zv9.75 Danio_rerio Zv9.75 Dankookia_rubra_gca_004355005 Dankookia_rubra_gca_004355005 Dankookia_rubra_gca_004355005 @@ -16407,7 +16321,6 @@ Daphnia_magna_gca020631705v2 Daphnia_magna_gca020631705v2 Daphnia_magna_gca0 Daphnia_pulex Daphnia_pulex Daphnia_pulex Daphnia_pulex_gca021134715v1rs Daphnia_pulex_gca021134715v1rs Daphnia_pulex_gca021134715v1rs Daphnia_pulicaria_gca021234035v2rs Daphnia_pulicaria_gca021234035v2rs Daphnia_pulicaria_gca021234035v2rs -Dasnov3.0.110 Dasypus_novemcinctus Dasnov3.0.110 Dasnov3.0.75 Dasypus_novemcinctus Dasnov3.0.75 Dasnov3.0.99 Dasypus_novemcinctus Dasnov3.0.99 Daucus_carota Daucus_carota Daucus_carota @@ -16548,7 +16461,6 @@ Delftia_tsuruhatensis_gca_004353655 Delftia_tsuruhatensis_gca_004353655 Delf Delftia_tsuruhatensis_gca_900111975 Delftia_tsuruhatensis_gca_900111975 Delftia_tsuruhatensis_gca_900111975 Dellaglioa_algida_dsm_15638_gca_001434695 Dellaglioa_algida_dsm_15638_gca_001434695 Dellaglioa_algida_dsm_15638_gca_001434695 Dellaglioa_algida_gca_900206325 Dellaglioa_algida_gca_900206325 Dellaglioa_algida_gca_900206325 -ASM228892v3.110 Delphinapterus_leucas ASM228892v3.110 Delta_proteobacterium_ml8_d_gca_002029965 Delta_proteobacterium_ml8_d_gca_002029965 Delta_proteobacterium_ml8_d_gca_002029965 Delta_proteobacterium_mlms_1 Delta_proteobacterium_mlms_1 Delta_proteobacterium_mlms_1 Delta_proteobacterium_mlms_1_gca_000168275 Delta_proteobacterium_mlms_1_gca_000168275 Delta_proteobacterium_mlms_1_gca_000168275 @@ -16607,7 +16519,6 @@ Denitrobacterium_detoxificans Denitrobacterium_detoxificans Denitrobacterium Denitrovibrio_acetiphilus_dsm_12809 Denitrovibrio_acetiphilus_dsm_12809 Denitrovibrio_acetiphilus_dsm_12809 Denitrovibrio_acetiphilus_dsm_12809_gca_000025725 Denitrovibrio_acetiphilus_dsm_12809_gca_000025725 Denitrovibrio_acetiphilus_dsm_12809_gca_000025725 Denitrovibrio_sp__gca_002869145 Denitrovibrio_sp__gca_002869145 Denitrovibrio_sp__gca_002869145 -fDenClu1.1.110 Denticeps_clupeoides fDenClu1.1.110 fDenClu1.1.99 Denticeps_clupeoides fDenClu1.1.99 Dentipellis_fragilis_gca_004679275 Dentipellis_fragilis_gca_004679275 Dentipellis_fragilis_gca_004679275 Dentipellis_sp_kuc8613_gca_002286715 Dentipellis_sp_kuc8613_gca_002286715 Dentipellis_sp_kuc8613_gca_002286715 @@ -16992,7 +16903,6 @@ Diaphorobacter_sp_j5_51_gca_001023515 Diaphorobacter_sp_j5_51_gca_001023515 Diaphorobacter_sp_lr2014_1_gca_002916785 Diaphorobacter_sp_lr2014_1_gca_002916785 Diaphorobacter_sp_lr2014_1_gca_002916785 Diaporthe_ampelina_gca_001006365 Diaporthe_ampelina_gca_001006365 Diaporthe_ampelina_gca_001006365 Diaporthe_helianthi_gca_001702395 Diaporthe_helianthi_gca_001702395 Diaporthe_helianthi_gca_001702395 -dlabrax2021.110 Dicentrarchus_labrax dlabrax2021.110 Dichelobacter_nodosus Dichelobacter_nodosus Dichelobacter_nodosus Dichelobacter_nodosus_vcs1703a Dichelobacter_nodosus_vcs1703a Dichelobacter_nodosus_vcs1703a Dichelobacter_nodosus_vcs1703a_gca_000015345 Dichelobacter_nodosus_vcs1703a_gca_000015345 Dichelobacter_nodosus_vcs1703a_gca_000015345 @@ -17066,7 +16976,6 @@ Diplocarpon_rosae_gca_002317995 Diplocarpon_rosae_gca_002317995 Diplocarpon_ Diplodia_corticola_gca_001883845 Diplodia_corticola_gca_001883845 Diplodia_corticola_gca_001883845 Diplodia_seriata_gca_001006355 Diplodia_seriata_gca_001006355 Diplodia_seriata_gca_001006355 Diplodia_seriata_gca_001975905 Diplodia_seriata_gca_001975905 Diplodia_seriata_gca_001975905 -Dord_2.0.110 Dipodomys_ordii Dord_2.0.110 Dord_2.0.99 Dipodomys_ordii Dord_2.0.99 dipOrd1.75 Dipodomys_ordii dipOrd1.75 Dissulfuribacter_thermophilus Dissulfuribacter_thermophilus Dissulfuribacter_thermophilus @@ -17168,14 +17077,12 @@ Drancourtella_sp_an210_gca_002159995 Drancourtella_sp_an210_gca_002159995 Dr Drancourtella_sp_an57_gca_002161525 Drancourtella_sp_an57_gca_002161525 Drancourtella_sp_an57_gca_002161525 Drechmeria_coniospora_gca_001625195 Drechmeria_coniospora_gca_001625195 Drechmeria_coniospora_gca_001625195 Drechslerella_stenobrocha_248_gca_000525045 Drechslerella_stenobrocha_248_gca_000525045 Drechslerella_stenobrocha_248_gca_000525045 -droNov1.110 Dromaius_novaehollandiae droNov1.110 droNov1.99 Dromaius_novaehollandiae droNov1.99 Drosophila_ananassae Drosophila_ananassae Drosophila_ananassae Drosophila_erecta Drosophila_erecta Drosophila_erecta Drosophila_grimshawi Drosophila_grimshawi Drosophila_grimshawi BDGP5.75 Drosophila_melanogaster BDGP5.75 BDGP6.28.99 Drosophila_melanogaster BDGP6.28.99 -BDGP6.46.110 Drosophila_melanogaster BDGP6.46.110 Drosophila_melanogaster Drosophila_melanogaster Drosophila_melanogaster Drosophila_mojavensis Drosophila_mojavensis Drosophila_mojavensis Drosophila_persimilis Drosophila_persimilis Drosophila_persimilis @@ -17261,14 +17168,12 @@ Dysgonomonas_mossii_dsm_22836_gca_000213575 Dysgonomonas_mossii_dsm_22836_gca_ Dysgonomonas_sp_37_18_gca_001899125 Dysgonomonas_sp_37_18_gca_001899125 Dysgonomonas_sp_37_18_gca_001899125 Dysosmobacter_welbionis_gca_005121165 Dysosmobacter_welbionis_gca_005121165 Dysosmobacter_welbionis_gca_005121165 ebola_zaire Ebola ebola_zaire -fEcheNa1.1.110 Echeneis_naucrates fEcheNa1.1.110 fEcheNa1.1.99 Echeneis_naucrates fEcheNa1.1.99 Echinicola_strongylocentroti_gca_003260975 Echinicola_strongylocentroti_gca_003260975 Echinicola_strongylocentroti_gca_003260975 Echinicola_vietnamensis_dsm_17526 Echinicola_vietnamensis_dsm_17526 Echinicola_vietnamensis_dsm_17526 Echinicola_vietnamensis_dsm_17526_gca_000325705 Echinicola_vietnamensis_dsm_17526_gca_000325705 Echinicola_vietnamensis_dsm_17526_gca_000325705 Echinochloa_crusgalli Echinochloa_crusgalli Echinochloa_crusgalli Echinococcus_granulosus_gca000524195v1rs Echinococcus_granulosus_gca000524195v1rs Echinococcus_granulosus_gca000524195v1rs -TENREC.110 Echinops_telfairi TENREC.110 TENREC.75 Echinops_telfairi TENREC.75 TENREC.99 Echinops_telfairi TENREC.99 Ectocarpus_siliculosus_gca_000310025 Ectocarpus_siliculosus_gca_000310025 Ectocarpus_siliculosus_gca_000310025 @@ -17387,7 +17292,6 @@ Eisenbergiella_tayi_gca_001717135 Eisenbergiella_tayi_gca_001717135 Eisenber Eisenbergiella_tayi_gca_001722555 Eisenbergiella_tayi_gca_001722555 Eisenbergiella_tayi_gca_001722555 Ekhidna_lutea_gca_900188325 Ekhidna_lutea_gca_900188325 Ekhidna_lutea_gca_900188325 Elaphomyces_granulatus_gca_002240705 Elaphomyces_granulatus_gca_002240705 Elaphomyces_granulatus_gca_002240705 -Ee_SOAP_WITH_SSPACE.110 Electrophorus_electricus Ee_SOAP_WITH_SSPACE.110 Ee_SOAP_WITH_SSPACE.99 Electrophorus_electricus Ee_SOAP_WITH_SSPACE.99 Elizabethkingia_anophelis Elizabethkingia_anophelis Elizabethkingia_anophelis Elizabethkingia_anophelis_502 Elizabethkingia_anophelis_502 Elizabethkingia_anophelis_502 @@ -19412,16 +19316,13 @@ Epilithonimonas_xixisoli_gca_004365655 Epilithonimonas_xixisoli_gca_004365655 Epilithonimonas_zeae_gca_900141765 Epilithonimonas_zeae_gca_900141765 Epilithonimonas_zeae_gca_900141765 Epsilonproteobacteria_bacterium_ex_lamellibrachia_satsuma__gca_003934925 Epsilonproteobacteria_bacterium_ex_lamellibrachia_satsuma__gca_003934925 Epsilonproteobacteria_bacterium_ex_lamellibrachia_satsuma__gca_003934925 Epsilonproteobacteria_bacterium_gca_003643835 Epsilonproteobacteria_bacterium_gca_003643835 Epsilonproteobacteria_bacterium_gca_003643835 -Eburgeri_3.2.110 Eptatretus_burgeri Eburgeri_3.2.110 Eburgeri_3.2.99 Eptatretus_burgeri Eburgeri_3.2.99 Epulopiscium_sp_as2m_bin001_gca_002007295 Epulopiscium_sp_as2m_bin001_gca_002007295 Epulopiscium_sp_as2m_bin001_gca_002007295 Epulopiscium_sp_nuni2h_mbin001_gca_001994995 Epulopiscium_sp_nuni2h_mbin001_gca_001994995 Epulopiscium_sp_nuni2h_mbin001_gca_001994995 Epulopiscium_sp_scg_b11wga_epuloa1_gca_001983455 Epulopiscium_sp_scg_b11wga_epuloa1_gca_001983455 Epulopiscium_sp_scg_b11wga_epuloa1_gca_001983455 Epulopiscium_sp_scg_c07wga_epuloa2_gca_001983555 Epulopiscium_sp_scg_c07wga_epuloa2_gca_001983555 Epulopiscium_sp_scg_c07wga_epuloa2_gca_001983555 -ASM1607732v2.110 Equus_asinus ASM1607732v2.110 ASM303372v1.99 Equus_asinus_asinus ASM303372v1.99 EquCab2.75 Equus_caballus EquCab2.75 -EquCab3.0.110 Equus_caballus EquCab3.0.110 EquCab3.0.99 Equus_caballus EquCab3.0.99 Eragrostis_curvula Eragrostis_curvula Eragrostis_curvula Eragrostis_tef Eragrostis_tef Eragrostis_tef @@ -19431,10 +19332,8 @@ Eremococcus_coleocola_acs_139_v_col8_gca_000183205 Eremococcus_coleocola_acs_1 Eremomyces_bilateralis_cbs_781_70_gca_010015585 Eremomyces_bilateralis_cbs_781_70_gca_010015585 Eremomyces_bilateralis_cbs_781_70_gca_010015585 Eremothecium_cymbalariae_dbvpg_7215_gca_000235365 Eremothecium_cymbalariae_dbvpg_7215_gca_000235365 Eremothecium_cymbalariae_dbvpg_7215_gca_000235365 Eremothecium_gossypii_fdag1_gca_000968835 Eremothecium_gossypii_fdag1_gca_000968835 Eremothecium_gossypii_fdag1_gca_000968835 -HEDGEHOG.110 Erinaceus_europaeus HEDGEHOG.110 HEDGEHOG.75 Erinaceus_europaeus HEDGEHOG.75 HEDGEHOG.99 Erinaceus_europaeus HEDGEHOG.99 -fErpCal1.1.110 Erpetoichthys_calabaricus fErpCal1.1.110 fErpCal1.1.99 Erpetoichthys_calabaricus fErpCal1.1.99 Erwinia_amylovora_01sfr_bo Erwinia_amylovora_01sfr_bo Erwinia_amylovora_01sfr_bo Erwinia_amylovora_acw56400 Erwinia_amylovora_acw56400 Erwinia_amylovora_acw56400 @@ -19576,7 +19475,6 @@ Erythrobacter_sp_yt30_gca_001542875 Erythrobacter_sp_yt30_gca_001542875 Eryt Erythrobacteraceae_bacterium_cfh_75059_gca_004331795 Erythrobacteraceae_bacterium_cfh_75059_gca_004331795 Erythrobacteraceae_bacterium_cfh_75059_gca_004331795 Erythrobacteraceae_bacterium_hl_111 Erythrobacteraceae_bacterium_hl_111 Erythrobacteraceae_bacterium_hl_111 Erythrobacteraceae_bacterium_hl_111_gca_001314765 Erythrobacteraceae_bacterium_hl_111_gca_001314765 Erythrobacteraceae_bacterium_hl_111_gca_001314765 -GouldianFinch.110 Erythrura_gouldiae GouldianFinch.110 GouldianFinch.99 Erythrura_gouldiae GouldianFinch.99 Escherichia_albertii Escherichia_albertii Escherichia_albertii Escherichia_albertii_b156_gca_002109845 Escherichia_albertii_b156_gca_002109845 Escherichia_albertii_b156_gca_002109845 @@ -23521,7 +23419,6 @@ Escherichia_sp_mr_gca_005280595 Escherichia_sp_mr_gca_005280595 Escherichia_ Escherichia_vulneris_nbrc_102420 Escherichia_vulneris_nbrc_102420 Escherichia_vulneris_nbrc_102420 Escovopsis_weberi_gca_001278495 Escovopsis_weberi_gca_001278495 Escovopsis_weberi_gca_001278495 Eluc_V3.99 Esox_lucius Eluc_V3.99 -Eluc_v4.110 Esox_lucius Eluc_v4.110 Estrella_lausannensis_gca_900000175 Estrella_lausannensis_gca_900000175 Estrella_lausannensis_gca_900000175 Ethanoligenens_harbinense_gca_003612855 Ethanoligenens_harbinense_gca_003612855 Ethanoligenens_harbinense_gca_003612855 Ethanoligenens_harbinense_yuan_3 Ethanoligenens_harbinense_yuan_3 Ethanoligenens_harbinense_yuan_3 @@ -23788,7 +23685,6 @@ Faecalitalea_cylindroides_atcc_27803 Faecalitalea_cylindroides_atcc_27803 Fa Faecalitalea_cylindroides_atcc_27803_gca_000469305 Faecalitalea_cylindroides_atcc_27803_gca_000469305 Faecalitalea_cylindroides_atcc_27803_gca_000469305 Faecalitalea_cylindroides_gca_002160375 Faecalitalea_cylindroides_gca_002160375 Faecalitalea_cylindroides_gca_002160375 Faecalitalea_cylindroides_t2_87 Faecalitalea_cylindroides_t2_87 Faecalitalea_cylindroides_t2_87 -FalTin1.0.110 Falco_tinnunculus FalTin1.0.110 Falseniella_ignava_ccug_37419_gca_000301055 Falseniella_ignava_ccug_37419_gca_000301055 Falseniella_ignava_ccug_37419_gca_000301055 Falseniella_ignava_gca_002847645 Falseniella_ignava_gca_002847645 Falseniella_ignava_gca_002847645 Falsibacillus_albus_gca_003668575 Falsibacillus_albus_gca_003668575 Falsibacillus_albus_gca_003668575 @@ -23802,7 +23698,6 @@ Falsochrobactrum_ovis_gca_003259955 Falsochrobactrum_ovis_gca_003259955 Fals Falsochrobactrum_shanghaiense_gca_003149535 Falsochrobactrum_shanghaiense_gca_003149535 Falsochrobactrum_shanghaiense_gca_003149535 Felis_catus Felis_catus Felis_catus Felis_catus_6.2.75 Felis_catus Felis_catus_6.2.75 -Felis_catus_9.0.110 Felis_catus Felis_catus_9.0.110 Felis_catus_9.0.99 Felis_catus Felis_catus_9.0.99 Fermentimonas_caenicola Fermentimonas_caenicola Fermentimonas_caenicola Fermentimonas_caenicola_gca_000953535 Fermentimonas_caenicola_gca_000953535 Fermentimonas_caenicola_gca_000953535 @@ -23889,7 +23784,6 @@ Fibrobacter_succinogenes_subsp_succinogenes_s85 Fibrobacter_succinogenes_subsp Fibrobacter_succinogenes_subsp_succinogenes_s85_gca_000146505 Fibrobacter_succinogenes_subsp_succinogenes_s85_gca_000146505 Fibrobacter_succinogenes_subsp_succinogenes_s85_gca_000146505 Fibroporia_radiculosa_gca_000313525 Fibroporia_radiculosa_gca_000313525 Fibroporia_radiculosa_gca_000313525 Fibularhizoctonia_sp_cbs_109695_gca_001630335 Fibularhizoctonia_sp_cbs_109695_gca_001630335 Fibularhizoctonia_sp_cbs_109695_gca_001630335 -FicAlb1.5.110 Ficedula_albicollis FicAlb1.5.110 FicAlb_1.4.75 Ficedula_albicollis FicAlb_1.4.75 FicAlb_1.4.99 Ficedula_albicollis FicAlb_1.4.99 Fictibacillus_aquaticus_gca_002245695 Fictibacillus_aquaticus_gca_002245695 Fictibacillus_aquaticus_gca_002245695 @@ -24694,7 +24588,6 @@ Fructobacillus_sp_efb_n1 Fructobacillus_sp_efb_n1 Fructobacillus_sp_efb_n1 Fructobacillus_sp_efb_n1_gca_001038455 Fructobacillus_sp_efb_n1_gca_001038455 Fructobacillus_sp_efb_n1_gca_001038455 Fructobacillus_tropaeoli_gca_001047135 Fructobacillus_tropaeoli_gca_001047135 Fructobacillus_tropaeoli_gca_001047135 Fuerstiella_marisgermanici_gca_001983935 Fuerstiella_marisgermanici_gca_001983935 Fuerstiella_marisgermanici_gca_001983935 -DMR_v1.0.110 Fukomys_damarensis DMR_v1.0.110 DMR_v1.0.99 Fukomys_damarensis DMR_v1.0.99 Fulvimarina_endophytica_gca_003403015 Fulvimarina_endophytica_gca_003403015 Fulvimarina_endophytica_gca_003403015 Fulvimarina_manganoxydans_gca_900176465 Fulvimarina_manganoxydans_gca_900176465 Fulvimarina_manganoxydans_gca_900176465 @@ -24704,7 +24597,6 @@ Fulvimarina_sp__gca_002700095 Fulvimarina_sp__gca_002700095 Fulvimarina_sp__ Fulvimonas_soli_gca_003148905 Fulvimonas_soli_gca_003148905 Fulvimonas_soli_gca_003148905 Fulvivirga_imtechensis_ak7 Fulvivirga_imtechensis_ak7 Fulvivirga_imtechensis_ak7 Fulvivirga_imtechensis_ak7_gca_000331535 Fulvivirga_imtechensis_ak7_gca_000331535 Fulvivirga_imtechensis_ak7_gca_000331535 -Fundulus_heteroclitus-3.0.2.110 Fundulus_heteroclitus Fundulus_heteroclitus-3.0.2.110 Fundulus_heteroclitus-3.0.2.99 Fundulus_heteroclitus Fundulus_heteroclitus-3.0.2.99 Furfurilactobacillus_rossiae_dsm_15814_gca_001435135 Furfurilactobacillus_rossiae_dsm_15814_gca_001435135 Furfurilactobacillus_rossiae_dsm_15814_gca_001435135 Furfurilactobacillus_siliginis_gca_001437435 Furfurilactobacillus_siliginis_gca_001437435 Furfurilactobacillus_siliginis_gca_001437435 @@ -24952,7 +24844,6 @@ test_GRCh38.mane.1.0.refseq.chr21 GRCh38 test_GRCh38.mane.1.0.refseq.chr21 GRCh38.86 GRCh38.86 GRCh38.86 gadMor1.75 Gadus_morhua gadMor1.75 gadMor1.99 Gadus_morhua gadMor1.99 -gadMor3.0.110 Gadus_morhua gadMor3.0.110 Gaetbulibacter_sp_4g1_gca_002741945 Gaetbulibacter_sp_4g1_gca_002741945 Gaetbulibacter_sp_4g1_gca_002741945 Gaetbulibacter_sp_5u11_gca_002742325 Gaetbulibacter_sp_5u11_gca_002742325 Gaetbulibacter_sp_5u11_gca_002742325 Gaeumannomyces_graminis Gaeumannomyces_graminis Gaeumannomyces_graminis @@ -25016,10 +24907,6 @@ Gallionellales_bacterium_rifcsplowo2_02_full_57_47_gca_001801175 Gallionellale Gallionellales_bacterium_rifcsplowo2_12_full_59_22_gca_001801255 Gallionellales_bacterium_rifcsplowo2_12_full_59_22_gca_001801255 Gallionellales_bacterium_rifcsplowo2_12_full_59_22_gca_001801255 GRCg6a.99 Gallus_gallus GRCg6a.99 Galgal4.75 Gallus_gallus Galgal4.75 -bGalGal1.mat.broiler.GRCg7b.110 Gallus_gallus bGalGal1.mat.broiler.GRCg7b.110 -GRCg6a.110 Gallus_gallus_gca000002315v5 GRCg6a.110 -bGalGal1.pat.whiteleghornlayer.GRCg7w.110 Gallus_gallus_gca016700215v2 bGalGal1.pat.whiteleghornlayer.GRCg7w.110 -ASM309773v1.110 Gambusia_affinis ASM309773v1.110 ASM309773v1.99 Gambusia_affinis ASM309773v1.99 Gamma_proteobacterium_bdw918 Gamma_proteobacterium_bdw918 Gamma_proteobacterium_bdw918 Gamma_proteobacterium_bdw918_gca_000259575 Gamma_proteobacterium_bdw918_gca_000259575 Gamma_proteobacterium_bdw918_gca_000259575 @@ -25202,7 +25089,6 @@ Gardnerella_vaginalis_jcp8481a Gardnerella_vaginalis_jcp8481a Gardnerella_va Gardnerella_vaginalis_jcp8481b Gardnerella_vaginalis_jcp8481b Gardnerella_vaginalis_jcp8481b Gardnerella_vaginalis_jcp8522 Gardnerella_vaginalis_jcp8522 Gardnerella_vaginalis_jcp8522 Gardnerella_vaginalis_jcp8522_gca_000414425 Gardnerella_vaginalis_jcp8522_gca_000414425 Gardnerella_vaginalis_jcp8522_gca_000414425 -BROADS1.110 Gasterosteus_aculeatus BROADS1.110 BROADS1.75 Gasterosteus_aculeatus BROADS1.75 BROADS1.99 Gasterosteus_aculeatus BROADS1.99 Geitlerinema_sp_pcc_7407 Geitlerinema_sp_pcc_7407 Geitlerinema_sp_pcc_7407 @@ -25447,7 +25333,6 @@ Georgenia_satyanarayanai_gca_900116375 Georgenia_satyanarayanai_gca_900116375 Georgenia_soli_gca_002563695 Georgenia_soli_gca_002563695 Georgenia_soli_gca_002563695 Georgenia_sp_subg003 Georgenia_sp_subg003 Georgenia_sp_subg003 Georgenia_yuyongxinii_gca_006352065 Georgenia_yuyongxinii_gca_006352065 Georgenia_yuyongxinii_gca_006352065 -GeoFor_1.0.110 Geospiza_fortis GeoFor_1.0.110 Geosporobacter_ferrireducens Geosporobacter_ferrireducens Geosporobacter_ferrireducens Geosporobacter_ferrireducens_gca_001750685 Geosporobacter_ferrireducens_gca_001750685 Geosporobacter_ferrireducens_gca_001750685 Geosporobacter_subterraneus_dsm_17957_gca_900142145 Geosporobacter_subterraneus_dsm_17957_gca_900142145 Geosporobacter_subterraneus_dsm_17957_gca_900142145 @@ -25642,9 +25527,7 @@ Golovinomyces_cichoracearum_gca_003611215 Golovinomyces_cichoracearum_gca_0036 Golovinomyces_cichoracearum_gca_003611235 Golovinomyces_cichoracearum_gca_003611235 Golovinomyces_cichoracearum_gca_003611235 Golovinomyces_magnicellulatus_gca_006912115 Golovinomyces_magnicellulatus_gca_006912115 Golovinomyces_magnicellulatus_gca_006912115 Gonapodya_prolifera_jel478_gca_001574975 Gonapodya_prolifera_jel478_gca_001574975 Gonapodya_prolifera_jel478_gca_001574975 -ASM289641v1.110 Gopherus_agassizii ASM289641v1.110 ASM289641v1.99 Gopherus_agassizii ASM289641v1.99 -rGopEvg1_v1.p.110 Gopherus_evgoodei rGopEvg1_v1.p.110 Gordonia_aichiensis_nbrc_108223 Gordonia_aichiensis_nbrc_108223 Gordonia_aichiensis_nbrc_108223 Gordonia_aichiensis_nbrc_108223_gca_000332975 Gordonia_aichiensis_nbrc_108223_gca_000332975 Gordonia_aichiensis_nbrc_108223_gca_000332975 Gordonia_alkanivorans_cgmcc_6845 Gordonia_alkanivorans_cgmcc_6845 Gordonia_alkanivorans_cgmcc_6845 @@ -25726,13 +25609,11 @@ Gordonia_terrae_nbrc_100016_gca_000248035 Gordonia_terrae_nbrc_100016_gca_0002 Gordonia_westfalica_gca_900105725 Gordonia_westfalica_gca_900105725 Gordonia_westfalica_gca_900105725 Gordonibacter_pamelaeae_7_10_1_b Gordonibacter_pamelaeae_7_10_1_b Gordonibacter_pamelaeae_7_10_1_b gorGor3.1.75 Gorilla_gorilla gorGor3.1.75 -gorGor4.110 Gorilla_gorilla gorGor4.110 gorGor4.99 Gorilla_gorilla gorGor4.99 Gossypium_raimondii Gossypium_raimondii Gossypium_raimondii Gottfriedia_luciferensis_gca_001712755 Gottfriedia_luciferensis_gca_001712755 Gottfriedia_luciferensis_gca_001712755 Gottschalkia_acidurici_9a_gca_000299355 Gottschalkia_acidurici_9a_gca_000299355 Gottschalkia_acidurici_9a_gca_000299355 Gottschalkia_purinilytica_gca_001190785 Gottschalkia_purinilytica_gca_001190785 Gottschalkia_purinilytica_gca_001190785 -fGouWil2.1.110 Gouania_willdenowi fGouWil2.1.110 fGouWil2.1.99 Gouania_willdenowi fGouWil2.1.99 Gracilibacillus_boraciitolerans_jcm_21714 Gracilibacillus_boraciitolerans_jcm_21714 Gracilibacillus_boraciitolerans_jcm_21714 Gracilibacillus_boraciitolerans_jcm_21714_gca_000521485 Gracilibacillus_boraciitolerans_jcm_21714_gca_000521485 Gracilibacillus_boraciitolerans_jcm_21714_gca_000521485 @@ -26619,7 +26500,6 @@ Hanstruepera_neustonica_gca_002895005 Hanstruepera_neustonica_gca_002895005 Hapalosiphon_sp_mrb220 Hapalosiphon_sp_mrb220 Hapalosiphon_sp_mrb220 Hapalosiphon_sp_mrb220_gca_001275395 Hapalosiphon_sp_mrb220_gca_001275395 Hapalosiphon_sp_mrb220_gca_001275395 Hapalosiphonaceae_cyanobacterium_jju2_gca_003261315 Hapalosiphonaceae_cyanobacterium_jju2_gca_003261315 Hapalosiphonaceae_cyanobacterium_jju2_gca_003261315 -AstBur1.0.110 Haplochromis_burtoni AstBur1.0.110 AstBur1.0.99 Haplochromis_burtoni AstBur1.0.99 Harpegnathos_saltator_gca003227715v2rs Harpegnathos_saltator_gca003227715v2rs Harpegnathos_saltator_gca003227715v2rs Harryflintia_acetispora_gca_003433795 Harryflintia_acetispora_gca_003433795 Harryflintia_acetispora_gca_003433795 @@ -27692,15 +27572,12 @@ Hespellia_stercorisuis_dsm_15480_gca_900142165 Hespellia_stercorisuis_dsm_1548 Hesseltinella_vesiculosa_gca_002104935 Hesseltinella_vesiculosa_gca_002104935 Hesseltinella_vesiculosa_gca_002104935 Heterobasidion_irregulare_tc_32_1_gca_000320585 Heterobasidion_irregulare_tc_32_1_gca_000320585 Heterobasidion_irregulare_tc_32_1_gca_000320585 HetGla_female_1.0.99 Heterocephalus_glaber_female HetGla_female_1.0.99 -Naked_mole-rat_maternal.110 Heterocephalus_glaber_female Naked_mole-rat_maternal.110 HetGla_1.0.99 Heterocephalus_glaber_male HetGla_1.0.99 -Naked_mole-rat_paternal.110 Heterocephalus_glaber_male Naked_mole-rat_paternal.110 Heyndrickxia_sporothermodurans_gca_001587375 Heyndrickxia_sporothermodurans_gca_001587375 Heyndrickxia_sporothermodurans_gca_001587375 Heyndrickxia_sporothermodurans_gca_003055045 Heyndrickxia_sporothermodurans_gca_003055045 Heyndrickxia_sporothermodurans_gca_003055045 Heyndrickxia_sporothermodurans_gca_003055065 Heyndrickxia_sporothermodurans_gca_003055065 Heyndrickxia_sporothermodurans_gca_003055065 Hippea_maritima_dsm_10411 Hippea_maritima_dsm_10411 Hippea_maritima_dsm_10411 Hippea_maritima_dsm_10411_gca_000194135 Hippea_maritima_dsm_10411_gca_000194135 Hippea_maritima_dsm_10411_gca_000194135 -H_comes_QL1_v1.110 Hippocampus_comes H_comes_QL1_v1.110 H_comes_QL1_v1.99 Hippocampus_comes H_comes_QL1_v1.99 Hirschia_baltica_atcc_49814 Hirschia_baltica_atcc_49814 Hirschia_baltica_atcc_49814 Hirschia_baltica_atcc_49814_gca_000023785 Hirschia_baltica_atcc_49814_gca_000023785 Hirschia_baltica_atcc_49814_gca_000023785 @@ -27752,7 +27629,6 @@ Holzapfelia_floricola_dsm_23037_jcm_16512_gca_001436605 Holzapfelia_floricola_ Homalodisca_vitripennis_gca021130785v2rs Homalodisca_vitripennis_gca021130785v2rs Homalodisca_vitripennis_gca021130785v2rs Homarus_americanus_gca018991925v1 Homarus_americanus_gca018991925v1 Homarus_americanus_gca018991925v1 GRCh37.75 Homo_sapiens GRCh37.75 -GRCh38.110 Homo_sapiens GRCh38.110 GRCh38.99 Homo_sapiens GRCh38.99 hg19kg Homo_sapiens hg19kg hg38kg Homo_sapiens hg38kg @@ -27777,7 +27653,6 @@ Hortaea_werneckii_gca_003704675 Hortaea_werneckii_gca_003704675 Hortaea_wern Hortaea_werneckii_gca_003704685 Hortaea_werneckii_gca_003704685 Hortaea_werneckii_gca_003704685 Hoyosella_subflava_dqs3_9a1 Hoyosella_subflava_dqs3_9a1 Hoyosella_subflava_dqs3_9a1 Hoyosella_subflava_dqs3_9a1_gca_000214175 Hoyosella_subflava_dqs3_9a1_gca_000214175 Hoyosella_subflava_dqs3_9a1_gca_000214175 -ASM331708v1.110 Hucho_hucho ASM331708v1.110 ASM331708v1.99 Hucho_hucho ASM331708v1.99 GRCh37.87 Human GRCh37.87 GRCh37.p13 Human GRCh37.p13 @@ -28024,9 +27899,7 @@ Hyunsoonleella_jejuensis_gca_900111025 Hyunsoonleella_jejuensis_gca_900111025 Hyunsoonleella_pacifica_gca_004310335 Hyunsoonleella_pacifica_gca_004310335 Hyunsoonleella_pacifica_gca_004310335 Ichthyenterobacterium_magnum_gca_003610635 Ichthyenterobacterium_magnum_gca_003610635 Ichthyenterobacterium_magnum_gca_003610635 Ichthyophthirius_multifiliis_gca_000220395 Ichthyophthirius_multifiliis_gca_000220395 Ichthyophthirius_multifiliis_gca_000220395 -IpCoco_1.2.110 Ictalurus_punctatus IpCoco_1.2.110 IpCoco_1.2.99 Ictalurus_punctatus IpCoco_1.2.99 -SpeTri2.0.110 Ictidomys_tridecemlineatus SpeTri2.0.110 SpeTri2.0.99 Ictidomys_tridecemlineatus SpeTri2.0.99 spetri2.75 Ictidomys_tridecemlineatus spetri2.75 Ideonella_sakaiensis Ideonella_sakaiensis Ideonella_sakaiensis @@ -28166,7 +28039,6 @@ Ixodes_scapularis_ise6 Ixodes_scapularis_ise6 Ixodes_scapularis_ise6 Izhakiella_australiensis_gca_002006995 Izhakiella_australiensis_gca_002006995 Izhakiella_australiensis_gca_002006995 Izhakiella_capsodis_gca_900115045 Izhakiella_capsodis_gca_900115045 Izhakiella_capsodis_gca_900115045 Jaapia_argillacea_mucl_33604_gca_000697665 Jaapia_argillacea_mucl_33604_gca_000697665 Jaapia_argillacea_mucl_33604_gca_000697665 -JacJac1.0.110 Jaculus_jaculus JacJac1.0.110 JacJac1.0.99 Jaculus_jaculus JacJac1.0.99 Jaminaea_rosea_gca_003144245 Jaminaea_rosea_gca_003144245 Jaminaea_rosea_gca_003144245 Janibacter_hoylei_pvas_1 Janibacter_hoylei_pvas_1 Janibacter_hoylei_pvas_1 @@ -28302,7 +28174,6 @@ Jonquetella_sp_bv3c21 Jonquetella_sp_bv3c21 Jonquetella_sp_bv3c21 Joostella_marina_dsm_19592 Joostella_marina_dsm_19592 Joostella_marina_dsm_19592 Joostella_marina_dsm_19592_gca_000260115 Joostella_marina_dsm_19592_gca_000260115 Joostella_marina_dsm_19592_gca_000260115 Juglans_regia Juglans_regia Juglans_regia -ASM382977v1.110 Junco_hyemalis ASM382977v1.110 ASM382977v1.99 Junco_hyemalis ASM382977v1.99 Kaistella_antarctica_gca_900637895 Kaistella_antarctica_gca_900637895 Kaistella_antarctica_gca_900637895 Kaistella_carnis_gca_003860585 Kaistella_carnis_gca_003860585 Kaistella_carnis_gca_003860585 @@ -30765,7 +30636,6 @@ Kribbella_speibonae_gca_004331375 Kribbella_speibonae_gca_004331375 Kribbell Kribbella_turkmenica_gca_004348725 Kribbella_turkmenica_gca_004348725 Kribbella_turkmenica_gca_004348725 Kriegella_aquimaris_gca_900103215 Kriegella_aquimaris_gca_900103215 Kriegella_aquimaris_gca_900103215 Kroppenstedtia_eburnea_gca_900156615 Kroppenstedtia_eburnea_gca_900156615 Kroppenstedtia_eburnea_gca_900156615 -ASM164957v1.110 Kryptolebias_marmoratus ASM164957v1.110 ASM164957v1.99 Kryptolebias_marmoratus ASM164957v1.99 Ktedonobacter_racemifer_dsm_44963 Ktedonobacter_racemifer_dsm_44963 Ktedonobacter_racemifer_dsm_44963 Ktedonobacter_racemifer_dsm_44963_gca_000178855 Ktedonobacter_racemifer_dsm_44963_gca_000178855 Ktedonobacter_racemifer_dsm_44963_gca_000178855 @@ -30834,7 +30704,6 @@ Labrenzia_sp_ob1 Labrenzia_sp_ob1 Labrenzia_sp_ob1 Labrenzia_sp_ob1_gca_001624695 Labrenzia_sp_ob1_gca_001624695 Labrenzia_sp_ob1_gca_001624695 Labrenzia_sp_pt13c1_gca_004365135 Labrenzia_sp_pt13c1_gca_004365135 Labrenzia_sp_pt13c1_gca_004365135 Labrenzia_sp_vg12_gca_002237595 Labrenzia_sp_vg12_gca_002237595 Labrenzia_sp_vg12_gca_002237595 -BallGen_V1.110 Labrus_bergylta BallGen_V1.110 BallGen_V1.99 Labrus_bergylta BallGen_V1.99 Labrys_okinawensis_gca_002982075 Labrys_okinawensis_gca_002982075 Labrys_okinawensis_gca_002982075 Laccaria_amethystina_laam_08_1_gca_000827195 Laccaria_amethystina_laam_08_1_gca_000827195 Laccaria_amethystina_laam_08_1_gca_000827195 @@ -32051,7 +31920,6 @@ Lapidilactobacillus_dextrinicus_dsm_20335_gca_001436095 Lapidilactobacillus_de Laribacter_hongkongensis_gca_002215055 Laribacter_hongkongensis_gca_002215055 Laribacter_hongkongensis_gca_002215055 Laribacter_hongkongensis_hlhk9 Laribacter_hongkongensis_hlhk9 Laribacter_hongkongensis_hlhk9 Laribacter_hongkongensis_hlhk9_gca_000021025 Laribacter_hongkongensis_hlhk9_gca_000021025 Laribacter_hongkongensis_hlhk9_gca_000021025 -L_crocea_2.0.110 Larimichthys_crocea L_crocea_2.0.110 L_crocea_2.0.99 Larimichthys_crocea L_crocea_2.0.99 Larkinella_arboricola_gca_003259745 Larkinella_arboricola_gca_003259745 Larkinella_arboricola_gca_003259745 Larkinella_knui_gca_003858645 Larkinella_knui_gca_003858645 Larkinella_knui_gca_003858645 @@ -32061,10 +31929,8 @@ Larkinella_sp_bk230_gca_004366505 Larkinella_sp_bk230_gca_004366505 Larkinel Lasallia_pustulata_gca_008636195 Lasallia_pustulata_gca_008636195 Lasallia_pustulata_gca_008636195 Lasallia_pustulata_gca_900169345 Lasallia_pustulata_gca_900169345 Lasallia_pustulata_gca_900169345 Lasiodiplodia_theobromae_gca_008931885 Lasiodiplodia_theobromae_gca_008931885 Lasiodiplodia_theobromae_gca_008931885 -ASB_HGAPassembly_v1.110 Lates_calcarifer ASB_HGAPassembly_v1.110 ASB_HGAPassembly_v1.99 Lates_calcarifer ASB_HGAPassembly_v1.99 Latescibacteria_bacterium_dg_63_gca_001302905 Latescibacteria_bacterium_dg_63_gca_001302905 Latescibacteria_bacterium_dg_63_gca_001302905 -latLat_1.0.110 Laticauda_laticaudata latLat_1.0.110 Latilactobacillus_curvatus_gca_000805355 Latilactobacillus_curvatus_gca_000805355 Latilactobacillus_curvatus_gca_000805355 Latilactobacillus_curvatus_gca_001698165 Latilactobacillus_curvatus_gca_001698165 Latilactobacillus_curvatus_gca_001698165 Latilactobacillus_curvatus_gca_003410375 Latilactobacillus_curvatus_gca_003410375 Latilactobacillus_curvatus_gca_003410375 @@ -32083,7 +31949,6 @@ Latilactobacillus_sakei_gca_900234355 Latilactobacillus_sakei_gca_900234355 Latilactobacillus_sakei_gca_900408275 Latilactobacillus_sakei_gca_900408275 Latilactobacillus_sakei_gca_900408275 Latilactobacillus_sakei_subsp_sakei_23k_gca_000026065 Latilactobacillus_sakei_subsp_sakei_23k_gca_000026065 Latilactobacillus_sakei_subsp_sakei_23k_gca_000026065 Latilactobacillus_sakei_subsp_sakei_gca_004354475 Latilactobacillus_sakei_subsp_sakei_gca_004354475 Latilactobacillus_sakei_subsp_sakei_gca_004354475 -LatCha1.110 Latimeria_chalumnae LatCha1.110 LatCha1.75 Latimeria_chalumnae LatCha1.75 LatCha1.99 Latimeria_chalumnae LatCha1.99 Lautropia_dentalis_gca_003892345 Lautropia_dentalis_gca_003892345 Lautropia_dentalis_gca_003892345 @@ -32555,13 +32420,10 @@ Lentzea_xinjiangensis_gca_900110955 Lentzea_xinjiangensis_gca_900110955 Lent Lepeophtheirus_salmonis Lepeophtheirus_salmonis Lepeophtheirus_salmonis Lepeophtheirus_salmonis_gca016086655v3rs Lepeophtheirus_salmonis_gca016086655v3rs Lepeophtheirus_salmonis_gca016086655v3rs Lepidopterella_palustris_cbs_459_81_gca_001692735 Lepidopterella_palustris_cbs_459_81_gca_001692735 Lepidopterella_palustris_cbs_459_81_gca_001692735 -Lepidothrix_coronata-1.0.110 Lepidothrix_coronata Lepidothrix_coronata-1.0.110 Lepidothrix_coronata-1.0.99 Lepidothrix_coronata Lepidothrix_coronata-1.0.99 -LepOcu1.110 Lepisosteus_oculatus LepOcu1.110 LepOcu1.75 Lepisosteus_oculatus LepOcu1.75 LepOcu1.99 Lepisosteus_oculatus LepOcu1.99 Leptinotarsa_decemlineata_gca000500325v2 Leptinotarsa_decemlineata_gca000500325v2 Leptinotarsa_decemlineata_gca000500325v2 -ASM966780v1.110 Leptobrachium_leishanense ASM966780v1.110 Leptolinea_tardivitalis Leptolinea_tardivitalis Leptolinea_tardivitalis Leptolinea_tardivitalis_gca_001306095 Leptolinea_tardivitalis_gca_001306095 Leptolinea_tardivitalis_gca_001306095 Leptolyngbya_boryana_nies_2135_gca_002368255 Leptolyngbya_boryana_nies_2135_gca_002368255 Leptolyngbya_boryana_nies_2135_gca_002368255 @@ -33715,7 +33577,6 @@ Loktanella_sp_s4079_gca_000967725 Loktanella_sp_s4079_gca_000967725 Loktanel Loktanella_vestfoldensis_ska53 Loktanella_vestfoldensis_ska53 Loktanella_vestfoldensis_ska53 Lolium_perenne Lolium_perenne Lolium_perenne Lomentospora_prolificans_gca_002276285 Lomentospora_prolificans_gca_002276285 Lomentospora_prolificans_gca_002276285 -LonStrDom1.110 Lonchura_striata_domestica LonStrDom1.110 LonStrDom1.99 Lonchura_striata_domestica LonStrDom1.99 Lonepinella_koalarum_gca_004339625 Lonepinella_koalarum_gca_004339625 Lonepinella_koalarum_gca_004339625 Longibacter_salinarum_gca_002554795 Longibacter_salinarum_gca_002554795 Longibacter_salinarum_gca_002554795 @@ -33732,7 +33593,6 @@ Lophiostoma_macrostomum_cbs_122681_gca_010405375 Lophiostoma_macrostomum_cbs_1 Lophiotrema_nucula_gca_010015825 Lophiotrema_nucula_gca_010015825 Lophiotrema_nucula_gca_010015825 Lophium_mytilinum_gca_010093605 Lophium_mytilinum_gca_010093605 Lophium_mytilinum_gca_010093605 Lottia_gigantea Lottia_gigantea Lottia_gigantea -loxAfr3.110 Loxodonta_africana loxAfr3.110 loxAfr3.75 Loxodonta_africana loxAfr3.75 loxAfr3.99 Loxodonta_africana loxAfr3.99 Lucifera_butyrica_gca_900476375 Lucifera_butyrica_gca_900476375 Lucifera_butyrica_gca_900476375 @@ -33792,7 +33652,6 @@ Lyngbya_aestuarii_bl_j_gca_000478195 Lyngbya_aestuarii_bl_j_gca_000478195 Ly Lyngbya_confervoides_bdu141951 Lyngbya_confervoides_bdu141951 Lyngbya_confervoides_bdu141951 Lyngbya_confervoides_bdu141951_gca_000817775 Lyngbya_confervoides_bdu141951_gca_000817775 Lyngbya_confervoides_bdu141951_gca_000817775 Lyngbya_sp_pcc_8106 Lyngbya_sp_pcc_8106 Lyngbya_sp_pcc_8106 -mLynCan4_v1.p.110 Lynx_canadensis mLynCan4_v1.p.110 mLynCan4_v1.p.99 Lynx_canadensis mLynCan4_v1.p.99 Lysinibacillus_antri_gca_003977595 Lysinibacillus_antri_gca_003977595 Lysinibacillus_antri_gca_003977595 Lysinibacillus_boronitolerans_jcm_21713_10a_nbrc_103108 Lysinibacillus_boronitolerans_jcm_21713_10a_nbrc_103108 Lysinibacillus_boronitolerans_jcm_21713_10a_nbrc_103108 @@ -33920,11 +33779,8 @@ Lysobacter_spongiicola_dsm_21749_gca_900167055 Lysobacter_spongiicola_dsm_2174 Lysobacter_tolerans_gca_900155935 Lysobacter_tolerans_gca_900155935 Lysobacter_tolerans_gca_900155935 Lytechinus_variegatus_gca018143015v1 Lytechinus_variegatus_gca018143015v1 Lytechinus_variegatus_gca018143015v1 Macaca_fascicularis_5.0.99 Macaca_fascicularis Macaca_fascicularis_5.0.99 -Macaca_fascicularis_6.0.110 Macaca_fascicularis Macaca_fascicularis_6.0.110 MMUL_1.75 Macaca_mulatta MMUL_1.75 -Mmul_10.110 Macaca_mulatta Mmul_10.110 Mmul_10.99 Macaca_mulatta Mmul_10.99 -Mnem_1.0.110 Macaca_nemestrina Mnem_1.0.110 Mnem_1.0.99 Macaca_nemestrina Mnem_1.0.99 Macellibacteroides_sp_hh_zs Macellibacteroides_sp_hh_zs Macellibacteroides_sp_hh_zs Macellibacteroides_sp_hh_zs_gca_001704385 Macellibacteroides_sp_hh_zs_gca_001704385 Macellibacteroides_sp_hh_zs_gca_001704385 @@ -34005,7 +33861,6 @@ Malikia_granosa_gca_002980595 Malikia_granosa_gca_002980595 Malikia_granosa_ Malikia_spinosa_gca_002980625 Malikia_spinosa_gca_002980625 Malikia_spinosa_gca_002980625 Maliponia_aquimaris_gca_900184945 Maliponia_aquimaris_gca_900184945 Maliponia_aquimaris_gca_900184945 Malonomonas_rubra_dsm_5091_gca_900142125 Malonomonas_rubra_dsm_5091_gca_900142125 Malonomonas_rubra_dsm_5091_gca_900142125 -mCya_1.0.110 Malurus_cyaneus_samueli mCya_1.0.110 Malus_domestica_golden Malus_domestica_golden Malus_domestica_golden Mameliella_alba Mameliella_alba Mameliella_alba Mameliella_alba_gca_000807715 Mameliella_alba_gca_000807715 Mameliella_alba_gca_000807715 @@ -34019,9 +33874,7 @@ Mammaliicoccus_sciuri_gca_003580455 Mammaliicoccus_sciuri_gca_003580455 Mamm Mammaliicoccus_sciuri_gca_003970475 Mammaliicoccus_sciuri_gca_003970475 Mammaliicoccus_sciuri_gca_003970475 Mammaliicoccus_stepanovicii_gca_900187075 Mammaliicoccus_stepanovicii_gca_900187075 Mammaliicoccus_stepanovicii_gca_900187075 Mammaliicoccus_vitulinus_gca_003043315 Mammaliicoccus_vitulinus_gca_003043315 Mammaliicoccus_vitulinus_gca_003043315 -ASM171598v2.110 Manacus_vitellinus ASM171598v2.110 ASM171598v2.99 Manacus_vitellinus ASM171598v2.99 -Mleu.le_1.0.110 Mandrillus_leucophaeus Mleu.le_1.0.110 Mleu.le_1.0.99 Mandrillus_leucophaeus Mleu.le_1.0.99 Manduca_sexta_gca014839805v1rs Manduca_sexta_gca014839805v1rs Manduca_sexta_gca014839805v1rs Mangrovibacter_phragmitis_gca_001655675 Mangrovibacter_phragmitis_gca_001655675 Mangrovibacter_phragmitis_gca_001655675 @@ -34372,7 +34225,6 @@ Marmoricola_scoriae_gca_900104965 Marmoricola_scoriae_gca_900104965 Marmoric Marmoricola_solisilvae_gca_003725775 Marmoricola_solisilvae_gca_003725775 Marmoricola_solisilvae_gca_003725775 Marmoricola_sp_leaf446 Marmoricola_sp_leaf446 Marmoricola_sp_leaf446 Marmoricola_sp_leaf446_gca_001424755 Marmoricola_sp_leaf446_gca_001424755 Marmoricola_sp_leaf446_gca_001424755 -marMar2.1.110 Marmota_marmota_marmota marMar2.1.110 marMar2.1.99 Marmota_marmota_marmota marMar2.1.99 Marortus_luteolus_gca_002915595 Marortus_luteolus_gca_002915595 Marortus_luteolus_gca_002915595 Marssonina_brunnea_f_sp_multigermtubi_mb_m1_gca_000298775 Marssonina_brunnea_f_sp_multigermtubi_mb_m1_gca_000298775 Marssonina_brunnea_f_sp_multigermtubi_mb_m1_gca_000298775 @@ -34435,12 +34287,10 @@ Massilimicrobiota_sp_an142_gca_002160725 Massilimicrobiota_sp_an142_gca_002160 Massilimicrobiota_sp_an80_gca_002159255 Massilimicrobiota_sp_an80_gca_002159255 Massilimicrobiota_sp_an80_gca_002159255 Massilimicrobiota_timonensis_gca_002160865 Massilimicrobiota_timonensis_gca_002160865 Massilimicrobiota_timonensis_gca_002160865 fMasArm1.1.99 Mastacembelus_armatus fMasArm1.1.99 -fMasArm1.2.110 Mastacembelus_armatus fMasArm1.2.110 Mastigocladus_laminosus_uu774 Mastigocladus_laminosus_uu774 Mastigocladus_laminosus_uu774 Mastigocoleus_testarum_bc008 Mastigocoleus_testarum_bc008 Mastigocoleus_testarum_bc008 Mastigocoleus_testarum_bc008_gca_001456025 Mastigocoleus_testarum_bc008_gca_001456025 Mastigocoleus_testarum_bc008_gca_001456025 Mayetiola_destructor Mayetiola_destructor Mayetiola_destructor -M_zebra_UMD2a.110 Maylandia_zebra M_zebra_UMD2a.110 M_zebra_UMD2a.99 Maylandia_zebra M_zebra_UMD2a.99 Medicago_truncatula Medicago_truncatula Medicago_truncatula Mediterranea_sp_an20_gca_002160055 Mediterranea_sp_an20_gca_002160055 Mediterranea_sp_an20_gca_002160055 @@ -34514,7 +34364,6 @@ Melaminivora_sp_sc2_9_gca_003008575 Melaminivora_sp_sc2_9_gca_003008575 Mela Melampsora_laricipopulina Melampsora_laricipopulina Melampsora_laricipopulina Melanomma_pulvis_pyrius_cbs_109_77_gca_010093585 Melanomma_pulvis_pyrius_cbs_109_77_gca_010093585 Melanomma_pulvis_pyrius_cbs_109_77_gca_010093585 Turkey_2.01.99 Meleagris_gallopavo Turkey_2.01.99 -Turkey_5.1.110 Meleagris_gallopavo Turkey_5.1.110 UMD2.75 Meleagris_gallopavo UMD2.75 Melghiribacillus_thermohalophilus_gca_004342905 Melghiribacillus_thermohalophilus_gca_004342905 Melghiribacillus_thermohalophilus_gca_004342905 Melghirimyces_profundicolus_gca_003054245 Melghirimyces_profundicolus_gca_003054245 Melghirimyces_profundicolus_gca_003054245 @@ -34545,11 +34394,9 @@ Melitaea_cinxia Melitaea_cinxia Melitaea_cinxia Melitaea_cinxia_gca905220565v1 Melitaea_cinxia_gca905220565v1 Melitaea_cinxia_gca905220565v1 Melittangium_boletus_dsm_14713_gca_002305855 Melittangium_boletus_dsm_14713_gca_002305855 Melittangium_boletus_dsm_14713_gca_002305855 Melopsittacus_undulatus_6.3.99 Melopsittacus_undulatus Melopsittacus_undulatus_6.3.99 -bMelUnd1.mat.Z.110 Melopsittacus_undulatus bMelUnd1.mat.Z.110 Mercenaria_mercenaria_gca014805675v2 Mercenaria_mercenaria_gca014805675v2 Mercenaria_mercenaria_gca014805675v2 Meridianimaribacter_sp_cl38_gca_004328055 Meridianimaribacter_sp_cl38_gca_004328055 Meridianimaribacter_sp_cl38_gca_004328055 Meridianimarinicoccus_roseus_gca_003172915 Meridianimarinicoccus_roseus_gca_003172915 Meridianimarinicoccus_roseus_gca_003172915 -MunDraft-v1.0.110 Meriones_unguiculatus MunDraft-v1.0.110 MunDraft-v1.0.99 Meriones_unguiculatus MunDraft-v1.0.99 Merismopedia_glauca_ccap_1448_3_gca_003003775 Merismopedia_glauca_ccap_1448_3_gca_003003775 Merismopedia_glauca_ccap_1448_3_gca_003003775 Mesoaciditoga_sp__gca_002878315 Mesoaciditoga_sp__gca_002878315 Mesoaciditoga_sp__gca_002878315 @@ -34563,7 +34410,6 @@ Mesobacillus_subterraneus_gca_003937825 Mesobacillus_subterraneus_gca_00393782 Mesobacillus_zeae_gca_003570705 Mesobacillus_zeae_gca_003570705 Mesobacillus_zeae_gca_003570705 Mesobaculum_littorinae_gca_004011175 Mesobaculum_littorinae_gca_004011175 Mesobaculum_littorinae_gca_004011175 Mesocricetibacter_intestinalis_gca_004363295 Mesocricetibacter_intestinalis_gca_004363295 Mesocricetibacter_intestinalis_gca_004363295 -MesAur1.0.110 Mesocricetus_auratus MesAur1.0.110 MesAur1.0.99 Mesocricetus_auratus MesAur1.0.99 Mesoflavibacter_sp_hg96_gca_003008415 Mesoflavibacter_sp_hg96_gca_003008415 Mesoflavibacter_sp_hg96_gca_003008415 Mesoflavibacter_zeaxanthinifaciens_subsp_sabulilitoris_gca_003008435 Mesoflavibacter_zeaxanthinifaciens_subsp_sabulilitoris_gca_003008435 Mesoflavibacter_zeaxanthinifaciens_subsp_sabulilitoris_gca_003008435 @@ -36108,7 +35954,6 @@ Microbulbifer_thermotolerans Microbulbifer_thermotolerans Microbulbifer_ther Microbulbifer_thermotolerans_gca_001617625 Microbulbifer_thermotolerans_gca_001617625 Microbulbifer_thermotolerans_gca_001617625 Microbulbifer_thermotolerans_gca_900112305 Microbulbifer_thermotolerans_gca_900112305 Microbulbifer_thermotolerans_gca_900112305 Microbulbifer_yueqingensis_gca_900100355 Microbulbifer_yueqingensis_gca_900100355 Microbulbifer_yueqingensis_gca_900100355 -Mmur_3.0.110 Microcebus_murinus Mmur_3.0.110 Mmur_3.0.99 Microcebus_murinus Mmur_3.0.99 micMur1.75 Microcebus_murinus micMur1.75 Microcella_alkaliphila_gca_002355395 Microcella_alkaliphila_gca_002355395 Microcella_alkaliphila_gca_002355395 @@ -36396,7 +36241,6 @@ Microterricola_viridarii Microterricola_viridarii Microterricola_viridarii Microterricola_viridarii_gca_001542775 Microterricola_viridarii_gca_001542775 Microterricola_viridarii_gca_001542775 Microterricola_viridarii_gca_900104895 Microterricola_viridarii_gca_900104895 Microterricola_viridarii_gca_900104895 Microthyrium_microscopicum_gca_010405405 Microthyrium_microscopicum_gca_010405405 Microthyrium_microscopicum_gca_010405405 -MicOch1.0.110 Microtus_ochrogaster MicOch1.0.110 MicOch1.0.99 Microtus_ochrogaster MicOch1.0.99 Microvirga_guangxiensis_gca_900102135 Microvirga_guangxiensis_gca_900102135 Microvirga_guangxiensis_gca_900102135 Microvirga_lotononidis Microvirga_lotononidis Microvirga_lotononidis @@ -36489,7 +36333,6 @@ Mogibacterium_sp_cm50_gca_000293155 Mogibacterium_sp_cm50_gca_000293155 Mogi Mogibacterium_timidum_atcc_33093 Mogibacterium_timidum_atcc_33093 Mogibacterium_timidum_atcc_33093 Mogibacterium_timidum_atcc_33093_gca_000525775 Mogibacterium_timidum_atcc_33093_gca_000525775 Mogibacterium_timidum_atcc_33093_gca_000525775 Moheibacter_sediminis_gca_900176425 Moheibacter_sediminis_gca_900176425 Moheibacter_sediminis_gca_900176425 -ASM169857v1.110 Mola_mola ASM169857v1.110 ASM169857v1.99 Mola_mola ASM169857v1.99 Monaibacterium_marinum_gca_900231835 Monaibacterium_marinum_gca_900231835 Monaibacterium_marinum_gca_900231835 Monascus_purpureus_gca_006542485 Monascus_purpureus_gca_006542485 Monascus_purpureus_gca_006542485 @@ -36500,13 +36343,10 @@ Monilinia_laxa_gca_009299455 Monilinia_laxa_gca_009299455 Monilinia_laxa_gca Moniliophthora_perniciosa_fa553_gca_000183025 Moniliophthora_perniciosa_fa553_gca_000183025 Moniliophthora_perniciosa_fa553_gca_000183025 Moniliophthora_roreri_gca_001466705 Moniliophthora_roreri_gca_001466705 Moniliophthora_roreri_gca_001466705 Moniliophthora_roreri_mca_2997_gca_000488995 Moniliophthora_roreri_mca_2997_gca_000488995 Moniliophthora_roreri_mca_2997_gca_000488995 -ASM229v1.110 Monodelphis_domestica ASM229v1.110 ASM229v1.99 Monodelphis_domestica ASM229v1.99 BROADO5.75 Monodelphis_domestica BROADO5.75 -NGI_Narwhal_1.110 Monodon_monoceros NGI_Narwhal_1.110 Monoglobus_pectinilyticus_gca_002874775 Monoglobus_pectinilyticus_gca_002874775 Monoglobus_pectinilyticus_gca_002874775 Monomorium_pharaonis_gca013373865v2 Monomorium_pharaonis_gca013373865v2 Monomorium_pharaonis_gca013373865v2 -M_albus_1.0.110 Monopterus_albus M_albus_1.0.110 M_albus_1.0.99 Monopterus_albus M_albus_1.0.99 Monosiga_brevicollis_mx1_gca_000002865 Monosiga_brevicollis_mx1_gca_000002865 Monosiga_brevicollis_mx1_gca_000002865 Monosporascus_cannonballus_gca_004154925 Monosporascus_cannonballus_gca_004154925 Monosporascus_cannonballus_gca_004154925 @@ -36656,7 +36496,6 @@ Morococcus_cerebrosus Morococcus_cerebrosus Morococcus_cerebrosus Morococcus_cerebrosus_gca_000813705 Morococcus_cerebrosus_gca_000813705 Morococcus_cerebrosus_gca_000813705 Mortierella_elongata_ag_77_gca_001651415 Mortierella_elongata_ag_77_gca_001651415 Mortierella_elongata_ag_77_gca_001651415 Mortierella_verticillata_nrrl_6337_gca_000739165 Mortierella_verticillata_nrrl_6337_gca_000739165 Mortierella_verticillata_nrrl_6337_gca_000739165 -MosMos_v2_BIUU_UCD.110 Moschus_moschiferus MosMos_v2_BIUU_UCD.110 MosMos_v2_BIUU_UCD.99 Moschus_moschiferus MosMos_v2_BIUU_UCD.99 Motilibacter_peucedani_gca_003634695 Motilibacter_peucedani_gca_003634695 Motilibacter_peucedani_gca_003634695 Motilibacter_rhizosphaerae_gca_004216915 Motilibacter_rhizosphaerae_gca_004216915 Motilibacter_rhizosphaerae_gca_004216915 @@ -36771,52 +36610,31 @@ Muricomes_intestini_gca_004346165 Muricomes_intestini_gca_004346165 Muricome Muriicola_soli_gca_004139715 Muriicola_soli_gca_004139715 Muriicola_soli_gca_004139715 Murimonas_intestini_gca_003148945 Murimonas_intestini_gca_003148945 Murimonas_intestini_gca_003148945 Murinocardiopsis_flavida_gca_003014485 Murinocardiopsis_flavida_gca_003014485 Murinocardiopsis_flavida_gca_003014485 -CAROLI_EIJ_v1.1.110 Mus_caroli CAROLI_EIJ_v1.1.110 CAROLI_EIJ_v1.1.99 Mus_caroli CAROLI_EIJ_v1.1.99 GRCm38.75 Mus_musculus GRCm38.75 GRCm38.99 Mus_musculus GRCm38.99 -GRCm39.110 Mus_musculus GRCm39.110 testMm37.61 Mus_musculus testMm37.61 -129S1_SvImJ_v1.110 Mus_musculus_129s1svimj 129S1_SvImJ_v1.110 129S1_SvImJ_v1.99 Mus_musculus_129s1svimj 129S1_SvImJ_v1.99 -A_J_v1.110 Mus_musculus_aj A_J_v1.110 A_J_v1.99 Mus_musculus_aj A_J_v1.99 -AKR_J_v1.110 Mus_musculus_akrj AKR_J_v1.110 AKR_J_v1.99 Mus_musculus_akrj AKR_J_v1.99 -BALB_cJ_v1.110 Mus_musculus_balbcj BALB_cJ_v1.110 BALB_cJ_v1.99 Mus_musculus_balbcj BALB_cJ_v1.99 -C3H_HeJ_v1.110 Mus_musculus_c3hhej C3H_HeJ_v1.110 C3H_HeJ_v1.99 Mus_musculus_c3hhej C3H_HeJ_v1.99 -C57BL_6NJ_v1.110 Mus_musculus_c57bl6nj C57BL_6NJ_v1.110 C57BL_6NJ_v1.99 Mus_musculus_c57bl6nj C57BL_6NJ_v1.99 -CAST_EiJ_v1.110 Mus_musculus_casteij CAST_EiJ_v1.110 CAST_EiJ_v1.99 Mus_musculus_casteij CAST_EiJ_v1.99 -CBA_J_v1.110 Mus_musculus_cbaj CBA_J_v1.110 CBA_J_v1.99 Mus_musculus_cbaj CBA_J_v1.99 -DBA_2J_v1.110 Mus_musculus_dba2j DBA_2J_v1.110 DBA_2J_v1.99 Mus_musculus_dba2j DBA_2J_v1.99 -FVB_NJ_v1.110 Mus_musculus_fvbnj FVB_NJ_v1.110 FVB_NJ_v1.99 Mus_musculus_fvbnj FVB_NJ_v1.99 -LP_J_v1.110 Mus_musculus_lpj LP_J_v1.110 LP_J_v1.99 Mus_musculus_lpj LP_J_v1.99 -NOD_ShiLtJ_v1.110 Mus_musculus_nodshiltj NOD_ShiLtJ_v1.110 NOD_ShiLtJ_v1.99 Mus_musculus_nodshiltj NOD_ShiLtJ_v1.99 -NZO_HlLtJ_v1.110 Mus_musculus_nzohlltj NZO_HlLtJ_v1.110 NZO_HlLtJ_v1.99 Mus_musculus_nzohlltj NZO_HlLtJ_v1.99 -PWK_PhJ_v1.110 Mus_musculus_pwkphj PWK_PhJ_v1.110 PWK_PhJ_v1.99 Mus_musculus_pwkphj PWK_PhJ_v1.99 -WSB_EiJ_v1.110 Mus_musculus_wsbeij WSB_EiJ_v1.110 WSB_EiJ_v1.99 Mus_musculus_wsbeij WSB_EiJ_v1.99 -PAHARI_EIJ_v1.1.110 Mus_pahari PAHARI_EIJ_v1.1.110 PAHARI_EIJ_v1.1.99 Mus_pahari PAHARI_EIJ_v1.1.99 -MUSP714.110 Mus_spicilegus MUSP714.110 MUSP714.99 Mus_spicilegus MUSP714.99 -SPRET_EiJ_v1.110 Mus_spretus SPRET_EiJ_v1.110 SPRET_EiJ_v1.99 Mus_spretus SPRET_EiJ_v1.99 Musa_acuminata Musa_acuminata Musa_acuminata Musca_domestica Musca_domestica Musca_domestica Musicola_paradisiaca_ech703_gca_000023545 Musicola_paradisiaca_ech703_gca_000023545 Musicola_paradisiaca_ech703_gca_000023545 -MusPutFur1.0.110 Mustela_putorius_furo MusPutFur1.0.110 MusPutFur1.0.75 Mustela_putorius_furo MusPutFur1.0.75 MusPutFur1.0.99 Mustela_putorius_furo MusPutFur1.0.99 Myceligenerans_xiligouense_gca_003814695 Myceligenerans_xiligouense_gca_003814695 Myceligenerans_xiligouense_gca_003814695 @@ -41523,10 +41341,8 @@ Mycoplasmopsis_synoviae_gca_003147565 Mycoplasmopsis_synoviae_gca_003147565 Mycoplasmopsis_synoviae_gca_003586085 Mycoplasmopsis_synoviae_gca_003586085 Mycoplasmopsis_synoviae_gca_003586085 Mycoplasmopsis_verecunda_gca_900167035 Mycoplasmopsis_verecunda_gca_900167035 Mycoplasmopsis_verecunda_gca_900167035 Mycosphaerella_eumusae_gca_001578235 Mycosphaerella_eumusae_gca_001578235 Mycosphaerella_eumusae_gca_001578235 -Myoluc2.0.110 Myotis_lucifugus Myoluc2.0.110 Myoluc2.0.75 Myotis_lucifugus Myoluc2.0.75 Myoluc2.0.99 Myotis_lucifugus Myoluc2.0.99 -fMyrMur1.1.110 Myripristis_murdjan fMyrMur1.1.110 fMyrMur1.1.99 Myripristis_murdjan fMyrMur1.1.99 Myroides_aquimaris_gca_900108395 Myroides_aquimaris_gca_900108395 Myroides_aquimaris_gca_900108395 Myroides_guanonis_gca_900114085 Myroides_guanonis_gca_900114085 Myroides_guanonis_gca_900114085 @@ -41572,7 +41388,6 @@ Naasia_lichenicola_gca_004801885 Naasia_lichenicola_gca_004801885 Naasia_lic Nadsonia_fulvescens_var_elongata_dsm_6958_gca_001661315 Nadsonia_fulvescens_var_elongata_dsm_6958_gca_001661315 Nadsonia_fulvescens_var_elongata_dsm_6958_gca_001661315 Naegleria_gruberi_gca_000004985 Naegleria_gruberi_gca_000004985 Naegleria_gruberi_gca_000004985 Naematelia_encephala_gca_002105065 Naematelia_encephala_gca_002105065 Naematelia_encephala_gca_002105065 -Nana_v5.110 Naja_naja Nana_v5.110 Nakamurella_antarctica_gca_003860405 Nakamurella_antarctica_gca_003860405 Nakamurella_antarctica_gca_003860405 Nakamurella_flava_gca_005298075 Nakamurella_flava_gca_005298075 Nakamurella_flava_gca_005298075 Nakamurella_multipartita_dsm_44233 Nakamurella_multipartita_dsm_44233 Nakamurella_multipartita_dsm_44233 @@ -41583,7 +41398,6 @@ Nannizzia_gypsea_cbs_118893_gca_000150975 Nannizzia_gypsea_cbs_118893_gca_0001 Nannochloropsis_gaditana_ccmp526_gca_000240725 Nannochloropsis_gaditana_ccmp526_gca_000240725 Nannochloropsis_gaditana_ccmp526_gca_000240725 Nannochloropsis_gaditana_gca_000569095 Nannochloropsis_gaditana_gca_000569095 Nannochloropsis_gaditana_gca_000569095 Nannocystis_exedens_gca_900112715 Nannocystis_exedens_gca_900112715 Nannocystis_exedens_gca_900112715 -S.galili_v1.0.110 Nannospalax_galili S.galili_v1.0.110 S.galili_v1.0.99 Nannospalax_galili S.galili_v1.0.99 Nanoarchaeota_archaeon_gca_002687775 Nanoarchaeota_archaeon_gca_002687775 Nanoarchaeota_archaeon_gca_002687775 Nanoarchaeota_archaeon_gca_002687825 Nanoarchaeota_archaeon_gca_002687825 Nanoarchaeota_archaeon_gca_002687825 @@ -42551,10 +42365,8 @@ Neochlamydia_sp_tume1_gca_000813645 Neochlamydia_sp_tume1_gca_000813645 Neoc Neodiprion_lecontei_gca021901455v1rs Neodiprion_lecontei_gca021901455v1rs Neodiprion_lecontei_gca021901455v1rs Neodiprion_pinetum_gca021155775v1rs Neodiprion_pinetum_gca021155775v1rs Neodiprion_pinetum_gca021155775v1rs Neofusicoccum_parvum_ucrnp2_gca_000385595 Neofusicoccum_parvum_ucrnp2_gca_000385595 Neofusicoccum_parvum_ucrnp2_gca_000385595 -RGoby_Basel_V2.110 Neogobius_melanostomus RGoby_Basel_V2.110 RGoby_Basel_V2.99 Neogobius_melanostomus RGoby_Basel_V2.99 Neohortaea_acidophila_gca_010093505 Neohortaea_acidophila_gca_010093505 Neohortaea_acidophila_gca_010093505 -NeoBri1.0.110 Neolamprologus_brichardi NeoBri1.0.110 NeoBri1.0.99 Neolamprologus_brichardi NeoBri1.0.99 Neolecta_irregularis_dah_3_gca_001929475 Neolecta_irregularis_dah_3_gca_001929475 Neolecta_irregularis_dah_3_gca_001929475 Neolentinus_lepideus_hhb14362_ss_1_gca_001632425 Neolentinus_lepideus_hhb14362_ss_1_gca_001632425 Neolentinus_lepideus_hhb14362_ss_1_gca_001632425 @@ -42584,7 +42396,6 @@ Neorickettsia_sennetsu_str_miyayama Neorickettsia_sennetsu_str_miyayama Neor Neorickettsia_sennetsu_str_miyayama_gca_000013165 Neorickettsia_sennetsu_str_miyayama_gca_000013165 Neorickettsia_sennetsu_str_miyayama_gca_000013165 Neosartorya_fischeri Neosartorya_fischeri Neosartorya_fischeri Neosynechococcus_sphagnicola_sy1 Neosynechococcus_sphagnicola_sy1 Neosynechococcus_sphagnicola_sy1 -NNQGG.v01.110 Neovison_vison NNQGG.v01.110 NNQGG.v01.99 Neovison_vison NNQGG.v01.99 Neptuniibacter_caesariensis Neptuniibacter_caesariensis Neptuniibacter_caesariensis Neptunomonas_antarctica_gca_900156635 Neptunomonas_antarctica_gca_900156635 Neptunomonas_antarctica_gca_900156635 @@ -42984,7 +42795,6 @@ Nodularia_spumigena_ccy9414_gca_000340565 Nodularia_spumigena_ccy9414_gca_0003 Nodularia_spumigena_cena596 Nodularia_spumigena_cena596 Nodularia_spumigena_cena596 Nodularia_spumigena_cena596_gca_001623485 Nodularia_spumigena_cena596_gca_001623485 Nodularia_spumigena_cena596_gca_001623485 Nleu1.0.75 Nomascus_leucogenys Nleu1.0.75 -Nleu_3.0.110 Nomascus_leucogenys Nleu_3.0.110 Nleu_3.0.99 Nomascus_leucogenys Nleu_3.0.99 Nonlabens_agnitus_gca_002994045 Nonlabens_agnitus_gca_002994045 Nonlabens_agnitus_gca_002994045 Nonlabens_arenilitoris_gca_002954765 Nonlabens_arenilitoris_gca_002954765 Nonlabens_arenilitoris_gca_002954765 @@ -43069,13 +42879,9 @@ Nostoc_sp_peltigera_membranacea_cyanobiont_n6_gca_002949735 Nostoc_sp_peltiger Nostoc_sp_rf31ymg_gca_002155185 Nostoc_sp_rf31ymg_gca_002155185 Nostoc_sp_rf31ymg_gca_002155185 Nostoc_sp_t09_gca_002154695 Nostoc_sp_t09_gca_002154695 Nostoc_sp_t09_gca_002154695 Nostocales_cyanobacterium_ht_58_2_gca_002163975 Nostocales_cyanobacterium_ht_58_2_gca_002163975 Nostocales_cyanobacterium_ht_58_2_gca_002163975 -Meug_1.0.110 Notamacropus_eugenii Meug_1.0.110 Meug_1.0.99 Notamacropus_eugenii Meug_1.0.99 -TS10Xv2-PRI.110 Notechis_scutatus TS10Xv2-PRI.110 TS10Xv2-PRI.99 Notechis_scutatus TS10Xv2-PRI.99 -Nfu_20140520.110 Nothobranchius_furzeri Nfu_20140520.110 Nothophytophthora_sp_chile5_gca_001712635 Nothophytophthora_sp_chile5_gca_001712635 Nothophytophthora_sp_chile5_gca_001712635 -notPer1.110 Nothoprocta_perdicaria notPer1.110 notPer1.99 Nothoprocta_perdicaria notPer1.99 Notoacmeibacter_marinus_gca_002238045 Notoacmeibacter_marinus_gca_002238045 Notoacmeibacter_marinus_gca_002238045 Novacetimonas_cocois_gca_003311635 Novacetimonas_cocois_gca_003311635 Novacetimonas_cocois_gca_003311635 @@ -43165,7 +42971,6 @@ Novosphingobium_subterraneum Novosphingobium_subterraneum Novosphingobium_su Novosphingobium_subterraneum_gca_000807925 Novosphingobium_subterraneum_gca_000807925 Novosphingobium_subterraneum_gca_000807925 Novosphingobium_tardaugens_nbrc_16725 Novosphingobium_tardaugens_nbrc_16725 Novosphingobium_tardaugens_nbrc_16725 Novosphingobium_umbonatum_gca_004005905 Novosphingobium_umbonatum_gca_004005905 Novosphingobium_umbonatum_gca_004005905 -NumMel1.0.110 Numida_meleagris NumMel1.0.110 NumMel1.0.99 Numida_meleagris NumMel1.0.99 Nymphaea_colorata Nymphaea_colorata Nymphaea_colorata Obba_rivulosa_gca_001687445 Obba_rivulosa_gca_001687445 Obba_rivulosa_gca_001687445 @@ -43243,7 +43048,6 @@ Oceanospirillum_linum_gca_001995095 Oceanospirillum_linum_gca_001995095 Ocea Oceanospirillum_multiglobuliferum_gca_002059185 Oceanospirillum_multiglobuliferum_gca_002059185 Oceanospirillum_multiglobuliferum_gca_002059185 Oceanospirillum_sp__gca_002684995 Oceanospirillum_sp__gca_002684995 Oceanospirillum_sp__gca_002684995 Oceanotoga_teriensis_gca_003148465 Oceanotoga_teriensis_gca_003148465 Oceanotoga_teriensis_gca_003148465 -OchPri2.0-Ens.110 Ochotona_princeps OchPri2.0-Ens.110 OchPri2.0-Ens.99 Ochotona_princeps OchPri2.0-Ens.99 pika.75 Ochotona_princeps pika.75 Ochrobactrum_anthropi Ochrobactrum_anthropi Ochrobactrum_anthropi @@ -43278,7 +43082,6 @@ Octadecabacter_arcticus_238_gca_000155735 Octadecabacter_arcticus_238_gca_0001 Octadecabacter_ascidiaceicola_gca_900185015 Octadecabacter_ascidiaceicola_gca_900185015 Octadecabacter_ascidiaceicola_gca_900185015 Octadecabacter_temperatus Octadecabacter_temperatus Octadecabacter_temperatus Octadecabacter_temperatus_gca_001187845 Octadecabacter_temperatus_gca_001187845 Octadecabacter_temperatus_gca_001187845 -OctDeg1.0.110 Octodon_degus OctDeg1.0.110 OctDeg1.0.99 Octodon_degus OctDeg1.0.99 Octopus_bimaculoides Octopus_bimaculoides Octopus_bimaculoides Octopus_bimaculoides_gca001194135v1 Octopus_bimaculoides_gca001194135v1 Octopus_bimaculoides_gca001194135v1 @@ -43439,9 +43242,6 @@ Omnitrophica_wor_2_bacterium_rifcsplowo2_12_full_63_16_gca_001805925 Omnitroph Omnitrophica_wor_2_bacterium_rifoxya2_full_38_17_gca_001805965 Omnitrophica_wor_2_bacterium_rifoxya2_full_38_17_gca_001805965 Omnitrophica_wor_2_bacterium_rifoxya2_full_38_17_gca_001805965 Omnitrophica_wor_2_bacterium_sm23_72_gca_001304135 Omnitrophica_wor_2_bacterium_sm23_72_gca_001304135 Omnitrophica_wor_2_bacterium_sm23_72_gca_001304135 Onchocerca_volvulus Onchocerca_volvulus Onchocerca_volvulus -Okis_V2.110 Oncorhynchus_kisutch Okis_V2.110 -USDA_OmykA_1.1.110 Oncorhynchus_mykiss USDA_OmykA_1.1.110 -Otsh_v1.0.110 Oncorhynchus_tshawytscha Otsh_v1.0.110 Onion_yellows_phytoplasma_oy_m Onion_yellows_phytoplasma_oy_m Onion_yellows_phytoplasma_oy_m Onion_yellows_phytoplasma_oy_m_gca_000009845 Onion_yellows_phytoplasma_oy_m_gca_000009845 Onion_yellows_phytoplasma_oy_m_gca_000009845 Onthophagus_taurus_gca000648695v2 Onthophagus_taurus_gca000648695v2 Onthophagus_taurus_gca000648695v2 @@ -43483,9 +43283,7 @@ Ordospora_colligata_oc4_gca_000803265 Ordospora_colligata_oc4_gca_000803265 Orenia_marismortui_gca_004365685 Orenia_marismortui_gca_004365685 Orenia_marismortui_gca_004365685 Orenia_metallireducens Orenia_metallireducens Orenia_metallireducens Orenia_metallireducens_gca_900215265 Orenia_metallireducens_gca_900215265 Orenia_metallireducens_gca_900215265 -ASM587006v1.110 Oreochromis_aureus ASM587006v1.110 ASM587006v1.99 Oreochromis_aureus ASM587006v1.99 -O_niloticus_UMD_NMBU.110 Oreochromis_niloticus O_niloticus_UMD_NMBU.110 O_niloticus_UMD_NMBU.99 Oreochromis_niloticus O_niloticus_UMD_NMBU.99 Orenil1.0.75 Oreochromis_niloticus Orenil1.0.75 Oribacterium_asaccharolyticum_acb7 Oribacterium_asaccharolyticum_acb7 Oribacterium_asaccharolyticum_acb7 @@ -43532,12 +43330,10 @@ Ornithobacterium_rhinotracheale_h06_030791 Ornithobacterium_rhinotracheale_h06 Ornithobacterium_rhinotracheale_ort_umn_88 Ornithobacterium_rhinotracheale_ort_umn_88 Ornithobacterium_rhinotracheale_ort_umn_88 OANA5.75 Ornithorhynchus_anatinus OANA5.75 OANA5.99 Ornithorhynchus_anatinus OANA5.99 -mOrnAna1.p.v1.110 Ornithorhynchus_anatinus mOrnAna1.p.v1.110 Orrella_dioscoreae Orrella_dioscoreae Orrella_dioscoreae Orrella_dioscoreae_gca_900089455 Orrella_dioscoreae_gca_900089455 Orrella_dioscoreae_gca_900089455 Orrella_marina_gca_003058465 Orrella_marina_gca_003058465 Orrella_marina_gca_003058465 Orussus_abietinus_gca000612105v2 Orussus_abietinus_gca000612105v2 Orussus_abietinus_gca000612105v2 -OryCun2.0.110 Oryctolagus_cuniculus OryCun2.0.110 OryCun2.0.75 Oryctolagus_cuniculus OryCun2.0.75 OryCun2.0.99 Oryctolagus_cuniculus OryCun2.0.99 Oryza_barthii Oryza_barthii Oryza_barthii @@ -43566,17 +43362,11 @@ Oryza_sativa_n22 Oryza_sativa_n22 Oryza_sativa_n22 Oryza_sativa_natelboro Oryza_sativa_natelboro Oryza_sativa_natelboro Oryza_sativa_pr106 Oryza_sativa_pr106 Oryza_sativa_pr106 Oryza_sativa_zs97 Oryza_sativa_zs97 Oryza_sativa_zs97 -OJAV_1.1.110 Oryzias_javanicus OJAV_1.1.110 -ASM223467v1.110 Oryzias_latipes ASM223467v1.110 ASM223467v1.99 Oryzias_latipes ASM223467v1.99 MEDAKA1.75 Oryzias_latipes MEDAKA1.75 -ASM223471v1.110 Oryzias_latipes_hni ASM223471v1.110 ASM223471v1.99 Oryzias_latipes_hni ASM223471v1.99 -ASM223469v1.110 Oryzias_latipes_hsok ASM223469v1.110 ASM223469v1.99 Oryzias_latipes_hsok ASM223469v1.99 -Om_v0.7.RACA.110 Oryzias_melastigma Om_v0.7.RACA.110 Om_v0.7.RACA.99 Oryzias_melastigma Om_v0.7.RACA.99 -ASM858656v1.110 Oryzias_sinensis ASM858656v1.110 Oryzisolibacter_propanilivorax_gca_900103645 Oryzisolibacter_propanilivorax_gca_900103645 Oryzisolibacter_propanilivorax_gca_900103645 Oscillatoria_acuminata_pcc_6304 Oscillatoria_acuminata_pcc_6304 Oscillatoria_acuminata_pcc_6304 Oscillatoria_acuminata_pcc_6304_gca_000317105 Oscillatoria_acuminata_pcc_6304_gca_000317105 Oscillatoria_acuminata_pcc_6304_gca_000317105 @@ -43623,17 +43413,13 @@ Osedax_symbiont_rs1_gca_000416275 Osedax_symbiont_rs1_gca_000416275 Osedax_s Osedax_symbiont_rs2_gca_000416315 Osedax_symbiont_rs2_gca_000416315 Osedax_symbiont_rs2_gca_000416315 Ostreococcus_lucimarinus Ostreococcus_lucimarinus Ostreococcus_lucimarinus Otariodibacter_oris_gca_003634665 Otariodibacter_oris_gca_003634665 Otariodibacter_oris_gca_003634665 -OtoGar3.110 Otolemur_garnettii OtoGar3.110 OtoGar3.75 Otolemur_garnettii OtoGar3.75 OtoGar3.99 Otolemur_garnettii OtoGar3.99 Ottowia_oryzae_gca_003008535 Ottowia_oryzae_gca_003008535 Ottowia_oryzae_gca_003008535 Ottowia_sp_oral_taxon_894 Ottowia_sp_oral_taxon_894 Ottowia_sp_oral_taxon_894 Ottowia_sp_oral_taxon_894_gca_001262075 Ottowia_sp_oral_taxon_894_gca_001262075 Ottowia_sp_oral_taxon_894_gca_001262075 -OtuSun1.0.110 Otus_sunia OtuSun1.0.110 -Oar_v3.1.110 Ovis_aries Oar_v3.1.110 Oar_v3.1.75 Ovis_aries Oar_v3.1.75 Oar_v3.1.99 Ovis_aries Oar_v3.1.99 -Oar_rambouillet_v1.0.110 Ovis_aries_rambouillet Oar_rambouillet_v1.0.110 Owenia_fusiformis_gca903813345v1 Owenia_fusiformis_gca903813345v1 Owenia_fusiformis_gca903813345v1 Owenweeksia_hongkongensis_dsm_17368 Owenweeksia_hongkongensis_dsm_17368 Owenweeksia_hongkongensis_dsm_17368 Owenweeksia_hongkongensis_dsm_17368_gca_000236705 Owenweeksia_hongkongensis_dsm_17368_gca_000236705 Owenweeksia_hongkongensis_dsm_17368_gca_000236705 @@ -44061,10 +43847,8 @@ Paludibacter_sp_47_17_gca_001898935 Paludibacter_sp_47_17_gca_001898935 Palu Paludibacterium_purpuratum_gca_004363805 Paludibacterium_purpuratum_gca_004363805 Paludibacterium_purpuratum_gca_004363805 Paludifilum_halophilum_gca_002245355 Paludifilum_halophilum_gca_002245355 Paludifilum_halophilum_gca_002245355 Paludisphaera_borealis_gca_001956985 Paludisphaera_borealis_gca_001956985 Paludisphaera_borealis_gca_001956985 -panpan1.1.110 Pan_paniscus panpan1.1.110 panpan1.1.99 Pan_paniscus panpan1.1.99 CHIMP2.1.4.75 Pan_troglodytes CHIMP2.1.4.75 -Pan_tro_3.0.110 Pan_troglodytes Pan_tro_3.0.110 Pan_tro_3.0.99 Pan_troglodytes Pan_tro_3.0.99 Panacagrimonas_perspica_gca_004364935 Panacagrimonas_perspica_gca_004364935 Panacagrimonas_perspica_gca_004364935 Panacagrimonas_perspica_gca_004799025 Panacagrimonas_perspica_gca_004799025 Panacagrimonas_perspica_gca_004799025 @@ -44107,10 +43891,7 @@ Pannonibacter_indicus_gca_001517385 Pannonibacter_indicus_gca_001517385 Pann Pannonibacter_phragmitetus Pannonibacter_phragmitetus Pannonibacter_phragmitetus Pannonibacter_phragmitetus_gca_001484065 Pannonibacter_phragmitetus_gca_001484065 Pannonibacter_phragmitetus_gca_001484065 Pannonibacter_phragmitetus_gca_900454465 Pannonibacter_phragmitetus_gca_900454465 Pannonibacter_phragmitetus_gca_900454465 -PanLeo1.0.110 Panthera_leo PanLeo1.0.110 -PanPar1.0.110 Panthera_pardus PanPar1.0.110 PanPar1.0.99 Panthera_pardus PanPar1.0.99 -PanTig1.0.110 Panthera_tigris_altaica PanTig1.0.110 PanTig1.0.99 Panthera_tigris_altaica PanTig1.0.99 Pantoea_agglomerans Pantoea_agglomerans Pantoea_agglomerans Pantoea_agglomerans_299r Pantoea_agglomerans_299r Pantoea_agglomerans_299r @@ -44217,7 +43998,6 @@ Pantoea_wallisii_gca_002095485 Pantoea_wallisii_gca_002095485 Pantoea_wallis Papaver_somniferum Papaver_somniferum Papaver_somniferum Papillibacter_cinnamivorans_dsm_12816_gca_900176335 Papillibacter_cinnamivorans_dsm_12816_gca_900176335 Papillibacter_cinnamivorans_dsm_12816_gca_900176335 Panu_3.0.99 Papio_anubis Panu_3.0.99 -Panubis1.0.110 Papio_anubis Panubis1.0.110 Parabacteroides_acidifaciens_gca_003363715 Parabacteroides_acidifaciens_gca_003363715 Parabacteroides_acidifaciens_gca_003363715 Parabacteroides_chartae_gca_900168155 Parabacteroides_chartae_gca_900168155 Parabacteroides_chartae_gca_900168155 Parabacteroides_chinchillae_gca_900108035 Parabacteroides_chinchillae_gca_900108035 Parabacteroides_chinchillae_gca_900108035 @@ -44550,13 +44330,11 @@ Paraliobacillus_ryukyuensis_gca_003315295 Paraliobacillus_ryukyuensis_gca_0033 Paraliobacillus_sp_pm_2 Paraliobacillus_sp_pm_2 Paraliobacillus_sp_pm_2 Paraliobacillus_sp_pm_2_gca_001368815 Paraliobacillus_sp_pm_2_gca_001368815 Paraliobacillus_sp_pm_2_gca_001368815 Paramaledivibacter_caminithermalis_dsm_15212_gca_900142245 Paramaledivibacter_caminithermalis_dsm_15212_gca_900142245 Paramaledivibacter_caminithermalis_dsm_15212_gca_900142245 -fParRan2.1.110 Parambassis_ranga fParRan2.1.110 fParRan2.1.99 Parambassis_ranga fParRan2.1.99 Paramecium_tetraurelia Paramecium_tetraurelia Paramecium_tetraurelia Paramesorhizobium_deserti Paramesorhizobium_deserti Paramesorhizobium_deserti Paramesorhizobium_deserti_gca_001558695 Paramesorhizobium_deserti_gca_001558695 Paramesorhizobium_deserti_gca_001558695 Paramicrosporidium_saccamoebae_gca_002794465 Paramicrosporidium_saccamoebae_gca_002794465 Paramicrosporidium_saccamoebae_gca_002794465 -PKINGS_0.1.110 Paramormyrops_kingsleyae PKINGS_0.1.110 PKINGS_0.1.99 Paramormyrops_kingsleyae PKINGS_0.1.99 Paramuribaculum_intestinale_gca_003024815 Paramuribaculum_intestinale_gca_003024815 Paramuribaculum_intestinale_gca_003024815 Paraoerskovia_marina_gca_900105445 Paraoerskovia_marina_gca_900105445 Paraoerskovia_marina_gca_900105445 @@ -44818,7 +44596,6 @@ Parendozoicomonas_haliclonae_gca_900174585 Parendozoicomonas_haliclonae_gca_90 Parenemella_sanctibonifatiensis_gca_002250475 Parenemella_sanctibonifatiensis_gca_002250475 Parenemella_sanctibonifatiensis_gca_002250475 Parenemella_sanctibonifatiensis_gca_002250565 Parenemella_sanctibonifatiensis_gca_002250565 Parenemella_sanctibonifatiensis_gca_002250565 Paroceanicella_profunda_gca_005887635 Paroceanicella_profunda_gca_005887635 Paroceanicella_profunda_gca_005887635 -Parus_major1.1.110 Parus_major Parus_major1.1.110 Parus_major1.1.99 Parus_major Parus_major1.1.99 Parvibacter_caecicola_gca_005046025 Parvibacter_caecicola_gca_005046025 Parvibacter_caecicola_gca_005046025 Parvibaculum_lavamentivorans_ds_1 Parvibaculum_lavamentivorans_ds_1 Parvibaculum_lavamentivorans_ds_1 @@ -44940,7 +44717,6 @@ Paucilactobacillus_vaccinostercus_dsm_20634_gca_001436295 Paucilactobacillus_v Paucilactobacillus_wasatchensis_gca_000876205 Paucilactobacillus_wasatchensis_gca_000876205 Paucilactobacillus_wasatchensis_gca_000876205 Paucimonas_lemoignei_gca_004342585 Paucimonas_lemoignei_gca_004342585 Paucimonas_lemoignei_gca_004342585 Paucimonas_lemoignei_gca_900475325 Paucimonas_lemoignei_gca_900475325 Paucimonas_lemoignei_gca_900475325 -AIIM_Pcri_1.0.110 Pavo_cristatus AIIM_Pcri_1.0.110 AIIM_Pcri_1.0.99 Pavo_cristatus AIIM_Pcri_1.0.99 Paxillus_involutus_atcc_200175_gca_000827475 Paxillus_involutus_atcc_200175_gca_000827475 Paxillus_involutus_atcc_200175_gca_000827475 Paxillus_rubicundulus_ve08_2h10_gca_000827395 Paxillus_rubicundulus_ve08_2h10_gca_000827395 Paxillus_rubicundulus_ve08_2h10_gca_000827395 @@ -45196,7 +44972,6 @@ Pelodictyon_luteolum_dsm_273_gca_000012485 Pelodictyon_luteolum_dsm_273_gca_00 Pelodictyon_luteolum_gca_001622165 Pelodictyon_luteolum_gca_001622165 Pelodictyon_luteolum_gca_001622165 Pelodictyon_phaeoclathratiforme_bu_1 Pelodictyon_phaeoclathratiforme_bu_1 Pelodictyon_phaeoclathratiforme_bu_1 Pelodictyon_phaeoclathratiforme_bu_1_gca_000020645 Pelodictyon_phaeoclathratiforme_bu_1_gca_000020645 Pelodictyon_phaeoclathratiforme_bu_1_gca_000020645 -PelSin_1.0.110 Pelodiscus_sinensis PelSin_1.0.110 PelSin_1.0.75 Pelodiscus_sinensis PelSin_1.0.75 PelSin_1.0.99 Pelodiscus_sinensis PelSin_1.0.99 Pelolinea_submarina_gca_003385075 Pelolinea_submarina_gca_003385075 Pelolinea_submarina_gca_003385075 @@ -45229,7 +45004,6 @@ Pelotomaculum_sp_ptau1_bin065_gca_002067395 Pelotomaculum_sp_ptau1_bin065_gca_ Pelotomaculum_thermopropionicum_si Pelotomaculum_thermopropionicum_si Pelotomaculum_thermopropionicum_si Pelotomaculum_thermopropionicum_si_gca_000010565 Pelotomaculum_thermopropionicum_si_gca_000010565 Pelotomaculum_thermopropionicum_si_gca_000010565 Peltaster_fructicola_gca_001592805 Peltaster_fructicola_gca_001592805 Peltaster_fructicola_gca_001592805 -Pelusios_castaneus-1.0.110 Pelusios_castaneus Pelusios_castaneus-1.0.110 Penaeus_chinensis_gca019202785v2rs Penaeus_chinensis_gca019202785v2rs Penaeus_chinensis_gca019202785v2rs Penaeus_japonicus_gca017312705v1 Penaeus_japonicus_gca017312705v1 Penaeus_japonicus_gca017312705v1 Penaeus_monodon_gca015228065v1 Penaeus_monodon_gca015228065v1 Penaeus_monodon_gca015228065v1 @@ -45371,13 +45145,11 @@ Peribacillus_simplex_gca_900000145 Peribacillus_simplex_gca_900000145 Periba Peribacillus_simplex_gca_900156045 Peribacillus_simplex_gca_900156045 Peribacillus_simplex_gca_900156045 Peribacillus_simplex_nbrc_15720_dsm_1321_gca_002243645 Peribacillus_simplex_nbrc_15720_dsm_1321_gca_002243645 Peribacillus_simplex_nbrc_15720_dsm_1321_gca_002243645 Periconia_macrospinosa_gca_003073855 Periconia_macrospinosa_gca_003073855 Periconia_macrospinosa_gca_003073855 -PM.fa.110 Periophthalmus_magnuspinnatus PM.fa.110 PM.fa.99 Periophthalmus_magnuspinnatus PM.fa.99 Periweissella_cryptocerci_gca_004358325 Periweissella_cryptocerci_gca_004358325 Periweissella_cryptocerci_gca_004358325 Perkinsela_sp_ccap_1560_4_gca_001235845 Perkinsela_sp_ccap_1560_4_gca_001235845 Perkinsela_sp_ccap_1560_4_gca_001235845 Perkinsus_marinus_atcc_50983_gca_000006405 Perkinsus_marinus_atcc_50983_gca_000006405 Perkinsus_marinus_atcc_50983_gca_000006405 Permianibacter_aggregans_gca_004363125 Permianibacter_aggregans_gca_004363125 Permianibacter_aggregans_gca_004363125 -HU_Pman_2.1.110 Peromyscus_maniculatus_bairdii HU_Pman_2.1.110 HU_Pman_2.1.99 Peromyscus_maniculatus_bairdii HU_Pman_2.1.99 Peronospora_effusa_gca_003704535 Peronospora_effusa_gca_003704535 Peronospora_effusa_gca_003704535 Peronospora_effusa_gca_003843895 Peronospora_effusa_gca_003843895 Peronospora_effusa_gca_003843895 @@ -45388,7 +45160,6 @@ Pestalotiopsis_fici_w106_1_gca_000516985 Pestalotiopsis_fici_w106_1_gca_000516 Petrimonas_mucosa_gca_900095795 Petrimonas_mucosa_gca_900095795 Petrimonas_mucosa_gca_900095795 Petrimonas_sp_ibaraki_gca_002356435 Petrimonas_sp_ibaraki_gca_002356435 Petrimonas_sp_ibaraki_gca_002356435 Petrocella_atlantisensis_gca_900538275 Petrocella_atlantisensis_gca_900538275 Petrocella_atlantisensis_gca_900538275 -Pmarinus_7.0.110 Petromyzon_marinus Pmarinus_7.0.110 Pmarinus_7.0.75 Petromyzon_marinus Pmarinus_7.0.75 Pmarinus_7.0.99 Petromyzon_marinus Pmarinus_7.0.99 Petrotoga_halophila_dsm_16923_gca_002924615 Petrotoga_halophila_dsm_16923_gca_002924615 Petrotoga_halophila_dsm_16923_gca_002924615 @@ -45453,10 +45224,8 @@ Phascolarctobacterium_succinatutens_gca_001916865 Phascolarctobacterium_succin Phascolarctobacterium_succinatutens_gca_003452535 Phascolarctobacterium_succinatutens_gca_003452535 Phascolarctobacterium_succinatutens_gca_003452535 Phascolarctobacterium_succinatutens_yit_12067 Phascolarctobacterium_succinatutens_yit_12067 Phascolarctobacterium_succinatutens_yit_12067 Phascolarctobacterium_succinatutens_yit_12067_gca_000188175 Phascolarctobacterium_succinatutens_yit_12067_gca_000188175 Phascolarctobacterium_succinatutens_yit_12067_gca_000188175 -phaCin_unsw_v4.1.110 Phascolarctos_cinereus phaCin_unsw_v4.1.110 phaCin_unsw_v4.1.99 Phascolarctos_cinereus phaCin_unsw_v4.1.99 Phaseolus_vulgaris Phaseolus_vulgaris Phaseolus_vulgaris -ASM414374v1.110 Phasianus_colchicus ASM414374v1.110 ASM414374v1.99 Phasianus_colchicus ASM414374v1.99 Phellinidium_pouzarii_gca_004802695 Phellinidium_pouzarii_gca_004802695 Phellinidium_pouzarii_gca_004802695 Phellinus_noxius_gca_002287475 Phellinus_noxius_gca_002287475 Phellinus_noxius_gca_002287475 @@ -45560,7 +45329,6 @@ Phocaeicola_vulgatus_gca_900109635 Phocaeicola_vulgatus_gca_900109635 Phocae Phocaeicola_vulgatus_gca_900445545 Phocaeicola_vulgatus_gca_900445545 Phocaeicola_vulgatus_gca_900445545 Phocaeicola_vulgatus_pc510_gca_000178195 Phocaeicola_vulgatus_pc510_gca_000178195 Phocaeicola_vulgatus_pc510_gca_000178195 Phocaeicola_vulgatus_str_3975_rp4_gca_000699865 Phocaeicola_vulgatus_str_3975_rp4_gca_000699865 Phocaeicola_vulgatus_str_3975_rp4_gca_000699865 -mPhoSin1.pri.110 Phocoena_sinus mPhoSin1.pri.110 Phocoenobacter_uteri_gca_900454895 Phocoenobacter_uteri_gca_900454895 Phocoenobacter_uteri_gca_900454895 Phorcysia_thermohydrogeniphila_gca_004339575 Phorcysia_thermohydrogeniphila_gca_004339575 Phorcysia_thermohydrogeniphila_gca_004339575 Phormidesmis_priestleyi_ana Phormidesmis_priestleyi_ana Phormidesmis_priestleyi_ana @@ -45767,7 +45535,6 @@ Phyllobacterium_sp_yr620_gca_900104165 Phyllobacterium_sp_yr620_gca_900104165 Phyllobacterium_zundukense_gca_002763465 Phyllobacterium_zundukense_gca_002763465 Phyllobacterium_zundukense_gca_002763465 Physcomitrella_patens Physcomitrella_patens Physcomitrella_patens Physcomitrium_patens Physcomitrium_patens Physcomitrium_patens -ASM283717v2.110 Physeter_catodon ASM283717v2.110 ASM283717v2.99 Physeter_catodon ASM283717v2.99 Phytoactinopolyspora_halophila_gca_003287285 Phytoactinopolyspora_halophila_gca_003287285 Phytoactinopolyspora_halophila_gca_003287285 Phytobacter_diazotrophicus_gca_004346725 Phytobacter_diazotrophicus_gca_004346725 Phytobacter_diazotrophicus_gca_004346725 @@ -45813,7 +45580,6 @@ Pigmentiphaga_sp_h8_gca_003854895 Pigmentiphaga_sp_h8_gca_003854895 Pigmenti Pigmentiphaga_sp_nml030171_gca_002188635 Pigmentiphaga_sp_nml030171_gca_002188635 Pigmentiphaga_sp_nml030171_gca_002188635 Pigmentiphaga_sp_nml080357_gca_002188465 Pigmentiphaga_sp_nml080357_gca_002188465 Pigmentiphaga_sp_nml080357_gca_002188465 Pilibacter_termitis_gca_900167335 Pilibacter_termitis_gca_900167335 Pilibacter_termitis_gca_900167335 -ASM277652v2.110 Piliocolobus_tephrosceles ASM277652v2.110 ASM277652v2.99 Piliocolobus_tephrosceles ASM277652v2.99 Piloderma_croceum_f_1598_gca_000827315 Piloderma_croceum_f_1598_gca_000827315 Piloderma_croceum_f_1598_gca_000827315 Pimelobacter_simplex Pimelobacter_simplex Pimelobacter_simplex @@ -46040,19 +45806,13 @@ Pneumocystis_murina_b123_gca_000349005 Pneumocystis_murina_b123_gca_000349005 Pochonia_chlamydosporia_123_gca_000411695 Pochonia_chlamydosporia_123_gca_000411695 Pochonia_chlamydosporia_123_gca_000411695 Pochonia_chlamydosporia_170_gca_001653235 Pochonia_chlamydosporia_170_gca_001653235 Pochonia_chlamydosporia_170_gca_001653235 Pocillopora_damicornis_gca003704095v1 Pocillopora_damicornis_gca003704095v1 Pocillopora_damicornis_gca003704095v1 -PodMur_1.0.110 Podarcis_muralis PodMur_1.0.110 PodMur_1.0.99 Podarcis_muralis PodMur_1.0.99 Podospora_anserina_s_mat__gca_000226545 Podospora_anserina_s_mat__gca_000226545 Podospora_anserina_s_mat__gca_000226545 Podospora_anserina_s_mat_gca_000226545 Podospora_anserina_s_mat_gca_000226545 Podospora_anserina_s_mat_gca_000226545 -PoeFor_5.1.2.110 Poecilia_formosa PoeFor_5.1.2.110 PoeFor_5.1.2.99 Poecilia_formosa PoeFor_5.1.2.99 -P_latipinna-1.0.110 Poecilia_latipinna P_latipinna-1.0.110 P_latipinna-1.0.99 Poecilia_latipinna P_latipinna-1.0.99 -P_mexicana-1.0.110 Poecilia_mexicana P_mexicana-1.0.110 P_mexicana-1.0.99 Poecilia_mexicana P_mexicana-1.0.99 -Guppy_female_1.0_MT.110 Poecilia_reticulata Guppy_female_1.0_MT.110 Guppy_female_1.0_MT.99 Poecilia_reticulata Guppy_female_1.0_MT.99 -pvi1.1.110 Pogona_vitticeps pvi1.1.110 pvi1.1.99 Pogona_vitticeps pvi1.1.99 Pogonomyrmex_barbatus_gca000187915v1rs Pogonomyrmex_barbatus_gca000187915v1rs Pogonomyrmex_barbatus_gca000187915v1rs Pokkaliibacter_plantistimulans_gca_003194385 Pokkaliibacter_plantistimulans_gca_003194385 Pokkaliibacter_plantistimulans_gca_003194385 @@ -46139,7 +45899,6 @@ Pomacea_canaliculata_gca003073045v1 Pomacea_canaliculata_gca003073045v1 Poma Pomphorhynchus_laevis_gca012934845v2gb Pomphorhynchus_laevis_gca012934845v2gb Pomphorhynchus_laevis_gca012934845v2gb PPYG2.75 Pongo_abelii PPYG2.75 PPYG2.99 Pongo_abelii PPYG2.99 -Susie_PABv2.110 Pongo_abelii Susie_PABv2.110 Pontibaca_methylaminivorans_gca_900156525 Pontibaca_methylaminivorans_gca_900156525 Pontibaca_methylaminivorans_gca_900156525 Pontibacillus_chungwhensis_bh030062 Pontibacillus_chungwhensis_bh030062 Pontibacillus_chungwhensis_bh030062 Pontibacillus_chungwhensis_bh030062_gca_000770675 Pontibacillus_chungwhensis_bh030062_gca_000770675 Pontibacillus_chungwhensis_bh030062_gca_000770675 @@ -46645,7 +46404,6 @@ Primorskyibacter_flagellatus_gca_900176485 Primorskyibacter_flagellatus_gca_90 Primorskyibacter_sedentarius_gca_004342065 Primorskyibacter_sedentarius_gca_004342065 Primorskyibacter_sedentarius_gca_004342065 Pristionchus_pacificus Pristionchus_pacificus Pristionchus_pacificus Procambarus_clarkii_gca020424385v2 Procambarus_clarkii_gca020424385v2 Procambarus_clarkii_gca020424385v2 -proCap1.110 Procavia_capensis proCap1.110 proCap1.75 Procavia_capensis proCap1.75 proCap1.99 Procavia_capensis proCap1.99 Prochlorococcus_marinus_str_as9601 Prochlorococcus_marinus_str_as9601 Prochlorococcus_marinus_str_as9601 @@ -46733,7 +46491,6 @@ Prochlorococcus_sp_rs01_gca_001989435 Prochlorococcus_sp_rs01_gca_001989435 Prochlorococcus_sp_ss52 Prochlorococcus_sp_ss52 Prochlorococcus_sp_ss52 Prochlorothrix_hollandica_pcc_9006_gca_000341585 Prochlorothrix_hollandica_pcc_9006_gca_000341585 Prochlorothrix_hollandica_pcc_9006_gca_000341585 Profundibacter_amoris_gca_003544895 Profundibacter_amoris_gca_003544895 Profundibacter_amoris_gca_003544895 -Prosim_1.0.110 Prolemur_simus Prosim_1.0.110 Prosim_1.0.99 Prolemur_simus Prosim_1.0.99 Prolinoborus_fasciculus_gca_900322255 Prolinoborus_fasciculus_gca_900322255 Prolinoborus_fasciculus_gca_900322255 Prolixibacter_denitrificans_gca_003014495 Prolixibacter_denitrificans_gca_003014495 Prolixibacter_denitrificans_gca_003014495 @@ -46926,7 +46683,6 @@ Propionispora_sp_2_2_37 Propionispora_sp_2_2_37 Propionispora_sp_2_2_37 Propionispora_sp_2_2_37_gca_001298735 Propionispora_sp_2_2_37_gca_001298735 Propionispora_sp_2_2_37_gca_001298735 Propionispora_vibrioides_gca_900110485 Propionispora_vibrioides_gca_900110485 Propionispora_vibrioides_gca_900110485 Propionivibrio_dicarboxylicus_gca_900099695 Propionivibrio_dicarboxylicus_gca_900099695 Propionivibrio_dicarboxylicus_gca_900099695 -Pcoq_1.0.110 Propithecus_coquereli Pcoq_1.0.110 Pcoq_1.0.99 Propithecus_coquereli Pcoq_1.0.99 Prosthecobacter_debontii_gca_900167535 Prosthecobacter_debontii_gca_900167535 Prosthecobacter_debontii_gca_900167535 Prosthecobacter_fusiformis_gca_004364345 Prosthecobacter_fusiformis_gca_004364345 Prosthecobacter_fusiformis_gca_004364345 @@ -49748,7 +49504,6 @@ Pseudomonas_yangmingensis_gca_900114825 Pseudomonas_yangmingensis_gca_90011482 Pseudomonas_zeshuii_gca_900141925 Pseudomonas_zeshuii_gca_900141925 Pseudomonas_zeshuii_gca_900141925 Pseudomonas_zhaodongensis_gca_003293815 Pseudomonas_zhaodongensis_gca_003293815 Pseudomonas_zhaodongensis_gca_003293815 Pseudomonas_zhaodongensis_gca_003696365 Pseudomonas_zhaodongensis_gca_003696365 Pseudomonas_zhaodongensis_gca_003696365 -EBS10Xv2-PRI.110 Pseudonaja_textilis EBS10Xv2-PRI.110 EBS10Xv2-PRI.99 Pseudonaja_textilis EBS10Xv2-PRI.99 Pseudonitzschia_multistriata Pseudonitzschia_multistriata Pseudonitzschia_multistriata Pseudonocardia_alni_gca_002813375 Pseudonocardia_alni_gca_002813375 Pseudonocardia_alni_gca_002813375 @@ -49970,7 +49725,6 @@ Psychromonas_sp_psych_6c06_gca_002835465 Psychromonas_sp_psych_6c06_gca_002835 Psychromonas_sp_urea_02u_13_gca_002835995 Psychromonas_sp_urea_02u_13_gca_002835995 Psychromonas_sp_urea_02u_13_gca_002835995 Psychroserpens_sp_njdz02_gca_004843725 Psychroserpens_sp_njdz02_gca_004843725 Psychroserpens_sp_njdz02_gca_004843725 Psychrosphaera_saromensis_gca_002954545 Psychrosphaera_saromensis_gca_002954545 Psychrosphaera_saromensis_gca_002954545 -pteVam1.110 Pteropus_vampyrus pteVam1.110 pteVam1.75 Pteropus_vampyrus pteVam1.75 pteVam1.99 Pteropus_vampyrus pteVam1.99 Pterula_gracilis_gca_004369125 Pterula_gracilis_gca_004369125 Pterula_gracilis_gca_004369125 @@ -49990,7 +49744,6 @@ Pueribacillus_theae_gca_003097615 Pueribacillus_theae_gca_003097615 Pueribac Pukyongia_salina_gca_002966125 Pukyongia_salina_gca_002966125 Pukyongia_salina_gca_002966125 Pukyongiella_litopenaei_gca_003008555 Pukyongiella_litopenaei_gca_003008555 Pukyongiella_litopenaei_gca_003008555 Punctularia_strigosozonata_hhb_11173_ss5_gca_000264995 Punctularia_strigosozonata_hhb_11173_ss5_gca_000264995 Punctularia_strigosozonata_hhb_11173_ss5_gca_000264995 -PunNye1.0.110 Pundamilia_nyererei PunNye1.0.110 PunNye1.0.99 Pundamilia_nyererei PunNye1.0.99 Puniceibacterium_antarcticum_gca_002760615 Puniceibacterium_antarcticum_gca_002760615 Puniceibacterium_antarcticum_gca_002760615 Puniceibacterium_sediminis_gca_900188035 Puniceibacterium_sediminis_gca_900188035 Puniceibacterium_sediminis_gca_900188035 @@ -50019,7 +49772,6 @@ Pustulibacterium_marinum_gca_900116665 Pustulibacterium_marinum_gca_900116665 Puteibacter_caeruleilacunae_gca_005217565 Puteibacter_caeruleilacunae_gca_005217565 Puteibacter_caeruleilacunae_gca_005217565 Putridiphycobacter_roseus_gca_003234935 Putridiphycobacter_roseus_gca_003234935 Putridiphycobacter_roseus_gca_003234935 Pvc_group_bacterium_ex_bugula_neritina_ab1__gca_001730085 Pvc_group_bacterium_ex_bugula_neritina_ab1__gca_001730085 Pvc_group_bacterium_ex_bugula_neritina_ab1__gca_001730085 -Pygocentrus_nattereri-1.0.2.110 Pygocentrus_nattereri Pygocentrus_nattereri-1.0.2.110 Pygocentrus_nattereri-1.0.2.99 Pygocentrus_nattereri Pygocentrus_nattereri-1.0.2.99 Pyramidobacter_piscolens_w5455 Pyramidobacter_piscolens_w5455 Pyramidobacter_piscolens_w5455 Pyramidobacter_piscolens_w5455_gca_000177335 Pyramidobacter_piscolens_w5455_gca_000177335 Pyramidobacter_piscolens_w5455_gca_000177335 @@ -50262,10 +50014,6 @@ Rathayibacter_tritici_gca_001641005 Rathayibacter_tritici_gca_001641005 Rath Rathayibacter_tritici_gca_002931485 Rathayibacter_tritici_gca_002931485 Rathayibacter_tritici_gca_002931485 Rnor_5.0.75 Rattus_norvegicus Rnor_5.0.75 Rnor_6.0.99 Rattus_norvegicus Rnor_6.0.99 -mRatBN7.2.110 Rattus_norvegicus mRatBN7.2.110 -UTH_Rnor_SHRSP_BbbUtx_1.0.110 Rattus_norvegicus_shrspbbbutx UTH_Rnor_SHRSP_BbbUtx_1.0.110 -UTH_Rnor_SHR_Utx.110 Rattus_norvegicus_shrutx UTH_Rnor_SHR_Utx.110 -UTH_Rnor_WKY_Bbb_1.0.110 Rattus_norvegicus_wkybbb UTH_Rnor_WKY_Bbb_1.0.110 Reichenbachiella_agariperforans_gca_900142205 Reichenbachiella_agariperforans_gca_900142205 Reichenbachiella_agariperforans_gca_900142205 Reichenbachiella_faecimaris_gca_900176375 Reichenbachiella_faecimaris_gca_900176375 Reichenbachiella_faecimaris_gca_900176375 Reichenbachiella_sp_5m10_gca_002742335 Reichenbachiella_sp_5m10_gca_002742335 Reichenbachiella_sp_5m10_gca_002742335 @@ -50301,11 +50049,8 @@ Rheinheimera_sp_sa_1_gca_001669775 Rheinheimera_sp_sa_1_gca_001669775 Rheinh Rheinheimera_sp_yqf_1_gca_004005375 Rheinheimera_sp_yqf_1_gca_004005375 Rheinheimera_sp_yqf_1_gca_004005375 Rhinocladiella_mackenziei_cbs_650_93_gca_000835555 Rhinocladiella_mackenziei_cbs_650_93_gca_000835555 Rhinocladiella_mackenziei_cbs_650_93_gca_000835555 KF569996.1 Rhinolophus KF569996.1 -mRhiFer1_v1.p.110 Rhinolophus_ferrumequinum mRhiFer1_v1.p.110 mRhiFer1_v1.p.99 Rhinolophus_ferrumequinum mRhiFer1_v1.p.99 -ASM169854v1.110 Rhinopithecus_bieti ASM169854v1.110 ASM169854v1.99 Rhinopithecus_bieti ASM169854v1.99 -Rrox_v1.110 Rhinopithecus_roxellana Rrox_v1.110 Rrox_v1.99 Rhinopithecus_roxellana Rrox_v1.99 Rhipicephalus_microplus_gca013339725v1 Rhipicephalus_microplus_gca013339725v1 Rhipicephalus_microplus_gca013339725v1 Rhipicephalus_sanguineus_gca013339695v1 Rhipicephalus_sanguineus_gca013339695v1 Rhipicephalus_sanguineus_gca013339695v1 @@ -52028,7 +51773,6 @@ Saccharomonospora_xinjiangensis_xj_54_gca_000258175 Saccharomonospora_xinjiang Saccharomyces_arboricola_h_6_gca_000292725 Saccharomyces_arboricola_h_6_gca_000292725 Saccharomyces_arboricola_h_6_gca_000292725 Saccharomyces_boulardii_nom_inval_gca_001298375 Saccharomyces_boulardii_nom_inval_gca_001298375 Saccharomyces_boulardii_nom_inval_gca_001298375 Saccharomyces_boulardii_nom_inval_gca_001413975 Saccharomyces_boulardii_nom_inval_gca_001413975 Saccharomyces_boulardii_nom_inval_gca_001413975 -R64-1-1.110 Saccharomyces_cerevisiae R64-1-1.110 R64-1-1.75 Saccharomyces_cerevisiae R64-1-1.75 R64-1-1.99 Saccharomyces_cerevisiae R64-1-1.99 Saccharomyces_cerevisiae Saccharomyces_cerevisiae Saccharomyces_cerevisiae @@ -52195,14 +51939,12 @@ Saccoglossus_kowalevskii_gca000003605v1 Saccoglossus_kowalevskii_gca000003605v Saezia_sanguinis_gca_003991585 Saezia_sanguinis_gca_003991585 Saezia_sanguinis_gca_003991585 Sagittula_sp_p11_gca_002814095 Sagittula_sp_p11_gca_002814095 Sagittula_sp_p11_gca_002814095 Sagittula_stellata_e_37 Sagittula_stellata_e_37 Sagittula_stellata_e_37 -SaiBol1.0.110 Saimiri_boliviensis_boliviensis SaiBol1.0.110 SaiBol1.0.99 Saimiri_boliviensis_boliviensis SaiBol1.0.99 Saitoella_complicata_nrrl_y_17804_gca_000227095 Saitoella_complicata_nrrl_y_17804_gca_000227095 Saitoella_complicata_nrrl_y_17804_gca_000227095 Saitoella_complicata_nrrl_y_17804_gca_001661265 Saitoella_complicata_nrrl_y_17804_gca_001661265 Saitoella_complicata_nrrl_y_17804_gca_001661265 Saitozyma_podzolica_gca_003942215 Saitozyma_podzolica_gca_003942215 Saitozyma_podzolica_gca_003942215 Sala_cibi_gca_003722095 Sala_cibi_gca_003722095 Sala_cibi_gca_003722095 Salana_multivorans_gca_003751805 Salana_multivorans_gca_003751805 Salana_multivorans_gca_003751805 -fSalaFa1.1.110 Salarias_fasciatus fSalaFa1.1.110 fSalaFa1.1.99 Salarias_fasciatus fSalaFa1.1.99 Salegentibacter_agarivorans_gca_900113135 Salegentibacter_agarivorans_gca_900113135 Salegentibacter_agarivorans_gca_900113135 Salegentibacter_echinorum_gca_900129445 Salegentibacter_echinorum_gca_900129445 Salegentibacter_echinorum_gca_900129445 @@ -52313,8 +52055,6 @@ Salisediminibacterium_beveridgei_gca_001721685 Salisediminibacterium_beveridge Salisediminibacterium_haloalkalitolerans_gca_900111285 Salisediminibacterium_haloalkalitolerans_gca_900111285 Salisediminibacterium_haloalkalitolerans_gca_900111285 Saliterribacillus_persicus_gca_003337485 Saliterribacillus_persicus_gca_003337485 Saliterribacillus_persicus_gca_003337485 ICSASG_v2.99 Salmo_salar ICSASG_v2.99 -Ssal_v3.1.110 Salmo_salar Ssal_v3.1.110 -fSalTru1.1.110 Salmo_trutta fSalTru1.1.110 fSalTru1.1.99 Salmo_trutta fSalTru1.1.99 Salmonella_bongori_gca_900635485 Salmonella_bongori_gca_900635485 Salmonella_bongori_gca_900635485 Salmonella_bongori_n268_08 Salmonella_bongori_n268_08 Salmonella_bongori_n268_08 @@ -56662,7 +56402,6 @@ Salmonella_enterica_subsp_salamae_serovar_58_l_z13_z28_z6_str_00_0163 Salmonel Salmonella_sp_hmsc13b08_gca_001808015 Salmonella_sp_hmsc13b08_gca_001808015 Salmonella_sp_hmsc13b08_gca_001808015 Salpingoeca_rosetta_gca_000188695 Salpingoeca_rosetta_gca_000188695 Salpingoeca_rosetta_gca_000188695 Salsuginibacillus_halophilus_gca_003014715 Salsuginibacillus_halophilus_gca_003014715 Salsuginibacillus_halophilus_gca_003014715 -HLtupMer3.110 Salvator_merianae HLtupMer3.110 HLtupMer3.99 Salvator_merianae HLtupMer3.99 Samsonia_erythrinae_gca_004342665 Samsonia_erythrinae_gca_004342665 Samsonia_erythrinae_gca_004342665 Sandaracinomonas_limnophila_gca_004005965 Sandaracinomonas_limnophila_gca_004005965 Sandaracinomonas_limnophila_gca_004005965 @@ -56671,7 +56410,6 @@ Sandaracinus_amylolyticus_gca_000737325 Sandaracinus_amylolyticus_gca_00073732 Sandaracinus_sp__gca_002699025 Sandaracinus_sp__gca_002699025 Sandaracinus_sp__gca_002699025 Sandaracinus_sp__gca_002703625 Sandaracinus_sp__gca_002703625 Sandaracinus_sp__gca_002703625 Sandarakinorhabdus_cyanobacteriorum_gca_002251755 Sandarakinorhabdus_cyanobacteriorum_gca_002251755 Sandarakinorhabdus_cyanobacteriorum_gca_002251755 -SLUC_FBN_1.110 Sander_lucioperca SLUC_FBN_1.110 Sanguibacter_antarcticus_gca_002564005 Sanguibacter_antarcticus_gca_002564005 Sanguibacter_antarcticus_gca_002564005 Sanguibacter_gelidistatuariae_gca_900096585 Sanguibacter_gelidistatuariae_gca_900096585 Sanguibacter_gelidistatuariae_gca_900096585 Sanguibacter_keddieii_dsm_10542 Sanguibacter_keddieii_dsm_10542 Sanguibacter_keddieii_dsm_10542 @@ -56713,7 +56451,6 @@ Sarcina_sp_dsm_11001_gca_900101015 Sarcina_sp_dsm_11001_gca_900101015 Sarcin Sarcina_ventriculi_gca_001404895 Sarcina_ventriculi_gca_001404895 Sarcina_ventriculi_gca_001404895 DEVIL7.0.75 Sarcophilus_harrisii DEVIL7.0.75 DEVIL7.0.99 Sarcophilus_harrisii DEVIL7.0.99 -mSarHar1.11.110 Sarcophilus_harrisii mSarHar1.11.110 Sarcoptes_scabiei Sarcoptes_scabiei Sarcoptes_scabiei Scandinavium_goeteborgense_gca_003208195 Scandinavium_goeteborgense_gca_003208195 Scandinavium_goeteborgense_gca_003208195 Scandinavium_goeteborgense_gca_003935895 Scandinavium_goeteborgense_gca_003935895 Scandinavium_goeteborgense_gca_003935895 @@ -56766,14 +56503,11 @@ Schleiferilactobacillus_shenzhenensis_ly_73_gca_000469325 Schleiferilactobacil Schleiferilactobacillus_silagei_jcm_19001_gca_002217945 Schleiferilactobacillus_silagei_jcm_19001_gca_002217945 Schleiferilactobacillus_silagei_jcm_19001_gca_002217945 Schleiferilactobacillus_similis_dsm_23365_jcm_2765_gca_001436595 Schleiferilactobacillus_similis_dsm_23365_jcm_2765_gca_001436595 Schleiferilactobacillus_similis_dsm_23365_jcm_2765_gca_001436595 Schwartzia_succinivorans_dsm_10502_gca_900129225 Schwartzia_succinivorans_dsm_10502_gca_900129225 Schwartzia_succinivorans_dsm_10502_gca_900129225 -mSciVul1.1.110 Sciurus_vulgaris mSciVul1.1.110 Scleroderma_citrinum_foug_a_gca_000827425 Scleroderma_citrinum_foug_a_gca_000827425 Scleroderma_citrinum_foug_a_gca_000827425 -fSclFor1.1.110 Scleropages_formosus fSclFor1.1.110 fSclFor1.1.99 Scleropages_formosus fSclFor1.1.99 Sclerotinia_borealis_f_4128_gca_000503235 Sclerotinia_borealis_f_4128_gca_000503235 Sclerotinia_borealis_f_4128_gca_000503235 Sclerotinia_sclerotiorum Sclerotinia_sclerotiorum Sclerotinia_sclerotiorum Sclerotinia_sclerotiorum_1980_uf_70_gca_001857865 Sclerotinia_sclerotiorum_1980_uf_70_gca_001857865 Sclerotinia_sclerotiorum_1980_uf_70_gca_001857865 -ASM1334776v1.110 Scophthalmus_maximus ASM1334776v1.110 ASM318616v1.99 Scophthalmus_maximus ASM318616v1.99 Scopulibacillus_darangshiensis_gca_004341035 Scopulibacillus_darangshiensis_gca_004341035 Scopulibacillus_darangshiensis_gca_004341035 Scytalidium_lignicola_gca_002812745 Scytalidium_lignicola_gca_002812745 Scytalidium_lignicola_gca_002812745 @@ -56890,11 +56624,8 @@ Serinicoccus_hydrothermalis_gca_001685415 Serinicoccus_hydrothermalis_gca_0016 Serinicoccus_sp_cnj_927_gca_001942435 Serinicoccus_sp_cnj_927_gca_001942435 Serinicoccus_sp_cnj_927_gca_001942435 Serinicoccus_sp_cua_874_gca_001942225 Serinicoccus_sp_cua_874_gca_001942225 Serinicoccus_sp_cua_874_gca_001942225 Serinicoccus_sp_jlt9 Serinicoccus_sp_jlt9 Serinicoccus_sp_jlt9 -SCA1.110 Serinus_canaria SCA1.110 SCA1.99 Serinus_canaria SCA1.99 -Sdu_1.0.110 Seriola_dumerili Sdu_1.0.110 Sdu_1.0.99 Seriola_dumerili Sdu_1.0.99 -Sedor1.110 Seriola_lalandi_dorsalis Sedor1.110 Sedor1.99 Seriola_lalandi_dorsalis Sedor1.99 Serpentinicella_alkaliphila_gca_004345905 Serpentinicella_alkaliphila_gca_004345905 Serpentinicella_alkaliphila_gca_004345905 Serpentinimonas_maccroryi_gca_000828915 Serpentinimonas_maccroryi_gca_000828915 Serpentinimonas_maccroryi_gca_000828915 @@ -57885,11 +57616,8 @@ Sinirhodobacter_populi_gca_004022585 Sinirhodobacter_populi_gca_004022585 Si Sinobaca_qinghaiensis_gca_003610495 Sinobaca_qinghaiensis_gca_003610495 Sinobaca_qinghaiensis_gca_003610495 Sinobacteraceae_bacterium_gca_003730135 Sinobacteraceae_bacterium_gca_003730135 Sinobacteraceae_bacterium_gca_003730135 Sinobacterium_caligoides_gca_003752585 Sinobacterium_caligoides_gca_003752585 Sinobacterium_caligoides_gca_003752585 -SAMN03320099.WGS_v1.1.110 Sinocyclocheilus_anshuiensis SAMN03320099.WGS_v1.1.110 SAMN03320099.WGS_v1.1.99 Sinocyclocheilus_anshuiensis SAMN03320099.WGS_v1.1.99 -SAMN03320097.WGS_v1.1.110 Sinocyclocheilus_grahami SAMN03320097.WGS_v1.1.110 SAMN03320097.WGS_v1.1.99 Sinocyclocheilus_grahami SAMN03320097.WGS_v1.1.99 -SAMN03320098_v1.1.110 Sinocyclocheilus_rhinocerous SAMN03320098_v1.1.110 SAMN03320098_v1.1.99 Sinocyclocheilus_rhinocerous SAMN03320098_v1.1.99 Sinomicrobium_oceani_gca_900119185 Sinomicrobium_oceani_gca_900119185 Sinomicrobium_oceani_gca_900119185 Sinomicrobium_pectinilyticum_gca_003725735 Sinomicrobium_pectinilyticum_gca_003725735 Sinomicrobium_pectinilyticum_gca_003725735 @@ -58069,20 +57797,16 @@ Sorangium_cellulosum_so_ce56 Sorangium_cellulosum_so_ce56 Sorangium_cellulos Sorangium_cellulosum_so_ce56_gca_000067165 Sorangium_cellulosum_so_ce56_gca_000067165 Sorangium_cellulosum_so_ce56_gca_000067165 Sordaria_macrospora_gca_008692325 Sordaria_macrospora_gca_008692325 Sordaria_macrospora_gca_008692325 Sordaria_macrospora_k_hell_gca_000182805 Sordaria_macrospora_k_hell_gca_000182805 Sordaria_macrospora_k_hell_gca_000182805 -COMMON_SHREW1.110 Sorex_araneus COMMON_SHREW1.110 COMMON_SHREW1.75 Sorex_araneus COMMON_SHREW1.75 COMMON_SHREW1.99 Sorex_araneus COMMON_SHREW1.99 Sorghum_bicolor Sorghum_bicolor Sorghum_bicolor Sparassis_crispa_gca_003851025 Sparassis_crispa_gca_003851025 Sparassis_crispa_gca_003851025 Spartobacteria_bacterium_lr76_gca_003054655 Spartobacteria_bacterium_lr76_gca_003054655 Spartobacteria_bacterium_lr76_gca_003054655 -fSpaAur1.1.110 Sparus_aurata fSpaAur1.1.110 fSpaAur1.1.99 Sparus_aurata fSpaAur1.1.99 Spathaspora_passalidarum_nrrl_y_27907_gca_000223485 Spathaspora_passalidarum_nrrl_y_27907_gca_000223485 Spathaspora_passalidarum_nrrl_y_27907_gca_000223485 Spathaspora_sp_ja1_gca_003676035 Spathaspora_sp_ja1_gca_003676035 Spathaspora_sp_ja1_gca_003676035 -ASM240643v1.110 Spermophilus_dauricus ASM240643v1.110 ASM240643v1.99 Spermophilus_dauricus ASM240643v1.99 Sphaceloma_murrayae_gca_002895985 Sphaceloma_murrayae_gca_002895985 Sphaceloma_murrayae_gca_002895985 -fSphaOr1.1.110 Sphaeramia_orbicularis fSphaOr1.1.110 fSphaOr1.1.99 Sphaeramia_orbicularis fSphaOr1.1.99 Sphaerisporangium_album_gca_003323745 Sphaerisporangium_album_gca_003323745 Sphaerisporangium_album_gca_003323745 Sphaerisporangium_cinnabarinum_gca_003052455 Sphaerisporangium_cinnabarinum_gca_003052455 Sphaerisporangium_cinnabarinum_gca_003052455 @@ -58103,7 +57827,6 @@ Sphaerotilus_hippei_gca_003201595 Sphaerotilus_hippei_gca_003201595 Sphaerot Sphaerotilus_natans_subsp_natans_dsm_6575 Sphaerotilus_natans_subsp_natans_dsm_6575 Sphaerotilus_natans_subsp_natans_dsm_6575 Sphaerotilus_natans_subsp_natans_dsm_6575_gca_000689195 Sphaerotilus_natans_subsp_natans_dsm_6575_gca_000689195 Sphaerotilus_natans_subsp_natans_dsm_6575_gca_000689195 Sphaerulina_musiva_so2202_gca_000320565 Sphaerulina_musiva_so2202_gca_000320565 Sphaerulina_musiva_so2202_gca_000320565 -ASM311381v1.110 Sphenodon_punctatus ASM311381v1.110 ASM311381v1.99 Sphenodon_punctatus ASM311381v1.99 Sphingobacteriaceae_bacterium_gca_002319075 Sphingobacteriaceae_bacterium_gca_002319075 Sphingobacteriaceae_bacterium_gca_002319075 Sphingobacteriaceae_bacterium_gca_004176105 Sphingobacteriaceae_bacterium_gca_004176105 Sphingobacteriaceae_bacterium_gca_004176105 @@ -58755,7 +58478,6 @@ Stachybotrys_chartarum_ibt_40288_gca_000732765 Stachybotrys_chartarum_ibt_4028 Stachybotrys_chartarum_ibt_40293_gca_000732565 Stachybotrys_chartarum_ibt_40293_gca_000732565 Stachybotrys_chartarum_ibt_40293_gca_000732565 Stachybotrys_chartarum_ibt_7711_gca_000730325 Stachybotrys_chartarum_ibt_7711_gca_000730325 Stachybotrys_chartarum_ibt_7711_gca_000730325 Stachybotrys_chlorohalonata_ibt_40285_gca_000732775 Stachybotrys_chlorohalonata_ibt_40285_gca_000732775 Stachybotrys_chlorohalonata_ibt_40285_gca_000732775 -ASM869450v1.110 Stachyris_ruficeps ASM869450v1.110 Stackebrandtia_nassauensis_dsm_44728 Stackebrandtia_nassauensis_dsm_44728 Stackebrandtia_nassauensis_dsm_44728 Stackebrandtia_nassauensis_dsm_44728_gca_000024545 Stackebrandtia_nassauensis_dsm_44728_gca_000024545 Stackebrandtia_nassauensis_dsm_44728_gca_000024545 Stagonospora_sp_src1lsm3a_gca_001644525 Stagonospora_sp_src1lsm3a_gca_001644525 Stagonospora_sp_src1lsm3a_gca_001644525 @@ -64312,7 +64034,6 @@ Starkeya_novella_dsm_506_gca_000092925 Starkeya_novella_dsm_506_gca_000092925 Starkeya_novella_gca_003241485 Starkeya_novella_gca_003241485 Starkeya_novella_gca_003241485 Starkeya_novella_gca_003241695 Starkeya_novella_gca_003241695 Starkeya_novella_gca_003241695 Steccherinum_ochraceum_gca_004332605 Steccherinum_ochraceum_gca_004332605 Steccherinum_ochraceum_gca_004332605 -Stegastes_partitus-1.0.2.110 Stegastes_partitus Stegastes_partitus-1.0.2.110 Stegastes_partitus-1.0.2.99 Stegastes_partitus Stegastes_partitus-1.0.2.99 Stegodyphus_dumicola_gca010614865v2rs Stegodyphus_dumicola_gca010614865v2rs Stegodyphus_dumicola_gca010614865v2rs Stegodyphus_mimosarum Stegodyphus_mimosarum Stegodyphus_mimosarum @@ -72530,12 +72251,9 @@ Streptosporangium_sp_caverna__gca_003203775 Streptosporangium_sp_caverna__gca_ Streptosporangium_subroseum_gca_900188345 Streptosporangium_subroseum_gca_900188345 Streptosporangium_subroseum_gca_900188345 Strigamia_maritima Strigamia_maritima Strigamia_maritima Strigomonas_culicis_gca_000442495 Strigomonas_culicis_gca_000442495 Strigomonas_culicis_gca_000442495 -bStrHab1_v1.p.110 Strigops_habroptila bStrHab1_v1.p.110 bStrHab1_v1.p.99 Strigops_habroptila bStrHab1_v1.p.99 -Soccid_v01.110 Strix_occidentalis_caurina Soccid_v01.110 Strongylocentrotus_purpuratus Strongylocentrotus_purpuratus Strongylocentrotus_purpuratus Strongyloides_ratti Strongyloides_ratti Strongyloides_ratti -ASM69896v1.110 Struthio_camelus_australis ASM69896v1.110 ASM69896v1.99 Struthio_camelus_australis ASM69896v1.99 Stutzerimonas_balearica_dsm_6083_gca_900103375 Stutzerimonas_balearica_dsm_6083_gca_900103375 Stutzerimonas_balearica_dsm_6083_gca_900103375 Stutzerimonas_chloritidismutans_aw_1_gca_000495915 Stutzerimonas_chloritidismutans_aw_1_gca_000495915 Stutzerimonas_chloritidismutans_aw_1_gca_000495915 @@ -72770,34 +72488,20 @@ Sunxiuqinia_dokdonensis_gca_001270965 Sunxiuqinia_dokdonensis_gca_001270965 Sunxiuqinia_elliptica_gca_004361925 Sunxiuqinia_elliptica_gca_004361925 Sunxiuqinia_elliptica_gca_004361925 Sunxiuqinia_elliptica_gca_900113005 Sunxiuqinia_elliptica_gca_900113005 Sunxiuqinia_elliptica_gca_900113005 Superficieibacter_electus_gca_002915575 Superficieibacter_electus_gca_002915575 Superficieibacter_electus_gca_002915575 -meerkat_22Aug2017_6uvM2_HiC.110 Suricata_suricatta meerkat_22Aug2017_6uvM2_HiC.110 meerkat_22Aug2017_6uvM2_HiC.99 Suricata_suricatta meerkat_22Aug2017_6uvM2_HiC.99 Sscrofa10.2.75 Sus_scrofa Sscrofa10.2.75 -Sscrofa11.1.110 Sus_scrofa Sscrofa11.1.110 Sscrofa11.1.99 Sus_scrofa Sscrofa11.1.99 -Bamei_pig_v1.110 Sus_scrofa_bamei Bamei_pig_v1.110 Bamei_pig_v1.99 Sus_scrofa_bamei Bamei_pig_v1.99 -Berkshire_pig_v1.110 Sus_scrofa_berkshire Berkshire_pig_v1.110 Berkshire_pig_v1.99 Sus_scrofa_berkshire Berkshire_pig_v1.99 -Hampshire_pig_v1.110 Sus_scrofa_hampshire Hampshire_pig_v1.110 Hampshire_pig_v1.99 Sus_scrofa_hampshire Hampshire_pig_v1.99 -Jinhua_pig_v1.110 Sus_scrofa_jinhua Jinhua_pig_v1.110 Jinhua_pig_v1.99 Sus_scrofa_jinhua Jinhua_pig_v1.99 -Landrace_pig_v1.110 Sus_scrofa_landrace Landrace_pig_v1.110 Landrace_pig_v1.99 Sus_scrofa_landrace Landrace_pig_v1.99 -Large_White_v1.110 Sus_scrofa_largewhite Large_White_v1.110 Large_White_v1.99 Sus_scrofa_largewhite Large_White_v1.99 -Meishan_pig_v1.110 Sus_scrofa_meishan Meishan_pig_v1.110 Meishan_pig_v1.99 Sus_scrofa_meishan Meishan_pig_v1.99 -Pietrain_pig_v1.110 Sus_scrofa_pietrain Pietrain_pig_v1.110 Pietrain_pig_v1.99 Sus_scrofa_pietrain Pietrain_pig_v1.99 -Rongchang_pig_v1.110 Sus_scrofa_rongchang Rongchang_pig_v1.110 Rongchang_pig_v1.99 Sus_scrofa_rongchang Rongchang_pig_v1.99 -Tibetan_Pig_v2.110 Sus_scrofa_tibetan Tibetan_Pig_v2.110 Tibetan_Pig_v2.99 Sus_scrofa_tibetan Tibetan_Pig_v2.99 -USMARCv1.0.110 Sus_scrofa_usmarc USMARCv1.0.110 USMARCv1.0.99 Sus_scrofa_usmarc USMARCv1.0.99 -minipig_v1.0.110 Sus_scrofa_wuzhishan minipig_v1.0.110 minipig_v1.0.99 Sus_scrofa_wuzhishan minipig_v1.0.99 Sutcliffiella_cohnii_gca_002250055 Sutcliffiella_cohnii_gca_002250055 Sutcliffiella_cohnii_gca_002250055 Sutcliffiella_horikoshii_gca_002157855 Sutcliffiella_horikoshii_gca_002157855 Sutcliffiella_horikoshii_gca_002157855 @@ -72951,7 +72655,6 @@ test_t_urticae_p3 T. test_t_urticae_p3 Tabrizicola_alkalilacus_gca_003443995 Tabrizicola_alkalilacus_gca_003443995 Tabrizicola_alkalilacus_gca_003443995 Tabrizicola_piscis_gca_003940805 Tabrizicola_piscis_gca_003940805 Tabrizicola_piscis_gca_003940805 Tabrizicola_sp_th137_gca_002855575 Tabrizicola_sp_th137_gca_002855575 Tabrizicola_sp_th137_gca_002855575 -bTaeGut1_v1.p.110 Taeniopygia_guttata bTaeGut1_v1.p.110 bTaeGut1_v1.p.99 Taeniopygia_guttata bTaeGut1_v1.p.99 taeGut3.2.4.75 Taeniopygia_guttata taeGut3.2.4.75 Tahibacter_aquaticus_gca_004363655 Tahibacter_aquaticus_gca_004363655 Tahibacter_aquaticus_gca_004363655 @@ -72960,7 +72663,6 @@ Taibaiella_soli_gca_003236175 Taibaiella_soli_gca_003236175 Taibaiella_soli_ Taibaiella_sp_kbw10_gca_003852495 Taibaiella_sp_kbw10_gca_003852495 Taibaiella_sp_kbw10_gca_003852495 FUGU4.75 Takifugu_rubripes FUGU4.75 Takifugu_rubripes Takifugu_rubripes Takifugu_rubripes -fTakRub1.2.110 Takifugu_rubripes fTakRub1.2.110 fTakRub1.2.99 Takifugu_rubripes fTakRub1.2.99 Talaromyces_amestolkiae_gca_001896365 Talaromyces_amestolkiae_gca_001896365 Talaromyces_amestolkiae_gca_001896365 Talaromyces_atroroseus_gca_001907595 Talaromyces_atroroseus_gca_001907595 Talaromyces_atroroseus_gca_001907595 @@ -73112,7 +72814,6 @@ Terrabacter_sp_soil810_gca_001429645 Terrabacter_sp_soil810_gca_001429645 Te Terrabacter_sp_soil811 Terrabacter_sp_soil811 Terrabacter_sp_soil811 Terrabacter_sp_soil811_gca_001429655 Terrabacter_sp_soil811_gca_001429655 Terrabacter_sp_soil811_gca_001429655 Terracoccus_luteus_gca_003635045 Terracoccus_luteus_gca_003635045 Terracoccus_luteus_gca_003635045 -T_m_triunguis-2.0.110 Terrapene_carolina_triunguis T_m_triunguis-2.0.110 T_m_triunguis-2.0.99 Terrapene_carolina_triunguis T_m_triunguis-2.0.99 Terribacillus_aidingensis Terribacillus_aidingensis Terribacillus_aidingensis Terribacillus_aidingensis_gca_900215625 Terribacillus_aidingensis_gca_900215625 Terribacillus_aidingensis_gca_900215625 @@ -73216,7 +72917,6 @@ Tetragenococcus_muriaticus_pmc_11_5_gca_000747235 Tetragenococcus_muriaticus_p Tetragenococcus_osmophilus_gca_003795125 Tetragenococcus_osmophilus_gca_003795125 Tetragenococcus_osmophilus_gca_003795125 Tetrahymena_thermophila Tetrahymena_thermophila Tetrahymena_thermophila Tetranychus_urticae Tetranychus_urticae Tetranychus_urticae -TETRAODON8.110 Tetraodon_nigroviridis TETRAODON8.110 TETRAODON8.75 Tetraodon_nigroviridis TETRAODON8.75 TETRAODON8.99 Tetraodon_nigroviridis TETRAODON8.99 Tetrapisispora_blattae_cbs_6284_gca_000315915 Tetrapisispora_blattae_cbs_6284_gca_000315915 Tetrapisispora_blattae_cbs_6284_gca_000315915 @@ -73741,7 +73441,6 @@ Thermus_thermophilus_jl_18 Thermus_thermophilus_jl_18 Thermus_thermophilus_j Thermus_thermophilus_jl_18_gca_000258245 Thermus_thermophilus_jl_18_gca_000258245 Thermus_thermophilus_jl_18_gca_000258245 Thermus_thermophilus_sg0_5jp17_16 Thermus_thermophilus_sg0_5jp17_16 Thermus_thermophilus_sg0_5jp17_16 Thermus_thermophilus_sg0_5jp17_16_gca_000214845 Thermus_thermophilus_sg0_5jp17_16_gca_000214845 Thermus_thermophilus_sg0_5jp17_16_gca_000214845 -Tgel_1.0.110 Theropithecus_gelada Tgel_1.0.110 Tgel_1.0.99 Theropithecus_gelada Tgel_1.0.99 Thielavia_terrestris_nrrl_8126_gca_000226115 Thielavia_terrestris_nrrl_8126_gca_000226115 Thielavia_terrestris_nrrl_8126_gca_000226115 Thielaviopsis_punctulata_gca_000968615 Thielaviopsis_punctulata_gca_000968615 Thielaviopsis_punctulata_gca_000968615 @@ -74193,7 +73892,6 @@ Tumebacillus_flagellatus Tumebacillus_flagellatus Tumebacillus_flagellatus Tumebacillus_flagellatus_gca_000714935 Tumebacillus_flagellatus_gca_000714935 Tumebacillus_flagellatus_gca_000714935 Tumebacillus_permanentifrigoris_gca_003148565 Tumebacillus_permanentifrigoris_gca_003148565 Tumebacillus_permanentifrigoris_gca_003148565 Tumebacillus_sp_bk434_gca_004340785 Tumebacillus_sp_bk434_gca_004340785 Tumebacillus_sp_bk434_gca_004340785 -TREESHREW.110 Tupaia_belangeri TREESHREW.110 TREESHREW.75 Tupaia_belangeri TREESHREW.75 TREESHREW.99 Tupaia_belangeri TREESHREW.99 Turicella_otitidis Turicella_otitidis Turicella_otitidis @@ -74210,7 +73908,6 @@ Turicibacter_sp_hgf1 Turicibacter_sp_hgf1 Turicibacter_sp_hgf1 Turicimonas_muris_gca_002221595 Turicimonas_muris_gca_002221595 Turicimonas_muris_gca_002221595 Turneriella_parva_dsm_21527 Turneriella_parva_dsm_21527 Turneriella_parva_dsm_21527 Turneriella_parva_dsm_21527_gca_000266885 Turneriella_parva_dsm_21527_gca_000266885 Turneriella_parva_dsm_21527_gca_000266885 -turTru1.110 Tursiops_truncatus turTru1.110 turTru1.75 Tursiops_truncatus turTru1.75 turTru1.99 Tursiops_truncatus turTru1.99 Tychonema_bourrellyi_fem_gt703_gca_002412335 Tychonema_bourrellyi_fem_gt703_gca_002412335 Tychonema_bourrellyi_fem_gt703_gca_002412335 @@ -74277,14 +73974,10 @@ Ureibacillus_massiliensis_4400831_cip_108448_ccug_49529_gca_000772965 Ureibaci Ureibacillus_sinduriensis_blb_1_jcm_15800_gca_000772955 Ureibacillus_sinduriensis_blb_1_jcm_15800_gca_000772955 Ureibacillus_sinduriensis_blb_1_jcm_15800_gca_000772955 Ureibacillus_thermophilus_gca_004331915 Ureibacillus_thermophilus_gca_004331915 Ureibacillus_thermophilus_gca_004331915 Ureibacillus_xyleni_gca_900217795 Ureibacillus_xyleni_gca_900217795 Ureibacillus_xyleni_gca_900217795 -ASM342692v1.110 Urocitellus_parryii ASM342692v1.110 ASM342692v1.99 Urocitellus_parryii ASM342692v1.99 lekn01 Ursidibacter lekn01 -ASM334442v1.110 Ursus_americanus ASM334442v1.110 ASM334442v1.99 Ursus_americanus ASM334442v1.99 -UrsMar_1.0.110 Ursus_maritimus UrsMar_1.0.110 UrsMar_1.0.99 Ursus_maritimus UrsMar_1.0.99 -ASM966005v1.110 Ursus_thibetanus_thibetanus ASM966005v1.110 Uruburuella_suis_gca_004341385 Uruburuella_suis_gca_004341385 Uruburuella_suis_gca_004341385 Ustilaginoidea_virens_gca_000687475 Ustilaginoidea_virens_gca_000687475 Ustilaginoidea_virens_gca_000687475 Ustilaginoidea_virens_gca_000965225 Ustilaginoidea_virens_gca_000965225 Ustilaginoidea_virens_gca_000965225 @@ -74329,7 +74022,6 @@ Vandammella_animalimorsus_gca_003703375 Vandammella_animalimorsus_gca_00370337 Vanderwaltozyma_polyspora_dsm_70294_gca_000150035 Vanderwaltozyma_polyspora_dsm_70294_gca_000150035 Vanderwaltozyma_polyspora_dsm_70294_gca_000150035 Vannielia_litorea_gca_900142295 Vannielia_litorea_gca_900142295 Vannielia_litorea_gca_900142295 Vanrija_humicola_gca_008065275 Vanrija_humicola_gca_008065275 Vanrija_humicola_gca_008065275 -ASM479886v1.110 Varanus_komodoensis ASM479886v1.110 ASM479886v1.99 Varanus_komodoensis ASM479886v1.99 Varibaculum_cambriense Varibaculum_cambriense Varibaculum_cambriense Varibaculum_cambriense_dora_20_gca_000508625 Varibaculum_cambriense_dora_20_gca_000508625 Varibaculum_cambriense_dora_20_gca_000508625 @@ -75665,7 +75357,6 @@ Vibrionales_bacterium_c3r12_gca_003318175 Vibrionales_bacterium_c3r12_gca_0033 Vibrionales_bacterium_swat_3 Vibrionales_bacterium_swat_3 Vibrionales_bacterium_swat_3 Victivallales_bacterium_ccug_44730_gca_002998355 Victivallales_bacterium_ccug_44730_gca_002998355 Victivallales_bacterium_ccug_44730_gca_002998355 Victivallis_vadensis_gca_003096415 Victivallis_vadensis_gca_003096415 Victivallis_vadensis_gca_003096415 -vicPac1.110 Vicugna_pacos vicPac1.110 vicPac1.75 Vicugna_pacos vicPac1.75 vicPac1.99 Vicugna_pacos vicPac1.99 Vigna_angularis Vigna_angularis Vigna_angularis @@ -75710,7 +75401,6 @@ Vogesella_sp_eb Vogesella_sp_eb Vogesella_sp_eb Vogesella_sp_eb_gca_001037925 Vogesella_sp_eb_gca_001037925 Vogesella_sp_eb_gca_001037925 Vogesella_sp_lig4_gca_900090205 Vogesella_sp_lig4_gca_900090205 Vogesella_sp_lig4_gca_900090205 Volucribacter_psittacicida_gca_004339025 Volucribacter_psittacicida_gca_004339025 Volucribacter_psittacicida_gca_004339025 -bare-nosed_wombat_genome_assembly.110 Vombatus_ursinus bare-nosed_wombat_genome_assembly.110 bare-nosed_wombat_genome_assembly.99 Vombatus_ursinus bare-nosed_wombat_genome_assembly.99 Vulcaniibacterium_tengchongense_gca_003814555 Vulcaniibacterium_tengchongense_gca_003814555 Vulcaniibacterium_tengchongense_gca_003814555 Vulcanisaeta_distributa_dsm_14429 Vulcanisaeta_distributa_dsm_14429 Vulcanisaeta_distributa_dsm_14429 @@ -75724,7 +75414,6 @@ Vulcanisaeta_sp_mg_3 Vulcanisaeta_sp_mg_3 Vulcanisaeta_sp_mg_3 Vulcanisaeta_sp_osp_8 Vulcanisaeta_sp_osp_8 Vulcanisaeta_sp_osp_8 Vulgatibacter_incomptus Vulgatibacter_incomptus Vulgatibacter_incomptus Vulgatibacter_incomptus_gca_001263175 Vulgatibacter_incomptus_gca_001263175 Vulgatibacter_incomptus_gca_001263175 -VulVul2.2.110 Vulpes_vulpes VulVul2.2.110 VulVul2.2.99 Vulpes_vulpes VulVul2.2.99 Waddlia_chondrophila_wsu_86_1044 Waddlia_chondrophila_wsu_86_1044 Waddlia_chondrophila_wsu_86_1044 Waddlia_chondrophila_wsu_86_1044_gca_000092785 Waddlia_chondrophila_wsu_86_1044_gca_000092785 Waddlia_chondrophila_wsu_86_1044_gca_000092785 @@ -76379,7 +76068,6 @@ Xenococcus_sp_pcc_7305 Xenococcus_sp_pcc_7305 Xenococcus_sp_pcc_7305 Xenococcus_sp_pcc_7305_gca_000332055 Xenococcus_sp_pcc_7305_gca_000332055 Xenococcus_sp_pcc_7305_gca_000332055 Xenophilus_sp_ap218f_gca_002213445 Xenophilus_sp_ap218f_gca_002213445 Xenophilus_sp_ap218f_gca_002213445 JGI_4.2.75 Xenopus_tropicalis JGI_4.2.75 -UCB_Xtro_10.0.110 Xenopus_tropicalis UCB_Xtro_10.0.110 Xenopus_tropicalis_v9.1.99 Xenopus_tropicalis Xenopus_tropicalis_v9.1.99 Xenorhabdus_beddingii_gca_002127545 Xenorhabdus_beddingii_gca_002127545 Xenorhabdus_beddingii_gca_002127545 Xenorhabdus_bovienii Xenorhabdus_bovienii Xenorhabdus_bovienii @@ -76444,9 +76132,7 @@ Xenorhabdus_szentirmaii_dsm_16338_gca_000531455 Xenorhabdus_szentirmaii_dsm_16 Xenorhabdus_thuongxuanensis_gca_001908095 Xenorhabdus_thuongxuanensis_gca_001908095 Xenorhabdus_thuongxuanensis_gca_001908095 Xenorhabdus_vietnamensis_gca_002127535 Xenorhabdus_vietnamensis_gca_002127535 Xenorhabdus_vietnamensis_gca_002127535 Xinfangfangia_humi_gca_900609055 Xinfangfangia_humi_gca_900609055 Xinfangfangia_humi_gca_900609055 -Xiphophorus_couchianus-4.0.1.110 Xiphophorus_couchianus Xiphophorus_couchianus-4.0.1.110 Xiphophorus_couchianus-4.0.1.99 Xiphophorus_couchianus Xiphophorus_couchianus-4.0.1.99 -X_maculatus-5.0-male.110 Xiphophorus_maculatus X_maculatus-5.0-male.110 X_maculatus-5.0-male.99 Xiphophorus_maculatus X_maculatus-5.0-male.99 Xipmac4.4.2.75 Xiphophorus_maculatus Xipmac4.4.2.75 Xylanibacterium_ulmi_gca_004216535 Xylanibacterium_ulmi_gca_004216535 Xylanibacterium_ulmi_gca_004216535 @@ -76980,7 +76666,6 @@ Yoonia_vestfoldensis_gca_002158905 Yoonia_vestfoldensis_gca_002158905 Yoonia Youngiibacter_fragilis_232_1 Youngiibacter_fragilis_232_1 Youngiibacter_fragilis_232_1 Youngiibacter_fragilis_232_1_gca_000495435 Youngiibacter_fragilis_232_1_gca_000495435 Youngiibacter_fragilis_232_1_gca_000495435 Youngimonas_vesicularis_gca_004799325 Youngimonas_vesicularis_gca_004799325 Youngimonas_vesicularis_gca_004799325 -mZalCal1.pri.110 Zalophus_californianus mZalCal1.pri.110 Zasmidium_cellare_atcc_36951_gca_010093935 Zasmidium_cellare_atcc_36951_gca_010093935 Zasmidium_cellare_atcc_36951_gca_010093935 Zavarzinia_aquatilis_gca_003173035 Zavarzinia_aquatilis_gca_003173035 Zavarzinia_aquatilis_gca_003173035 Zavarzinia_compransoris_gca_003173055 Zavarzinia_compransoris_gca_003173055 Zavarzinia_compransoris_gca_003173055 @@ -77015,13 +76700,11 @@ Zobellia_galactanivorans Zobellia_galactanivorans Zobellia_galactanivorans Zobellia_galactanivorans_gca_000973105 Zobellia_galactanivorans_gca_000973105 Zobellia_galactanivorans_gca_000973105 Zobellia_uliginosa_gca_900156625 Zobellia_uliginosa_gca_900156625 Zobellia_uliginosa_gca_900156625 Zongyanglinia_marina_gca_005771405 Zongyanglinia_marina_gca_005771405 Zongyanglinia_marina_gca_005771405 -Zonotrichia_albicollis-1.0.1.110 Zonotrichia_albicollis Zonotrichia_albicollis-1.0.1.110 Zonotrichia_albicollis-1.0.1.99 Zonotrichia_albicollis Zonotrichia_albicollis-1.0.1.99 Zoogloeaceae_bacteirum_par_f_2_gca_003054515 Zoogloeaceae_bacteirum_par_f_2_gca_003054515 Zoogloeaceae_bacteirum_par_f_2_gca_003054515 Zooshikella_ganghwensis_gca_002261065 Zooshikella_ganghwensis_gca_002261065 Zooshikella_ganghwensis_gca_002261065 Zootermopsis_nevadensis Zootermopsis_nevadensis Zootermopsis_nevadensis Zopfia_rhizophila_cbs_207_26_gca_010093925 Zopfia_rhizophila_cbs_207_26_gca_010093925 Zopfia_rhizophila_cbs_207_26_gca_010093925 -ASM128173v1.110 Zosterops_lateralis_melanops ASM128173v1.110 Zunongwangia_atlantica_22ii14_10f7_gca_002094855 Zunongwangia_atlantica_22ii14_10f7_gca_002094855 Zunongwangia_atlantica_22ii14_10f7_gca_002094855 Zunongwangia_mangrovi_gca_900112105 Zunongwangia_mangrovi_gca_900112105 Zunongwangia_mangrovi_gca_900112105 Zunongwangia_profunda_gca_003541615 Zunongwangia_profunda_gca_003541615 Zunongwangia_profunda_gca_003541615 diff --git a/pom.xml b/pom.xml index eef71a0c..5b5e9943 100644 --- a/pom.xml +++ b/pom.xml @@ -163,7 +163,7 @@ maven-compiler-plugin 3.8.1 - 11 + 21 ISO-8859-1 true true diff --git a/src/main/java/org/snpeff/interval/Genome.java b/src/main/java/org/snpeff/interval/Genome.java index 7f42bbfd..7c84c83d 100644 --- a/src/main/java/org/snpeff/interval/Genome.java +++ b/src/main/java/org/snpeff/interval/Genome.java @@ -6,10 +6,7 @@ import java.util.Comparator; import java.util.HashMap; import java.util.Iterator; -import java.util.LinkedList; import java.util.List; -import java.util.Properties; - import org.snpeff.binseq.GenomicSequences; import org.snpeff.fileIterator.FastaFileIterator; import org.snpeff.serializer.MarkerSerializer; From b10b19732155139496117d576f66265e1e18c65a Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Fri, 2 Aug 2024 11:20:35 -0400 Subject: [PATCH 04/21] Project updated --- src/main/java/org/snpeff/vcf/VcfEntry.java | 5 ----- src/main/java/org/snpeff/vcf/VcfHeader.java | 3 ++- src/main/java/org/snpeff/vcf/VcfHeaderEntry.java | 4 +++- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index 7f6bdd84..acb3bfdf 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -36,17 +36,12 @@ public enum AlleleFrequencyType { } public static final String FILTER_PASS = "PASS"; - public static final char WITHIN_FIELD_SEP = ','; public static final String SUB_FIELD_SEP = ";"; - public static final String[] EMPTY_STRING_ARRAY = new String[0]; - public static final double ALLELE_FEQUENCY_COMMON = 0.05; public static final double ALLELE_FEQUENCY_LOW = 0.01; - public static final Pattern INFO_KEY_PATTERN = Pattern.compile("[\\p{Alpha}_][\\p{Alnum}._]*"); - public static final String VCF_INFO_END = "END"; // Imprecise variants // In order to report sequencing data evidence for both variant and non-variant positions in the genome, the VCF diff --git a/src/main/java/org/snpeff/vcf/VcfHeader.java b/src/main/java/org/snpeff/vcf/VcfHeader.java index e5650563..b626b601 100644 --- a/src/main/java/org/snpeff/vcf/VcfHeader.java +++ b/src/main/java/org/snpeff/vcf/VcfHeader.java @@ -1,5 +1,6 @@ package org.snpeff.vcf; +import java.io.Serializable; import java.util.ArrayList; import java.util.Collection; import java.util.HashMap; @@ -15,7 +16,7 @@ * * @author pablocingolani */ -public class VcfHeader { +public class VcfHeader implements Serializable { public static final String INFO_PREFIX = "##INFO="; public static final String FORMAT_PREFIX = "##FORMAT="; diff --git a/src/main/java/org/snpeff/vcf/VcfHeaderEntry.java b/src/main/java/org/snpeff/vcf/VcfHeaderEntry.java index c0b76348..3de9a139 100644 --- a/src/main/java/org/snpeff/vcf/VcfHeaderEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfHeaderEntry.java @@ -1,5 +1,7 @@ package org.snpeff.vcf; +import java.io.Serializable; + /** * Represents a info elements in a VCF file's header * @@ -9,7 +11,7 @@ * * @author pablocingolani */ -public class VcfHeaderEntry { +public class VcfHeaderEntry implements Serializable { protected String line; protected String id; From b46def3dfd9bf5e795836e2be1c8cca862522ae6 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Mon, 9 Sep 2024 09:39:16 -0400 Subject: [PATCH 05/21] Project updated --- .vscode/launch.json | 2 +- src/main/java/org/snpeff/fileIterator/VcfFileIterator.java | 2 +- .../java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java | 5 +++-- .../java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java | 2 +- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/.vscode/launch.json b/.vscode/launch.json index e7381bca..8d133908 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -10,7 +10,7 @@ "request": "launch", "mainClass": "org.snpeff.SnpEff", "projectName": "SnpEff", - "args": "build -v hg19" + "args": "-v -tag MANE_Select GRCh38.mane.1.2.ensembl /Users/kqrw311/snpEff/z.vcf" }, ] } \ No newline at end of file diff --git a/src/main/java/org/snpeff/fileIterator/VcfFileIterator.java b/src/main/java/org/snpeff/fileIterator/VcfFileIterator.java index 852102c3..647725ce 100644 --- a/src/main/java/org/snpeff/fileIterator/VcfFileIterator.java +++ b/src/main/java/org/snpeff/fileIterator/VcfFileIterator.java @@ -128,7 +128,7 @@ public VcfEntry parseVcfLine(String line) { try { if (line.startsWith("#")) { // Header? header.addLine(line); - } else if ((line.length() > 0) && (!line.startsWith("#"))) { // Vcf entry? + } else if (line.length() > 0) { // Vcf entry? return new VcfEntry(this, line, lineNum, parseNow); } } catch (Throwable t) { diff --git a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java index 50f93989..7a9f485a 100644 --- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java +++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java @@ -229,7 +229,8 @@ void add(String trId, String seq, int lineNum, boolean check) { ); // Sanity check - if (checkNumOk && totalOk <= 0) fatalErrorNoTranscriptsChecked(); + + if (checkNumOk && (totalOk + totalErrors) <= 0 && (totalNotFound > 0)) fatalErrorNoTranscriptsChecked(); return perc; } @@ -244,7 +245,7 @@ void fatalErrorNoTranscriptsChecked() { int maxTrIds = 20; sb.append("Transcript IDs from database (sample):\n" + sampleTrIds(maxTrIds)); sb.append("Transcript IDs from database (fasta file):\n" + sampleTrIdsFasta(maxTrIds)); - Log.fatalError("No CDS checked. This is might be caused by differences in FASTA file transcript IDs respect to database's transcript's IDs.\n" + sb); + Log.fatalError("No CDS checked. This might be caused by differences in FASTA file transcript IDs respect to database's transcript's IDs.\n" + sb); } /** diff --git a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java index 491e906f..826362a0 100644 --- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java +++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java @@ -1007,7 +1007,7 @@ public void usage(String message) { } System.err.println("snpEff version " + VERSION); - System.err.println("Usage: snpEff [eff] [options] genome_version [input_file]"); + System.err.println("Usage: snpEff [ann] [options] genome_version [input_file]"); System.err.println("\n"); System.err.println("\tvariants_file : Default is STDIN"); System.err.println("\n"); From 2e3069feadb396e77e6a6e3742c03bf22f188bd9 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Mon, 9 Sep 2024 09:50:40 -0400 Subject: [PATCH 06/21] Project updated --- .vscode/launch.json | 2 +- .../java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.vscode/launch.json b/.vscode/launch.json index 8d133908..0cd90995 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -10,7 +10,7 @@ "request": "launch", "mainClass": "org.snpeff.SnpEff", "projectName": "SnpEff", - "args": "-v -tag MANE_Select GRCh38.mane.1.2.ensembl /Users/kqrw311/snpEff/z.vcf" + "args": "-v -noOut -tag MANE_Select GRCh38.mane.1.2.ensembl /Users/kqrw311/snpEff/z.vcf" }, ] } \ No newline at end of file diff --git a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java index 826362a0..0146fdf6 100644 --- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java +++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java @@ -1043,6 +1043,7 @@ public void usage(String message) { System.err.println("\t-lof : Add loss of function (LOF) and Nonsense mediated decay (NMD) tags."); System.err.println("\t-noHgvs : Do not add HGVS annotations."); System.err.println("\t-noLof : Do not add LOF and NMD annotations."); + System.err.println("\t-noOut : Do not write the output resuts to STDOUT (maybe used for debugging)."); System.err.println("\t-noShiftHgvs : Do not shift variants according to HGVS notation (most 3prime end)."); System.err.println("\t-oicr : Add OICR tag in VCF file. Default: " + useOicr); System.err.println("\t-sequenceOntology : Use Sequence Ontology terms. Default: " + useSequenceOntology); From 4190a386278525859ccbd169b7b004c8dfb1c7bb Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Thu, 12 Sep 2024 13:50:50 -0400 Subject: [PATCH 07/21] Imprved parsing --- .vscode/launch.json | 2 +- src/main/java/org/snpeff/interval/Marker.java | 1 + .../interval/codonChange/CodonChangeInv.java | 12 +++++- src/main/java/org/snpeff/vcf/VcfEntry.java | 7 +++- .../integration/TestCasesIntegrationBase.java | 4 ++ .../integration/TestCasesIntegrationZzz2.java | 28 ++++++++++++++ .../testCases/unity/TestCasesVcf.java | 38 +++++++++++++++++++ tests/integration/zzz2/test_inv.vcf | 3 ++ tests/unity/vcf/test_inv.vcf | 3 ++ 9 files changed, 94 insertions(+), 4 deletions(-) create mode 100644 src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java create mode 100644 tests/integration/zzz2/test_inv.vcf create mode 100644 tests/unity/vcf/test_inv.vcf diff --git a/.vscode/launch.json b/.vscode/launch.json index 0cd90995..8807eb42 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -10,7 +10,7 @@ "request": "launch", "mainClass": "org.snpeff.SnpEff", "projectName": "SnpEff", - "args": "-v -noOut -tag MANE_Select GRCh38.mane.1.2.ensembl /Users/kqrw311/snpEff/z.vcf" + "args": "-v -noOut testHg3882Chr22 /Users/kqrw311/snpEff/z.vcf" }, ] } \ No newline at end of file diff --git a/src/main/java/org/snpeff/interval/Marker.java b/src/main/java/org/snpeff/interval/Marker.java index 7fbb1119..36eeb64e 100644 --- a/src/main/java/org/snpeff/interval/Marker.java +++ b/src/main/java/org/snpeff/interval/Marker.java @@ -9,6 +9,7 @@ import org.snpeff.snpEffect.VariantEffect; import org.snpeff.snpEffect.VariantEffects; import org.snpeff.util.Gpr; +import org.snpeff.util.Log; import java.lang.reflect.Constructor; import java.util.ArrayList; diff --git a/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java b/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java index 4801bec1..3d222b17 100644 --- a/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java +++ b/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java @@ -7,6 +7,7 @@ import org.snpeff.snpEffect.EffectType; import org.snpeff.snpEffect.VariantEffects; import org.snpeff.snpEffect.VariantEffect.EffectImpact; +import org.snpeff.util.Log; /** * Calculate codon changes produced by an inversion @@ -55,7 +56,16 @@ void exons() { // Is the variant affecting a coding part of the exon? // If so, then this is a HIGH impact effect. - if (cdsMarker != null && variant.intersect(ex).intersects(cdsMarker)) impact = EffectImpact.HIGH; + if (cdsMarker != null ) { + var intersect = variant.intersect(ex); + Log.debug("INTERSECT:" // + + "\n\tCDS marker: " + cdsMarker + + "\n\tExon: " + ex + + "\n\tVariant: " + variant + + "\n\tIntersect: " + intersect + ); + if (intersect != null && intersect.intersects(cdsMarker)) impact = EffectImpact.HIGH; + } // Is the whole exon inverted or just part of it? EffectType effType = variant.includes(ex) ? EffectType.EXON_INVERSION : EffectType.EXON_INVERSION_PARTIAL; diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index acb3bfdf..db9a574d 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -53,10 +53,12 @@ public enum AlleleFrequencyType { public static final String VCF_ALT_NON_REF = "<*>"; // See VCF 4.2 section "5.5 Representing unspecified alleles and REF-only blocks (gVCF)" public static final String VCF_ALT_NON_REF_gVCF = ""; // NON_REF tag for ALT field (only in gVCF fields) public static final String VCF_ALT_MISSING_REF = "*"; // The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion (see VCF 4.3 spec., ALT definition) + public static final String VCF_ALT_INV = ""; // Inversion public static final String[] VCF_ALT_NON_REF_gVCF_ARRAY = { VCF_ALT_NON_REF_gVCF }; public static final String[] VCF_ALT_NON_REF_ARRAY = { VCF_ALT_NON_REF }; public static final String[] VCF_ALT_MISSING_REF_ARRAY = { VCF_ALT_MISSING_REF }; + public static final String[] VCF_ALT_INV_ARRAY = { VCF_ALT_INV }; public static final String VCF_INFO_HOMS = "HO"; public static final String VCF_INFO_HETS = "HE"; @@ -1074,6 +1076,7 @@ String[] parseAltSingle(String altsStr) { if (altsStr.equals(VCF_ALT_NON_REF)) { return VCF_ALT_NON_REF_ARRAY; } if (altsStr.equals(VCF_ALT_MISSING_REF)) { return VCF_ALT_MISSING_REF_ARRAY; } if (altsStr.equals(VCF_ALT_NON_REF_gVCF)) { return VCF_ALT_NON_REF_gVCF_ARRAY; } + if (altsStr.equals(VCF_ALT_INV)) { return VCF_ALT_INV_ARRAY; } // SNP IUB conversion table String alts[]; @@ -1539,8 +1542,8 @@ List variants(Chromosome chromo, int start, String reference, String al list = Variant.factory(chromo, startNew, ch, "", id, false); } else if (alt.startsWith("(); list.add(var); diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java index d3cd0951..604a03c9 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java @@ -882,6 +882,10 @@ public String showTranscripts(Genome genome, boolean hideProtein) { return sb.toString(); } + public List snpEffect(String genome, String vcfFile) { + return snpEffect(genome, vcfFile, null, EffFormatVersion.FORMAT_EFF_4); + } + /** * Calculate snp effect for an input VCF file */ diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java new file mode 100644 index 00000000..0e9a9d2d --- /dev/null +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java @@ -0,0 +1,28 @@ +package org.snpeff.snpEffect.testCases.integration; + +import org.junit.jupiter.api.Test; +import static org.junit.jupiter.api.Assertions.assertTrue; + +/** + * Test case + */ +public class TestCasesIntegrationZzz2 extends TestCasesIntegrationBase { + + @Test + public void test_01() { + verbose = true; + var vcfEntries = snpEffect("testHg3882Chr22", path("test_inv.vcf")); + + if (verbose) { + for (var vcfEntry : vcfEntries) { + System.out.println(vcfEntry); + for (var vcfEffect : vcfEntry.getVcfEffects()) { + System.out.println("\t" + vcfEffect); + } + } + } + + assertTrue(vcfEntries.size() > 0); + } + +} diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 20dbcb65..40907b9f 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -715,4 +715,42 @@ public void test_36_cleanupUnderscores() { assertEquals("a1_b2c3_d4", VcfEntry.cleanUnderscores("_____a1_b2c3_______d4________")); } + @Test + public void test_37_inversions_parsing() { + Log.debug("Test"); + String vcfFile = path("test_inv.vcf"); + + VcfFileIterator vcf = new VcfFileIterator(vcfFile); + // Read the first entry + VcfEntry ve = vcf.next(); + if (verbose) Log.info(ve); + var vars = ve.variants(); + var inv = (Variant) vars.get(0); + var refExpected = "GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC"; + var startExpected = 27360852; + var endExpected = startExpected + refExpected.length() - 1; + var altExpected = new StringBuilder(refExpected).reverse().toString(); + assertEquals(VariantType.INV, inv.getVariantType()); + assertEquals(refExpected, inv.getReference()); + assertEquals(altExpected, inv.getAlt()); + assertEquals(startExpected, inv.getStart()); + assertEquals(endExpected, inv.getEnd()); + + // Read the second entry + ve = vcf.next(); + if (verbose) Log.info(ve); + vars = ve.variants(); + inv = (Variant) vars.get(0); + refExpected = "CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; + altExpected = new StringBuilder(refExpected).reverse().toString(); + startExpected = 37973491; + endExpected = startExpected + refExpected.length() - 1; + assertEquals(VariantType.INV, inv.getVariantType()); + assertEquals(refExpected, inv.getReference()); + assertEquals(altExpected, inv.getAlt()); + assertEquals(startExpected, inv.getStart()); + assertEquals(endExpected, inv.getEnd()); + } + + } diff --git a/tests/integration/zzz2/test_inv.vcf b/tests/integration/zzz2/test_inv.vcf new file mode 100644 index 00000000..4e3e82ee --- /dev/null +++ b/tests/integration/zzz2/test_inv.vcf @@ -0,0 +1,3 @@ +#chr1 27360853 DRAGEN:INV:962:0:0:1:15:0 GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC . MinSomaticScore END=27360932;SVTYPE=INV;SVLEN=-79;CIGAR=1M79I79D;CONTIG=CACTATGTTCTTGTGGCGCAGGCGTCTGTGAAGAGCGATCTCTTCATGCAGGGGCTGAGAGAACCTGAGGGGAGGTAAGGGAGAGAGGAAAGGGACCGAGGTGGGCAGAGAAGCCCCGCCCATCCCACGCCAGCCTGGCCCCGCCCCAAGGACCCGCCCCGCCCACAAGCCCTCTCCGACCTTCCCCACCCTTACTACCCTGCCCACAGGACCCTCCAGACCTCAATCCCGCCCGCACGGTCCTGGCTGTTCCGCCCACGGGCCCAGTCCACAGGGCTCGAACTCTCAGGTCCTACGAGCCCGCCCACTAGGCCCCGCCCACAGGAGCCGCTCCGCTCGTGGCCCGGCTCACTCGGCCCTCGCGAGCCCTCAGCCCCACCCGCGCTGCCACGCACCGCACCTGCTGTCCCGCTCCGGGATCTCCTTGATGGCGATGCGCACCCTCGTGTGGCGATCGCGGCCCGCGTACACCACCCCATACGTGCCCTTGCCCAGCACCAGCCGCTCGCCCGTCTCCGTGTACTCATAATCAAACTGCCGGGCGCGGGGGAGATGTTGGAGGTGAGGACGCGGGACTGGGAGCTCGCGGAGGGCGAGGGGCCGCGGGCCCTGCTGAACTCCCATCTCACCCCGCGCCCTCCGCCTCCTCCGCGGGCGCCGTGGAATCCGGGTTCGTCACCCAGGCCTGGATCAGGCCGCAGAACCTGAAGGTGGGGGAGGTCAGACCCGCGGGAGGGGCATCTTGGTCCCCACCTAAGCCGGAGCATCCAACGGACGTCGTCCCTTTCTTTCCCCCACTCCCCCCCGGGCATCCTGGCCCTCAGAGTACCCCGACCATGAAAGGCTGCGCACCACTGGCAGTGCCCTACGCTGGGGAAGCACAGCTGGACGTCCTGAGCCGGGGGGAGTGCATAGAGGAAGCAGCAGCGCTCGTCGCGCTTTGAGGCG;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 1272,0:4027,3:3624,3 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B_1_Lymphoma +chr22 37973492 DRAGEN:INV:49554:0:0:0:16:0 CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT . MinSomaticScore END=37973553;SVTYPE=INV;SVLEN=-61;CIGAR=1M61I61D;CONTIG=AACCTCCTTCTCCTCTGTCCAGCCTGTTCTCCTGGGGCTTTGCTGCTGGAGCCTGGATGGGGCGGGTGGGTCATCAGGGCAGTGAGCCAGACAGAAAGCCCCCCGACCTGTCAGCCTCTTCAGCCTCCTCAGCCTCCTCCACTGCCACCACCAGGCCTGAGGTGGGCAAGGAACAGGGCACACAGGCTGGGGGCAGGGGCTGGGCGGGGGGTGGTGGCGACAGGGCCCCAGTCCCACAGCCCCACACACTGGGAGCAGCCAGTATATACGACACTGTCCCGGCCCTAAAGGGGGCCCTGAGGGGCTGGGGTCAGAGATGGCCGTGTAGAGGGGCCGCTGCGAGGGCCCCATATAGGAGAAGGCCGAGTAGAGGCCAGAGGCCTGGCCCGAGTGGCCATAATAGGGTCCTGAGGGCTGATGGTCAGAGTAGTCAAACTGGGGGCGGGAGATGGAGGGGAAGGCTGAGCCATAGTGGGGCAGGCTGAGGGAGGTGTAGGCGATCTGTGAGGTGGATGGCTGGTCGGTGTAGTGTGGGGGCCCCTGGGGCCCCGCGGTCTCTGTCTTCACCTGGGCTTTGGCATCCACACCAGGTGGTGAGACCGTGGGCAGAGCCACGCCTGGTGGCTTGGAGATCCAGGCGGAGTGTCCACTGGCCACGGCCAGGGCACTGCCCAGCCCATAGCCGGCTGCTGAGTAGCTGCTCACATGGCCTGGGTGCCCATTGGGCGGCAGGTACTGGTCCAACTCAGCCACATCAAAGGTCTCCATGTTGGACATTACCTCGTGGCTGATCTCACCAATGTCCACGTTGCCGAAGTCGATGTGAGGCTTCCCGCCCTCCCCCATGGAGCGCCCGTCCCGCTTCGGGTCTGCCTTGCCCGACTGCAGCTCTGTCTTCGGGGTGGTTGGAGGGGTGGGTGGGCCATGGCTCTGGCCTGGGTAGAAGGGAGACAGAGAGAGAGAGCGCAAGGGGGAAGCAGGTTAGAGGCAGGTGGGCGCACGTGAACTTCCATGGTTCACCTTCAGGCAGCGGGTGCCTCTGGGAAAACCTTGTAAGTTTCACATTTTGGCAGCATGAGTCGGGTTTTTTTTTGTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGACTGGAGTGCAGTGGCGCCATCTCGGCTCACTGCA;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 705,0:2396,2:2155,2 diff --git a/tests/unity/vcf/test_inv.vcf b/tests/unity/vcf/test_inv.vcf new file mode 100644 index 00000000..c32afb6d --- /dev/null +++ b/tests/unity/vcf/test_inv.vcf @@ -0,0 +1,3 @@ +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B_1_Lymphoma +chr1 27360853 DRAGEN:INV:962:0:0:1:15:0 GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC . MinSomaticScore END=27360932;SVTYPE=INV;SVLEN=-79;CIGAR=1M79I79D;CONTIG=CACTATGTTCTTGTGGCGCAGGCGTCTGTGAAGAGCGATCTCTTCATGCAGGGGCTGAGAGAACCTGAGGGGAGGTAAGGGAGAGAGGAAAGGGACCGAGGTGGGCAGAGAAGCCCCGCCCATCCCACGCCAGCCTGGCCCCGCCCCAAGGACCCGCCCCGCCCACAAGCCCTCTCCGACCTTCCCCACCCTTACTACCCTGCCCACAGGACCCTCCAGACCTCAATCCCGCCCGCACGGTCCTGGCTGTTCCGCCCACGGGCCCAGTCCACAGGGCTCGAACTCTCAGGTCCTACGAGCCCGCCCACTAGGCCCCGCCCACAGGAGCCGCTCCGCTCGTGGCCCGGCTCACTCGGCCCTCGCGAGCCCTCAGCCCCACCCGCGCTGCCACGCACCGCACCTGCTGTCCCGCTCCGGGATCTCCTTGATGGCGATGCGCACCCTCGTGTGGCGATCGCGGCCCGCGTACACCACCCCATACGTGCCCTTGCCCAGCACCAGCCGCTCGCCCGTCTCCGTGTACTCATAATCAAACTGCCGGGCGCGGGGGAGATGTTGGAGGTGAGGACGCGGGACTGGGAGCTCGCGGAGGGCGAGGGGCCGCGGGCCCTGCTGAACTCCCATCTCACCCCGCGCCCTCCGCCTCCTCCGCGGGCGCCGTGGAATCCGGGTTCGTCACCCAGGCCTGGATCAGGCCGCAGAACCTGAAGGTGGGGGAGGTCAGACCCGCGGGAGGGGCATCTTGGTCCCCACCTAAGCCGGAGCATCCAACGGACGTCGTCCCTTTCTTTCCCCCACTCCCCCCCGGGCATCCTGGCCCTCAGAGTACCCCGACCATGAAAGGCTGCGCACCACTGGCAGTGCCCTACGCTGGGGAAGCACAGCTGGACGTCCTGAGCCGGGGGGAGTGCATAGAGGAAGCAGCAGCGCTCGTCGCGCTTTGAGGCG;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 1272,0:4027,3:3624,3 +chr22 37973492 DRAGEN:INV:49554:0:0:0:16:0 CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT . MinSomaticScore END=37973553;SVTYPE=INV;SVLEN=-61;CIGAR=1M61I61D;CONTIG=AACCTCCTTCTCCTCTGTCCAGCCTGTTCTCCTGGGGCTTTGCTGCTGGAGCCTGGATGGGGCGGGTGGGTCATCAGGGCAGTGAGCCAGACAGAAAGCCCCCCGACCTGTCAGCCTCTTCAGCCTCCTCAGCCTCCTCCACTGCCACCACCAGGCCTGAGGTGGGCAAGGAACAGGGCACACAGGCTGGGGGCAGGGGCTGGGCGGGGGGTGGTGGCGACAGGGCCCCAGTCCCACAGCCCCACACACTGGGAGCAGCCAGTATATACGACACTGTCCCGGCCCTAAAGGGGGCCCTGAGGGGCTGGGGTCAGAGATGGCCGTGTAGAGGGGCCGCTGCGAGGGCCCCATATAGGAGAAGGCCGAGTAGAGGCCAGAGGCCTGGCCCGAGTGGCCATAATAGGGTCCTGAGGGCTGATGGTCAGAGTAGTCAAACTGGGGGCGGGAGATGGAGGGGAAGGCTGAGCCATAGTGGGGCAGGCTGAGGGAGGTGTAGGCGATCTGTGAGGTGGATGGCTGGTCGGTGTAGTGTGGGGGCCCCTGGGGCCCCGCGGTCTCTGTCTTCACCTGGGCTTTGGCATCCACACCAGGTGGTGAGACCGTGGGCAGAGCCACGCCTGGTGGCTTGGAGATCCAGGCGGAGTGTCCACTGGCCACGGCCAGGGCACTGCCCAGCCCATAGCCGGCTGCTGAGTAGCTGCTCACATGGCCTGGGTGCCCATTGGGCGGCAGGTACTGGTCCAACTCAGCCACATCAAAGGTCTCCATGTTGGACATTACCTCGTGGCTGATCTCACCAATGTCCACGTTGCCGAAGTCGATGTGAGGCTTCCCGCCCTCCCCCATGGAGCGCCCGTCCCGCTTCGGGTCTGCCTTGCCCGACTGCAGCTCTGTCTTCGGGGTGGTTGGAGGGGTGGGTGGGCCATGGCTCTGGCCTGGGTAGAAGGGAGACAGAGAGAGAGAGCGCAAGGGGGAAGCAGGTTAGAGGCAGGTGGGCGCACGTGAACTTCCATGGTTCACCTTCAGGCAGCGGGTGCCTCTGGGAAAACCTTGTAAGTTTCACATTTTGGCAGCATGAGTCGGGTTTTTTTTTGTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGACTGGAGTGCAGTGGCGCCATCTCGGCTCACTGCA;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 705,0:2396,2:2155,2 From 9828b7bb40798a61af225a7aaa165989ddc22c61 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Thu, 12 Sep 2024 13:53:10 -0400 Subject: [PATCH 08/21] Imprved parsing --- src/main/java/org/snpeff/vcf/VcfEntry.java | 4 ++-- .../org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java | 5 ++++- 2 files changed, 6 insertions(+), 3 deletions(-) diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index db9a574d..b214feb7 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -1549,8 +1549,8 @@ List variants(Chromosome chromo, int start, String reference, String al list.add(var); } else if (alt.startsWith("(); list.add(var); diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 40907b9f..4cf6e8df 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -726,16 +726,19 @@ public void test_37_inversions_parsing() { if (verbose) Log.info(ve); var vars = ve.variants(); var inv = (Variant) vars.get(0); + if (verbose) Log.info(inv); var refExpected = "GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC"; var startExpected = 27360852; var endExpected = startExpected + refExpected.length() - 1; var altExpected = new StringBuilder(refExpected).reverse().toString(); + assertEquals(1, vars.size()); assertEquals(VariantType.INV, inv.getVariantType()); assertEquals(refExpected, inv.getReference()); assertEquals(altExpected, inv.getAlt()); assertEquals(startExpected, inv.getStart()); assertEquals(endExpected, inv.getEnd()); + // Read the second entry ve = vcf.next(); if (verbose) Log.info(ve); @@ -745,6 +748,7 @@ public void test_37_inversions_parsing() { altExpected = new StringBuilder(refExpected).reverse().toString(); startExpected = 37973491; endExpected = startExpected + refExpected.length() - 1; + assertEquals(1, vars.size()); assertEquals(VariantType.INV, inv.getVariantType()); assertEquals(refExpected, inv.getReference()); assertEquals(altExpected, inv.getAlt()); @@ -752,5 +756,4 @@ public void test_37_inversions_parsing() { assertEquals(endExpected, inv.getEnd()); } - } From e2dc2df326ab3903a9adca48d9b1aff1a321bf88 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Fri, 13 Sep 2024 05:08:02 -0400 Subject: [PATCH 09/21] Project updated --- config/snpEff.test.config | 1 + src/main/java/org/snpeff/SnpEff.java | 13 ++++- .../java/org/snpeff/interval/Variant.java | 4 +- .../interval/codonChange/CodonChangeInv.java | 7 --- .../snpEffect/commandLine/SnpEffCmdEff.java | 2 + .../integration/TestCasesIntegrationBase.java | 2 + .../integration/TestCasesIntegrationInv.java | 53 +++++++++++++++++++ .../integration/TestCasesIntegrationZzz2.java | 28 ---------- tests/integration/{zzz2 => inv}/test_inv.vcf | 0 9 files changed, 73 insertions(+), 37 deletions(-) create mode 100644 src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java delete mode 100644 src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java rename tests/integration/{zzz2 => inv}/test_inv.vcf (100%) diff --git a/config/snpEff.test.config b/config/snpEff.test.config index ed8470a5..5f4a2259 100644 --- a/config/snpEff.test.config +++ b/config/snpEff.test.config @@ -114,6 +114,7 @@ test_GRCh38.mane.1.0.ensembl.chr19.genome : GRCh38 MANE 1.0 chr19 test_GRCh38.mane.1.0.ensembl.chr21.genome : GRCh38 MANE 1.0 chr21 test_GRCh38.mane.1.0.refseq.chr21.genome : GRCh38 MANE 1.0 chr21 test_GRCh38.mane.1.0.refseq.chr19.genome : GRCh38 MANE 1.0 chr19 +test_GRCh38.mane.1.2.ensembl.chr1.genome : GRCh38 MANE 1.2 chr1 #--- # Test cases: Non-human diff --git a/src/main/java/org/snpeff/SnpEff.java b/src/main/java/org/snpeff/SnpEff.java index f2abde72..2b663cc4 100644 --- a/src/main/java/org/snpeff/SnpEff.java +++ b/src/main/java/org/snpeff/SnpEff.java @@ -130,6 +130,7 @@ public enum OutputFormat { protected boolean strict = false; // Only use transcript that have been validated protected boolean saveOutput = false; // Save output to buffer (instead of printing it to STDOUT) protected boolean suppressOutput = false; // Only used for debugging purposes + protected boolean testing = false; // Testing mode protected boolean verbose; // Be verbose protected Boolean treatAllAsProteinCoding = null; // Only use coding genes. Default is 'null' which means 'auto' protected int numWorkers = Gpr.NUM_CORES; // Max number of threads (if multi-threaded version is available) @@ -392,6 +393,7 @@ void copyValues(SnpEff cmd) { cmd.configOverride = configOverride; cmd.tags = tags; cmd.tagsNo = tagsNo; + cmd.testing = testing; } /** @@ -1261,6 +1263,10 @@ public void setSupressOutput(boolean suppressOutput) { this.suppressOutput = suppressOutput; } + public void setTesting(boolean testing) { + this.testing = testing; + } + public void setUpDownStreamLength(int upDownStreamLength) { this.upDownStreamLength = upDownStreamLength; } @@ -1274,7 +1280,12 @@ public void setVerbose(boolean verbose) { */ @Override public void usage(String message) { - if (message != null) System.err.println("Error: " + message + "\n"); + if (message != null) { + System.err.println("Error: " + message + "\n"); + System.err.println("Command line :\t" + commandLineStr(false) + "\n"); + if( testing ) throw new RuntimeException("Error: " + message); + } + System.err.println("SnpEff version " + VERSION); System.err.println("Usage: snpEff [command] [options] [files]"); System.err.println("\nRun 'java -jar snpEff.jar command' for help on each specific command"); diff --git a/src/main/java/org/snpeff/interval/Variant.java b/src/main/java/org/snpeff/interval/Variant.java index 20cfc319..37911c6e 100644 --- a/src/main/java/org/snpeff/interval/Variant.java +++ b/src/main/java/org/snpeff/interval/Variant.java @@ -6,6 +6,7 @@ import org.snpeff.snpEffect.EffectType; import org.snpeff.util.GprSeq; import org.snpeff.util.IubString; +import org.snpeff.util.Log; import java.util.LinkedList; import java.util.List; @@ -367,7 +368,8 @@ public boolean isStructuralHuge() { // We only check if: a) that the chromosome exists and b) chromosome it is not small if (chr != null && chr.size() > HUGE_DELETION_SIZE_THRESHOLD) { - double ratio = (chr.size() > 0 ? size() / ((double) chr.size()) : 0); + double ratio = size() / ((double) chr.size()); + Log.debug("Structural variant size: " + size() + ", chromosome size: " + chr.size() + ", ratio: " + ratio); return size() > HUGE_DELETION_SIZE_THRESHOLD || ratio > HUGE_DELETION_RATIO_THRESHOLD; } diff --git a/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java b/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java index 3d222b17..6b75ec26 100644 --- a/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java +++ b/src/main/java/org/snpeff/interval/codonChange/CodonChangeInv.java @@ -58,18 +58,11 @@ void exons() { // If so, then this is a HIGH impact effect. if (cdsMarker != null ) { var intersect = variant.intersect(ex); - Log.debug("INTERSECT:" // - + "\n\tCDS marker: " + cdsMarker - + "\n\tExon: " + ex - + "\n\tVariant: " + variant - + "\n\tIntersect: " + intersect - ); if (intersect != null && intersect.intersects(cdsMarker)) impact = EffectImpact.HIGH; } // Is the whole exon inverted or just part of it? EffectType effType = variant.includes(ex) ? EffectType.EXON_INVERSION : EffectType.EXON_INVERSION_PARTIAL; - effectNoCodon(ex, effType, impact); } } diff --git a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java index 0146fdf6..196ea59c 100644 --- a/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java +++ b/src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdEff.java @@ -209,6 +209,7 @@ public boolean annotate(VcfEntry vcfEntry) { } catch (Throwable t) { totalErrs++; Log.error(t, "Error while processing VCF entry (line " + vcfFile.getLineNum() + ") :\n\t" + vcfEntry + "\n" + t); + if( testing ) throw new RuntimeException("Error while processing VCF entry (line " + vcfFile.getLineNum() + ") :\n\t" + vcfEntry + "\n" + t, t); } finally { if (!printed && !filteredOut) outputFormatter.printSection(vcfEntry); } @@ -1004,6 +1005,7 @@ public void usage(String message) { if (message != null) { System.err.println("Error :\t" + message); System.err.println("Command line :\t" + commandLineStr(false) + "\n"); + if( testing ) throw new RuntimeException("Error: " + message); } System.err.println("snpEff version " + VERSION); diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java index 604a03c9..b2f38847 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationBase.java @@ -907,9 +907,11 @@ public List snpEffect(String genome, String vcfFile, String[] otherArg args.add(vcfFile); SnpEff cmd = new SnpEff(args.toArray(new String[0])); + cmd.setTesting(true); SnpEffCmdEff cmdEff = (SnpEffCmdEff) cmd.cmd(); cmdEff.setVerbose(verbose); cmdEff.setSupressOutput(!verbose); + cmdEff.setTesting(true); if (effFormatVersion != null) cmdEff.setFormatVersion(effFormatVersion); // Run command diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java new file mode 100644 index 00000000..00ffbeb9 --- /dev/null +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java @@ -0,0 +1,53 @@ +package org.snpeff.snpEffect.testCases.integration; + +import org.junit.jupiter.api.Test; +import org.snpeff.snpEffect.EffectType; +import org.snpeff.snpEffect.VariantEffect.EffectImpact; +import org.snpeff.vcf.VcfEntry; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.util.List; + +/** + * Test cases for Inversions + */ +public class TestCasesIntegrationInv extends TestCasesIntegrationBase { + + + void hasInv(List vcfEntries) { + assertTrue(vcfEntries.size() > 0); + var found = false; + for (var vcfEntry : vcfEntries) { + System.out.println(vcfEntry); + for (var vcfEffect : vcfEntry.getVcfEffects()) { + System.out.println("\t" + vcfEffect.getEffectType() + "\t" + vcfEffect); + if( vcfEffect.getEffectType() == EffectType.CHROMOSOME_LARGE_INVERSION + || vcfEffect.getEffectType() == EffectType.EXON_INVERSION + || vcfEffect.getEffectType() == EffectType.EXON_INVERSION_PARTIAL + || vcfEffect.getEffectType() == EffectType.TRANSCRIPT_INVERSION + ) { + assertEquals(EffectImpact.HIGH, vcfEffect.getImpact()); + found = true; + } + } + } + assertTrue(found); + } + + @Test + public void test_01() { + verbose = true; + var vcfEntries = snpEffect("testHg3882Chr22", path("test_inv.vcf")); + hasInv(vcfEntries); + } + + @Test + public void test_02() { + verbose = true; + var vcfEntries = snpEffect("testHg3882Chr22", path("test_inv_02.vcf")); + hasInv(vcfEntries); + } + +} diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java deleted file mode 100644 index 0e9a9d2d..00000000 --- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationZzz2.java +++ /dev/null @@ -1,28 +0,0 @@ -package org.snpeff.snpEffect.testCases.integration; - -import org.junit.jupiter.api.Test; -import static org.junit.jupiter.api.Assertions.assertTrue; - -/** - * Test case - */ -public class TestCasesIntegrationZzz2 extends TestCasesIntegrationBase { - - @Test - public void test_01() { - verbose = true; - var vcfEntries = snpEffect("testHg3882Chr22", path("test_inv.vcf")); - - if (verbose) { - for (var vcfEntry : vcfEntries) { - System.out.println(vcfEntry); - for (var vcfEffect : vcfEntry.getVcfEffects()) { - System.out.println("\t" + vcfEffect); - } - } - } - - assertTrue(vcfEntries.size() > 0); - } - -} diff --git a/tests/integration/zzz2/test_inv.vcf b/tests/integration/inv/test_inv.vcf similarity index 100% rename from tests/integration/zzz2/test_inv.vcf rename to tests/integration/inv/test_inv.vcf From 532ae2491c748caa167d161074c0100c178df872 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Fri, 13 Sep 2024 05:09:33 -0400 Subject: [PATCH 10/21] Testing for --- .../testCases/integration/TestCasesIntegrationInv.java | 2 +- tests/integration/inv/test_inv.vcf | 1 - tests/integration/inv/test_inv_02.vcf | 2 ++ 3 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 tests/integration/inv/test_inv_02.vcf diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java index 00ffbeb9..483cf717 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java @@ -46,7 +46,7 @@ public void test_01() { @Test public void test_02() { verbose = true; - var vcfEntries = snpEffect("testHg3882Chr22", path("test_inv_02.vcf")); + var vcfEntries = snpEffect("test_GRCh38.mane.1.2.ensembl.chr1", path("test_inv_02.vcf")); hasInv(vcfEntries); } diff --git a/tests/integration/inv/test_inv.vcf b/tests/integration/inv/test_inv.vcf index 4e3e82ee..562bc801 100644 --- a/tests/integration/inv/test_inv.vcf +++ b/tests/integration/inv/test_inv.vcf @@ -1,3 +1,2 @@ -#chr1 27360853 DRAGEN:INV:962:0:0:1:15:0 GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC . MinSomaticScore END=27360932;SVTYPE=INV;SVLEN=-79;CIGAR=1M79I79D;CONTIG=CACTATGTTCTTGTGGCGCAGGCGTCTGTGAAGAGCGATCTCTTCATGCAGGGGCTGAGAGAACCTGAGGGGAGGTAAGGGAGAGAGGAAAGGGACCGAGGTGGGCAGAGAAGCCCCGCCCATCCCACGCCAGCCTGGCCCCGCCCCAAGGACCCGCCCCGCCCACAAGCCCTCTCCGACCTTCCCCACCCTTACTACCCTGCCCACAGGACCCTCCAGACCTCAATCCCGCCCGCACGGTCCTGGCTGTTCCGCCCACGGGCCCAGTCCACAGGGCTCGAACTCTCAGGTCCTACGAGCCCGCCCACTAGGCCCCGCCCACAGGAGCCGCTCCGCTCGTGGCCCGGCTCACTCGGCCCTCGCGAGCCCTCAGCCCCACCCGCGCTGCCACGCACCGCACCTGCTGTCCCGCTCCGGGATCTCCTTGATGGCGATGCGCACCCTCGTGTGGCGATCGCGGCCCGCGTACACCACCCCATACGTGCCCTTGCCCAGCACCAGCCGCTCGCCCGTCTCCGTGTACTCATAATCAAACTGCCGGGCGCGGGGGAGATGTTGGAGGTGAGGACGCGGGACTGGGAGCTCGCGGAGGGCGAGGGGCCGCGGGCCCTGCTGAACTCCCATCTCACCCCGCGCCCTCCGCCTCCTCCGCGGGCGCCGTGGAATCCGGGTTCGTCACCCAGGCCTGGATCAGGCCGCAGAACCTGAAGGTGGGGGAGGTCAGACCCGCGGGAGGGGCATCTTGGTCCCCACCTAAGCCGGAGCATCCAACGGACGTCGTCCCTTTCTTTCCCCCACTCCCCCCCGGGCATCCTGGCCCTCAGAGTACCCCGACCATGAAAGGCTGCGCACCACTGGCAGTGCCCTACGCTGGGGAAGCACAGCTGGACGTCCTGAGCCGGGGGGAGTGCATAGAGGAAGCAGCAGCGCTCGTCGCGCTTTGAGGCG;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 1272,0:4027,3:3624,3 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B_1_Lymphoma chr22 37973492 DRAGEN:INV:49554:0:0:0:16:0 CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT . MinSomaticScore END=37973553;SVTYPE=INV;SVLEN=-61;CIGAR=1M61I61D;CONTIG=AACCTCCTTCTCCTCTGTCCAGCCTGTTCTCCTGGGGCTTTGCTGCTGGAGCCTGGATGGGGCGGGTGGGTCATCAGGGCAGTGAGCCAGACAGAAAGCCCCCCGACCTGTCAGCCTCTTCAGCCTCCTCAGCCTCCTCCACTGCCACCACCAGGCCTGAGGTGGGCAAGGAACAGGGCACACAGGCTGGGGGCAGGGGCTGGGCGGGGGGTGGTGGCGACAGGGCCCCAGTCCCACAGCCCCACACACTGGGAGCAGCCAGTATATACGACACTGTCCCGGCCCTAAAGGGGGCCCTGAGGGGCTGGGGTCAGAGATGGCCGTGTAGAGGGGCCGCTGCGAGGGCCCCATATAGGAGAAGGCCGAGTAGAGGCCAGAGGCCTGGCCCGAGTGGCCATAATAGGGTCCTGAGGGCTGATGGTCAGAGTAGTCAAACTGGGGGCGGGAGATGGAGGGGAAGGCTGAGCCATAGTGGGGCAGGCTGAGGGAGGTGTAGGCGATCTGTGAGGTGGATGGCTGGTCGGTGTAGTGTGGGGGCCCCTGGGGCCCCGCGGTCTCTGTCTTCACCTGGGCTTTGGCATCCACACCAGGTGGTGAGACCGTGGGCAGAGCCACGCCTGGTGGCTTGGAGATCCAGGCGGAGTGTCCACTGGCCACGGCCAGGGCACTGCCCAGCCCATAGCCGGCTGCTGAGTAGCTGCTCACATGGCCTGGGTGCCCATTGGGCGGCAGGTACTGGTCCAACTCAGCCACATCAAAGGTCTCCATGTTGGACATTACCTCGTGGCTGATCTCACCAATGTCCACGTTGCCGAAGTCGATGTGAGGCTTCCCGCCCTCCCCCATGGAGCGCCCGTCCCGCTTCGGGTCTGCCTTGCCCGACTGCAGCTCTGTCTTCGGGGTGGTTGGAGGGGTGGGTGGGCCATGGCTCTGGCCTGGGTAGAAGGGAGACAGAGAGAGAGAGCGCAAGGGGGAAGCAGGTTAGAGGCAGGTGGGCGCACGTGAACTTCCATGGTTCACCTTCAGGCAGCGGGTGCCTCTGGGAAAACCTTGTAAGTTTCACATTTTGGCAGCATGAGTCGGGTTTTTTTTTGTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGACTGGAGTGCAGTGGCGCCATCTCGGCTCACTGCA;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 705,0:2396,2:2155,2 diff --git a/tests/integration/inv/test_inv_02.vcf b/tests/integration/inv/test_inv_02.vcf new file mode 100644 index 00000000..9d367f62 --- /dev/null +++ b/tests/integration/inv/test_inv_02.vcf @@ -0,0 +1,2 @@ +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B_1_Lymphoma +chr1 27360853 DRAGEN:INV:962:0:0:1:15:0 GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC . MinSomaticScore END=27360932;SVTYPE=INV;SVLEN=-79;CIGAR=1M79I79D;CONTIG=CACTATGTTCTTGTGGCGCAGGCGTCTGTGAAGAGCGATCTCTTCATGCAGGGGCTGAGAGAACCTGAGGGGAGGTAAGGGAGAGAGGAAAGGGACCGAGGTGGGCAGAGAAGCCCCGCCCATCCCACGCCAGCCTGGCCCCGCCCCAAGGACCCGCCCCGCCCACAAGCCCTCTCCGACCTTCCCCACCCTTACTACCCTGCCCACAGGACCCTCCAGACCTCAATCCCGCCCGCACGGTCCTGGCTGTTCCGCCCACGGGCCCAGTCCACAGGGCTCGAACTCTCAGGTCCTACGAGCCCGCCCACTAGGCCCCGCCCACAGGAGCCGCTCCGCTCGTGGCCCGGCTCACTCGGCCCTCGCGAGCCCTCAGCCCCACCCGCGCTGCCACGCACCGCACCTGCTGTCCCGCTCCGGGATCTCCTTGATGGCGATGCGCACCCTCGTGTGGCGATCGCGGCCCGCGTACACCACCCCATACGTGCCCTTGCCCAGCACCAGCCGCTCGCCCGTCTCCGTGTACTCATAATCAAACTGCCGGGCGCGGGGGAGATGTTGGAGGTGAGGACGCGGGACTGGGAGCTCGCGGAGGGCGAGGGGCCGCGGGCCCTGCTGAACTCCCATCTCACCCCGCGCCCTCCGCCTCCTCCGCGGGCGCCGTGGAATCCGGGTTCGTCACCCAGGCCTGGATCAGGCCGCAGAACCTGAAGGTGGGGGAGGTCAGACCCGCGGGAGGGGCATCTTGGTCCCCACCTAAGCCGGAGCATCCAACGGACGTCGTCCCTTTCTTTCCCCCACTCCCCCCCGGGCATCCTGGCCCTCAGAGTACCCCGACCATGAAAGGCTGCGCACCACTGGCAGTGCCCTACGCTGGGGAAGCACAGCTGGACGTCCTGAGCCGGGGGGAGTGCATAGAGGAAGCAGCAGCGCTCGTCGCGCTTTGAGGCG;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 1272,0:4027,3:3624,3 From b9967c1e49715bef5482c012667522f1ea92d85d Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Fri, 13 Sep 2024 05:20:11 -0400 Subject: [PATCH 11/21] Added INV test --- config/snpEff.config | 134282 ++++++++++++++- .../java/org/snpeff/interval/Variant.java | 1 - .../integration/TestCasesIntegrationInv.java | 8 +- 3 files changed, 134266 insertions(+), 25 deletions(-) diff --git a/config/snpEff.config b/config/snpEff.config index 2156ee94..3aa2710f 100644 --- a/config/snpEff.config +++ b/config/snpEff.config @@ -1,4 +1,8 @@ +#--- +# Core +#--- + #------------------------------------------------------------------------------- # # SnpEff configuration file @@ -130,6 +134,10 @@ codon.Thraustochytrium_Mitochondrial : TTT/F , TTC/F , TTA/* , TTG/L , TCT/S , # #------------------------------------------------------------------------------- + +#--- +# DBs +#--- #--- # Non-standard Databases #--- @@ -227,11 +235,10 @@ GRCh38.mane.1.2.refseq.genome: Human genome GRCh38, using MANE transcripts v1.2, GRCh38.GRCh38.mane.1.2.refseq.M.codonTable : Vertebrate_Mitochondrial GRCh38.GRCh38.mane.1.2.refseq.MT.codonTable : Vertebrate_Mitochondrial -# Mouse -mm9.genome : Mouse -mm10.genome : Mouse -mm39.genome : Mouse +#--- +# Test databases +#--- #--- # Test cases: Generic @@ -348,6 +355,7 @@ test_GRCh38.mane.1.0.ensembl.chr19.genome : GRCh38 MANE 1.0 chr19 test_GRCh38.mane.1.0.ensembl.chr21.genome : GRCh38 MANE 1.0 chr21 test_GRCh38.mane.1.0.refseq.chr21.genome : GRCh38 MANE 1.0 chr21 test_GRCh38.mane.1.0.refseq.chr19.genome : GRCh38 MANE 1.0 chr19 +test_GRCh38.mane.1.2.ensembl.chr1.genome : GRCh38 MANE 1.2 chr1 #--- # Test cases: Non-human @@ -402,32 +410,134268 @@ test_t_urticae_p3.genome: T. Urticae p3 #--- -# ENSEMBL release 110 +# ENSEMBL release 112 #--- -# Empty #--- -# NCBI genomes +# UCSC genomes #--- +allMis1.genome : allMis1 +allMis1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/allMis1/bigZips +allMis1.retrieval_date : 2024-01-02 -# Empty snpEff.NCBI.empty.config +aptMan1.genome : aptMan1 +aptMan1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/aptMan1/bigZips +aptMan1.retrieval_date : 2024-01-02 +bisBis1.genome : bisBis1 +bisBis1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bisBis1/bigZips +bisBis1.retrieval_date : 2024-01-02 -#--- -# ENSEMBL BFMPP release 57 -#--- -# Empty +bosTau3.genome : bosTau3 +bosTau3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau3/bigZips +bosTau3.retrieval_date : 2024-01-02 -#--- -# FLYBASE release FB2022_02 -#--- +bosTau4.genome : bosTau4 +bosTau4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau4/bigZips +bosTau4.retrieval_date : 2024-01-02 -dmel_r6.45.genome: dmel_r6.45 +bosTau6.genome : bosTau6 +bosTau6.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau6/bigZips +bosTau6.retrieval_date : 2024-01-02 + +bosTau7.genome : bosTau7 +bosTau7.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau7/bigZips +bosTau7.retrieval_date : 2024-01-02 + +bosTau8.genome : bosTau8 +bosTau8.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips +bosTau8.retrieval_date : 2024-01-02 + +bosTau9.genome : bosTau9 +bosTau9.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/bigZips +bosTau9.retrieval_date : 2024-01-02 + +calJac1.genome : calJac1 +calJac1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/calJac1/bigZips +calJac1.retrieval_date : 2024-01-02 + +calJac3.genome : calJac3 +calJac3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/calJac3/bigZips +calJac3.retrieval_date : 2024-01-02 + +canFam3.genome : canFam3 +canFam3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/canFam3/bigZips +canFam3.retrieval_date : 2024-01-02 + +cavPor3.genome : cavPor3 +cavPor3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/cavPor3/bigZips +cavPor3.retrieval_date : 2024-01-02 + +ce10.genome : ce10 +ce10.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ce10/bigZips +ce10.retrieval_date : 2024-01-02 + +ce11.genome : ce11 +ce11.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ce11/bigZips +ce11.retrieval_date : 2024-01-02 + +ce6.genome : ce6 +ce6.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ce6/bigZips +ce6.retrieval_date : 2024-01-02 + +ci3.genome : ci3 +ci3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ci3/bigZips +ci3.retrieval_date : 2024-01-02 + +criGri1.genome : criGri1 +criGri1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/criGri1/bigZips +criGri1.retrieval_date : 2024-01-02 + +criGriChoV1.genome : criGriChoV1 +criGriChoV1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV1/bigZips +criGriChoV1.retrieval_date : 2024-01-02 + +criGriChoV2.genome : criGriChoV2 +criGriChoV2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV2/bigZips +criGriChoV2.retrieval_date : 2024-01-02 + +danRer10.genome : danRer10 +danRer10.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips +danRer10.retrieval_date : 2024-01-02 + +danRer11.genome : danRer11 +danRer11.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer11/bigZips +danRer11.retrieval_date : 2024-01-02 + +danRer5.genome : danRer5 +danRer5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer5/bigZips +danRer5.retrieval_date : 2024-01-02 + +danRer6.genome : danRer6 +danRer6.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer6/bigZips +danRer6.retrieval_date : 2024-01-02 + +danRer7.genome : danRer7 +danRer7.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer7/bigZips +danRer7.retrieval_date : 2024-01-02 + +dm3.genome : dm3 +dm3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/dm3/bigZips +dm3.retrieval_date : 2024-01-02 + +dm6.genome : dm6 +dm6.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/dm6/bigZips +dm6.retrieval_date : 2024-01-02 + +equCab1.genome : equCab1 +equCab1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/equCab1/bigZips +equCab1.retrieval_date : 2024-01-02 + +equCab2.genome : equCab2 +equCab2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/equCab2/bigZips +equCab2.retrieval_date : 2024-01-02 + +equCab3.genome : equCab3 +equCab3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/equCab3/bigZips +equCab3.retrieval_date : 2024-01-02 + +felCat3.genome : felCat3 +felCat3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat3/bigZips +felCat3.retrieval_date : 2024-01-02 + +felCat4.genome : felCat4 +felCat4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat4/bigZips +felCat4.retrieval_date : 2024-01-02 + +felCat5.genome : felCat5 +felCat5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat5/bigZips +felCat5.retrieval_date : 2024-01-02 + +felCat8.genome : felCat8 +felCat8.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat8/bigZips +felCat8.retrieval_date : 2024-01-02 + +felCat9.genome : felCat9 +felCat9.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/felCat9/bigZips +felCat9.retrieval_date : 2024-01-02 + +fr3.genome : fr3 +fr3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/fr3/bigZips +fr3.retrieval_date : 2024-01-02 + +galGal3.genome : galGal3 +galGal3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal3/bigZips +galGal3.retrieval_date : 2024-01-02 + +galGal4.genome : galGal4 +galGal4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal4/bigZips +galGal4.retrieval_date : 2024-01-02 + +galGal5.genome : galGal5 +galGal5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips +galGal5.retrieval_date : 2024-01-02 + +galGal6.genome : galGal6 +galGal6.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/galGal6/bigZips +galGal6.retrieval_date : 2024-01-02 + +gasAcu1.genome : gasAcu1 +gasAcu1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/gasAcu1/bigZips +gasAcu1.retrieval_date : 2024-01-02 + +gorGor4.genome : gorGor4 +gorGor4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/gorGor4/bigZips +gorGor4.retrieval_date : 2024-01-02 + +gorGor5.genome : gorGor5 +gorGor5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/gorGor5/bigZips +gorGor5.retrieval_date : 2024-01-02 + +hg19.genome : hg19 +hg19.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips +hg19.retrieval_date : 2024-01-02 + +hg38.genome : hg38 +hg38.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips +hg38.retrieval_date : 2024-01-02 + +loxAfr3.genome : loxAfr3 +loxAfr3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/loxAfr3/bigZips +loxAfr3.retrieval_date : 2024-01-02 + +macFas5.genome : macFas5 +macFas5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/macFas5/bigZips +macFas5.retrieval_date : 2024-01-02 + +melGal5.genome : melGal5 +melGal5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/melGal5/bigZips +melGal5.retrieval_date : 2024-01-02 + +mm10.genome : mm10 +mm10.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips +mm10.retrieval_date : 2024-01-02 + +mm9.genome : mm9 +mm9.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips +mm9.retrieval_date : 2024-01-02 + +musFur1.genome : musFur1 +musFur1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/musFur1/bigZips +musFur1.retrieval_date : 2024-01-02 + +oreNil2.genome : oreNil2 +oreNil2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/oreNil2/bigZips +oreNil2.retrieval_date : 2024-01-02 + +ornAna1.genome : ornAna1 +ornAna1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ornAna1/bigZips +ornAna1.retrieval_date : 2024-01-02 + +ornAna2.genome : ornAna2 +ornAna2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ornAna2/bigZips +ornAna2.retrieval_date : 2024-01-02 + +oryCun2.genome : oryCun2 +oryCun2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/oryCun2/bigZips +oryCun2.retrieval_date : 2024-01-02 + +oryLat2.genome : oryLat2 +oryLat2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/oryLat2/bigZips +oryLat2.retrieval_date : 2024-01-02 + +oviAri1.genome : oviAri1 +oviAri1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/oviAri1/bigZips +oviAri1.retrieval_date : 2024-01-02 + +oviAri3.genome : oviAri3 +oviAri3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/oviAri3/bigZips +oviAri3.retrieval_date : 2024-01-02 + +oviAri4.genome : oviAri4 +oviAri4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/oviAri4/bigZips +oviAri4.retrieval_date : 2024-01-02 + +panPan1.genome : panPan1 +panPan1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/panPan1/bigZips +panPan1.retrieval_date : 2024-01-02 + +panTro3.genome : panTro3 +panTro3.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro3/bigZips +panTro3.retrieval_date : 2024-01-02 + +panTro4.genome : panTro4 +panTro4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro4/bigZips +panTro4.retrieval_date : 2024-01-02 + +panTro5.genome : panTro5 +panTro5.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro5/bigZips +panTro5.retrieval_date : 2024-01-02 + +panTro6.genome : panTro6 +panTro6.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips +panTro6.retrieval_date : 2024-01-02 + +papAnu2.genome : papAnu2 +papAnu2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/papAnu2/bigZips +papAnu2.retrieval_date : 2024-01-02 + +papAnu4.genome : papAnu4 +papAnu4.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/papAnu4/bigZips +papAnu4.retrieval_date : 2024-01-02 + +papHam1.genome : papHam1 +papHam1.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/papHam1/bigZips +papHam1.retrieval_date : 2024-01-02 + +ponAbe2.genome : ponAbe2 +ponAbe2.reference : rsync://hgdownload.soe.ucsc.edu/goldenPath/ponAbe2/bigZips +ponAbe2.retrieval_date 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ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_gnavus_gca_003475065.retrieval_date : 2024-01-06 + +_ruminococcus_gnavus_gca_003475365.genome : _ruminococcus_gnavus_gca_003475365 +_ruminococcus_gnavus_gca_003475365.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_gnavus_gca_003475365.retrieval_date : 2024-01-06 + +_ruminococcus_torques_atcc_27756_gca_000153925.genome : _ruminococcus_torques_atcc_27756_gca_000153925 +_ruminococcus_torques_atcc_27756_gca_000153925.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_atcc_27756_gca_000153925.retrieval_date : 2024-01-06 + +_ruminococcus_torques_cag_61_gca_000432115.genome : _ruminococcus_torques_cag_61_gca_000432115 +_ruminococcus_torques_cag_61_gca_000432115.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_cag_61_gca_000432115.retrieval_date : 2024-01-06 + +_ruminococcus_torques_gca_001405315.genome : _ruminococcus_torques_gca_001405315 +_ruminococcus_torques_gca_001405315.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_gca_001405315.retrieval_date : 2024-01-06 + +_ruminococcus_torques_gca_001406235.genome : _ruminococcus_torques_gca_001406235 +_ruminococcus_torques_gca_001406235.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_gca_001406235.retrieval_date : 2024-01-06 + +_ruminococcus_torques_gca_001406495.genome : _ruminococcus_torques_gca_001406495 +_ruminococcus_torques_gca_001406495.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_gca_001406495.retrieval_date : 2024-01-06 + +_ruminococcus_torques_gca_001406755.genome : _ruminococcus_torques_gca_001406755 +_ruminococcus_torques_gca_001406755.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_gca_001406755.retrieval_date : 2024-01-06 + +_ruminococcus_torques_gca_003470435.genome : _ruminococcus_torques_gca_003470435 +_ruminococcus_torques_gca_003470435.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_gca_003470435.retrieval_date : 2024-01-06 + +_ruminococcus_torques_gca_004167165.genome : _ruminococcus_torques_gca_004167165 +_ruminococcus_torques_gca_004167165.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_gca_004167165.retrieval_date : 2024-01-06 + +_ruminococcus_torques_l2_14_gca_000210035.genome : _ruminococcus_torques_l2_14_gca_000210035 +_ruminococcus_torques_l2_14_gca_000210035.reference : ftp.ensemblgenomes.org/pub/release-57 +_ruminococcus_torques_l2_14_gca_000210035.retrieval_date : 2024-01-06 + +#--- +# FLYBASE release FB2022_02 +#--- + +dmel_r6.45.genome: dmel_r6.45 #--- # Custom requests @@ -446,7 +134690,7 @@ GRCh38.86.reference: http://ftp.ensembl.org/pub/release-86/fasta/homo_sapiens/ #--- -# COVID19 +# COVID #--- #--- # SARS / COVID19 diff --git a/src/main/java/org/snpeff/interval/Variant.java b/src/main/java/org/snpeff/interval/Variant.java index 37911c6e..069780de 100644 --- a/src/main/java/org/snpeff/interval/Variant.java +++ b/src/main/java/org/snpeff/interval/Variant.java @@ -369,7 +369,6 @@ public boolean isStructuralHuge() { // We only check if: a) that the chromosome exists and b) chromosome it is not small if (chr != null && chr.size() > HUGE_DELETION_SIZE_THRESHOLD) { double ratio = size() / ((double) chr.size()); - Log.debug("Structural variant size: " + size() + ", chromosome size: " + chr.size() + ", ratio: " + ratio); return size() > HUGE_DELETION_SIZE_THRESHOLD || ratio > HUGE_DELETION_RATIO_THRESHOLD; } diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java index 483cf717..62e32703 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationInv.java @@ -16,13 +16,11 @@ public class TestCasesIntegrationInv extends TestCasesIntegrationBase { - void hasInv(List vcfEntries) { + void hasInvHighImpact(List vcfEntries) { assertTrue(vcfEntries.size() > 0); var found = false; for (var vcfEntry : vcfEntries) { - System.out.println(vcfEntry); for (var vcfEffect : vcfEntry.getVcfEffects()) { - System.out.println("\t" + vcfEffect.getEffectType() + "\t" + vcfEffect); if( vcfEffect.getEffectType() == EffectType.CHROMOSOME_LARGE_INVERSION || vcfEffect.getEffectType() == EffectType.EXON_INVERSION || vcfEffect.getEffectType() == EffectType.EXON_INVERSION_PARTIAL @@ -40,14 +38,14 @@ void hasInv(List vcfEntries) { public void test_01() { verbose = true; var vcfEntries = snpEffect("testHg3882Chr22", path("test_inv.vcf")); - hasInv(vcfEntries); + hasInvHighImpact(vcfEntries); } @Test public void test_02() { verbose = true; var vcfEntries = snpEffect("test_GRCh38.mane.1.2.ensembl.chr1", path("test_inv_02.vcf")); - hasInv(vcfEntries); + hasInvHighImpact(vcfEntries); } } From f34fd64ae82dab4042de8cc276deb44f10048b72 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Tue, 17 Sep 2024 10:25:05 +0200 Subject: [PATCH 12/21] Project updated --- papers/VCFv4.1.pdf | Bin 0 -> 712448 bytes papers/VCFv4.2.pdf | Bin 0 -> 713844 bytes papers/VCFv4.3.pdf | Bin 0 -> 859596 bytes papers/VCFv4.4.pdf | Bin 0 -> 881108 bytes papers/VCFv4.5.pdf | Bin 0 -> 896346 bytes .../snpeff/fileIterator/VcfFileIterator.java | 16 + src/main/java/org/snpeff/interval/Marker.java | 1 - .../java/org/snpeff/interval/Variant.java | 3 +- src/main/java/org/snpeff/vcf/VcfEntry.java | 359 ++++++++++++------ .../integration/TestCasesIntegrationDup.java | 4 +- .../testCases/unity/TestCasesVcf.java | 108 ++++-- test_04_TestCasesEff.csv | 4 +- 12 files changed, 348 insertions(+), 147 deletions(-) create mode 100644 papers/VCFv4.1.pdf create mode 100644 papers/VCFv4.2.pdf create mode 100644 papers/VCFv4.3.pdf create mode 100644 papers/VCFv4.4.pdf create mode 100644 papers/VCFv4.5.pdf diff --git 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java.util.List; @@ -68,6 +70,20 @@ public class VcfFileIterator extends MarkerFileIterator implements Par String chrPrev = ""; int posPrev = -1; + + /** + * Create a VcfFileIterator from a string containig VCF lines + */ + public static VcfFileIterator fromString(String vcfLines) { + try (var bais = new ByteArrayInputStream(vcfLines.getBytes("UTF-8"))) { + InputStreamReader isr = new InputStreamReader(bais); + BufferedReader br = new BufferedReader(isr); + return new VcfFileIterator(br); + } catch (IOException e) { + throw new RuntimeException(e); + } + } + public VcfFileIterator() { super((String) null, 1); init(); diff --git a/src/main/java/org/snpeff/interval/Marker.java b/src/main/java/org/snpeff/interval/Marker.java index 36eeb64e..7fbb1119 100644 --- a/src/main/java/org/snpeff/interval/Marker.java +++ b/src/main/java/org/snpeff/interval/Marker.java @@ -9,7 +9,6 @@ import org.snpeff.snpEffect.VariantEffect; import org.snpeff.snpEffect.VariantEffects; import org.snpeff.util.Gpr; -import org.snpeff.util.Log; import java.lang.reflect.Constructor; import java.util.ArrayList; diff --git a/src/main/java/org/snpeff/interval/Variant.java b/src/main/java/org/snpeff/interval/Variant.java index 069780de..39b3073a 100644 --- a/src/main/java/org/snpeff/interval/Variant.java +++ b/src/main/java/org/snpeff/interval/Variant.java @@ -6,7 +6,6 @@ import org.snpeff.snpEffect.EffectType; import org.snpeff.util.GprSeq; import org.snpeff.util.IubString; -import org.snpeff.util.Log; import java.util.LinkedList; import java.util.List; @@ -30,7 +29,7 @@ public class Variant extends Marker { protected VariantType variantType; // Variant type protected String ref; // Reference (i.e. original bases in the genome) protected String alt; // Changed bases - protected String genotype; // Genotype 'ALT' (e.g. A VCF entry may encode multiple ALTs). + protected String genotype; // Genotype (i.e. the original 'ALT' in the VCF file). A VCF entry may encode multiple ALTs, and 'ALT' migh get modified when creating the variant. Here we store ALT as originaly show in the VCF. protected boolean imprecise = false; // Imprecise variant: coordinates are not exact (E.g. see section "Encoding Structural Variants in VCF" from VCF spec. 4.1) public Variant() { diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index b214feb7..e829dfec 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -42,7 +42,9 @@ public enum AlleleFrequencyType { public static final double ALLELE_FEQUENCY_COMMON = 0.05; public static final double ALLELE_FEQUENCY_LOW = 0.01; public static final Pattern INFO_KEY_PATTERN = Pattern.compile("[\\p{Alpha}_][\\p{Alnum}._]*"); - public static final String VCF_INFO_END = "END"; // Imprecise variants + public static final String VCF_INFO_END = "END"; // Imprecise variants. Deprecated: "END has been deprecated in favour of INFO SVLEN and FORMAT LEN." + public static final String VCF_INFO_SVLEN = "SVLEN"; // "SVLEN must be specified for symbolic structural variant alleles" + public static final String VCF_INFO_IMPRECISE = "IMPRECISE"; // IMPRECISE must be specified for imprecise structural variant alleles // In order to report sequencing data evidence for both variant and non-variant positions in the genome, the VCF // specification allows to represent blocks of reference-only calls in a single record using the END INFO tag, an idea @@ -51,11 +53,11 @@ public enum AlleleFrequencyType { // other possible alternate allele (both SNP, indel, or otherwise). A symbolic alternate allele <*> is used to represent // this unspecified alternate allele public static final String VCF_ALT_NON_REF = "<*>"; // See VCF 4.2 section "5.5 Representing unspecified alleles and REF-only blocks (gVCF)" - public static final String VCF_ALT_NON_REF_gVCF = ""; // NON_REF tag for ALT field (only in gVCF fields) + public static final String VCF_ALT_NON_REF_OLD = ""; // NON_REF tag for ALT field (only in gVCF fields (olf version of '<*>') public static final String VCF_ALT_MISSING_REF = "*"; // The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion (see VCF 4.3 spec., ALT definition) public static final String VCF_ALT_INV = ""; // Inversion - public static final String[] VCF_ALT_NON_REF_gVCF_ARRAY = { VCF_ALT_NON_REF_gVCF }; + public static final String[] VCF_ALT_NON_REF_OLD_ARRAY = { VCF_ALT_NON_REF_OLD }; public static final String[] VCF_ALT_NON_REF_ARRAY = { VCF_ALT_NON_REF }; public static final String[] VCF_ALT_MISSING_REF_ARRAY = { VCF_ALT_MISSING_REF }; public static final String[] VCF_ALT_INV_ARRAY = { VCF_ALT_INV }; @@ -166,6 +168,16 @@ public static boolean isValidInfoValue(String value) { return !invalid; } + /** + * Pad with 'N' characters up length 'len' + */ + String padNs(String ref, int len) { + if( ref.length() <= len ) return ref; + char[] bases = new char[len]; + for( int i = 0; i < len; i++ ) bases[i] = (i < ref.length() ? ref.charAt(i) : 'N'); + return new String(bases); + } + /** * Decode INFO value */ @@ -224,13 +236,13 @@ public VcfEntry(VcfFileIterator vcfFileIterator, Marker parent, String chromosom super(parent, start, start + ref.length() - 1, false, id); this.chromosomeName = chromosomeName; this.ref = ref; - parseAlts(altsStr); + this.alts = parseAlts(altsStr); this.quality = quality; filter = filterPass; this.infoStr = infoStr; parseInfo(); this.format = format; - parseEnd(altsStr); + parseEnd(); } /** @@ -814,6 +826,16 @@ public VcfInfoType getVcfInfoNumber(String id) { return vcfInfo.getVcfInfoType(); } + public boolean hasAltNonRef() { + if (alts == null || alts.length == 0) return false; + + // Is any ALT is variant? + for (String alt : alts) + if (isAltNonRef(alt)) return true; + + return false; + } + public boolean hasField(String filedName) { return vcfFileIterator.getVcfHeader().getVcfHeaderInfo(filedName) != null; } @@ -831,6 +853,13 @@ public boolean hasQuality() { return quality != null; } + /** + * Is this ALT string a NON_REF? (gVCF) + */ + public boolean isAltNonRef(String alt) { + return alt != null && (alt.equals(VCF_ALT_NON_REF) || alt.equals(VCF_ALT_NON_REF_OLD)); + } + /** * Is this bi-allelic (based ONLY on the number of ALTs) * WARINIG: You should use 'calcHetero()' method for a more precise calculation. @@ -909,9 +938,9 @@ public boolean isVariant(String alt) { return alt != null // && !alt.isEmpty() // && !alt.equals(VcfFileIterator.MISSING) // Missing ALT (".")? - && !alt.equals(VCF_ALT_NON_REF) // '*' - && !alt.equals(VCF_ALT_NON_REF_gVCF) // '' - && !alt.equals(VCF_ALT_MISSING_REF) // '<*>' + && !alt.equals(VCF_ALT_NON_REF) // '<*>' + && !alt.equals(VCF_ALT_NON_REF_OLD) // '' + && !alt.equals(VCF_ALT_MISSING_REF) // '*' && !alt.equals(ref) // Is ALT different than REF? ; } @@ -1006,7 +1035,7 @@ public void parse() { // ALT altStr = vcfFileIterator.readField(fields, 4).toUpperCase(); - parseAlts(altStr); + this.alts = parseAlts(altStr); // Quality String qStr = vcfFileIterator.readField(fields, 5); @@ -1021,7 +1050,7 @@ public void parse() { info = null; // Start & End coordinates are anchored to the reference genome, thus based on REF field (ALT is not taken into account) - parseEnd(altStr); + parseEnd(); // Genotype format format = null; @@ -1035,11 +1064,11 @@ public void parse() { /** * Parse ALT field */ - void parseAlts(String altsStr) { + String[] parseAlts(String altsStr) { if (altsStr.length() == 1 || altsStr.indexOf(',') < 0) { // SNP or single field (no commas) alts = parseAltSingle(altsStr); - if (alts == null) alts = new String[0]; + return alts != null ? alts : new String[0]; } else { // Multiple fields (comma separated) List altsList = new ArrayList<>(); @@ -1056,7 +1085,7 @@ void parseAlts(String altsStr) { } } - alts = altsList.toArray(EMPTY_STRING_ARRAY); + return altsList.toArray(EMPTY_STRING_ARRAY); } } @@ -1075,7 +1104,7 @@ String[] parseAltSingle(String altsStr) { // Not a variant? if (altsStr.equals(VCF_ALT_NON_REF)) { return VCF_ALT_NON_REF_ARRAY; } if (altsStr.equals(VCF_ALT_MISSING_REF)) { return VCF_ALT_MISSING_REF_ARRAY; } - if (altsStr.equals(VCF_ALT_NON_REF_gVCF)) { return VCF_ALT_NON_REF_gVCF_ARRAY; } + if (altsStr.equals(VCF_ALT_NON_REF_OLD)) { return VCF_ALT_NON_REF_OLD_ARRAY; } if (altsStr.equals(VCF_ALT_INV)) { return VCF_ALT_INV_ARRAY; } // SNP IUB conversion table @@ -1173,17 +1202,43 @@ String[] parseAltSingle(String altsStr) { /** * Parse 'end' coordinate */ - void parseEnd(String altStr) { - end = start + ref.length() - 1; - + void parseEnd() { // Imprecise variants are indicated by an angle brackets '<...>' - if (altStr.indexOf('<') >= 0) { - // If there is an 'END' tag, we should use it - if ((getInfo(VCF_INFO_END) != null)) { + if (altStr.indexOf('<') >= 0 ) { + !!!!!!!! MOVE TO PARSE START + if( hasAltNonRef() ) { + // Non-ref alt: '<*>' or + } else { + // , , , , or similar + // "Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant." + start++; + } + + if ( hasInfo(VCF_INFO_SVLEN) ) { + // From VCF specification: + // ``` + // SVLEN must be specified for symbolic structural variant alleles. SVLEN is defined for INS, DUP, + // INV, and DEL symbolic alleles as the number of the inserted, duplicated, inverted, and deleted + // bases respectively. SVLEN is defined for CNV symbolic alleles as the length of the segment over + // which the copy number variant is defined. The missing value . should be used for all other ALT + // alleles, including ALT alleles using breakend notation. + // ``` + var svlen = (int) getInfoInt(VCF_INFO_SVLEN); + // "For backwards compatibility, the absolute value of SVLEN should be taken and a negative SVLEN + // should be treated as positive values." + if (svlen < 0) svlen = -svlen; + end = start + svlen - 1; + } else if ( hasInfo(VCF_INFO_END) ) { + // "For backwards compatibility, a missing SVLEN should be inferred from the END field." // Get 'END' field and do some sanity check end = (int) getInfoInt(VCF_INFO_END) - 1; if (end < start) { throw new RuntimeException("INFO field 'END' is before varaint's 'POS'\n\tEND : " + end + "\n\tPOS : " + start); } + } else { + // If no SVLEN or END field is present, we can't infer the end position, we'll use 'ref' length + end = start + ref.length() - 1; } + } else { + end = start + ref.length() - 1; } } @@ -1520,86 +1575,39 @@ List variants(Chromosome chromo, int start, String reference, String al list = Variant.factory(chromo, start, reference, null, id, false); } else if (reference.length() == 1 && alt.length() == 1) { // The most common case: SNPs - // SNPs - // 20 3 . C G . PASS DP=100 + // VCF entry example: + // 20 3 . C G . PASS DP=100 list = Variant.factory(chromo, start, reference, alt, id, vcfFileIterator.isExpandIub()); } else if (alt.charAt(0) == '<') { - // Structural variants - if (alt.startsWith(" 6 PASS IMPRECISE;SVTYPE=DEL;END=321887;SVLEN=-105;CIPOS=-56,20;CIEND=-10,62 - String ch = ref; - int startNew = start; - - if (end > start) { - startNew = start + reference.length(); - int size = end - startNew + 1; - char change[] = new char[size]; - for (int i = 0; i < change.length; i++) - change[i] = reference.length() > i ? reference.charAt(i) : 'N'; - ch = new String(change); - } - list = Variant.factory(chromo, startNew, ch, "", id, false); - } else if (alt.startsWith("(); - list.add(var); - } else if (alt.startsWith("(); - list.add(var); - } + list = variantsStructural(chromo, start, reference, alt, id); } else if ((alt.indexOf('[') >= 0) || (alt.indexOf(']') >= 0)) { - // Translocations - - // Parse ALT string - boolean left = alt.indexOf(']') >= 0; - String sep = (left ? "\\]" : "\\["); - String tpos[] = alt.split(sep); - String pos = tpos[1]; - boolean before = (alt.indexOf(']') == 0) || (alt.indexOf('[') == 0); - String altBases = (before ? tpos[2] : tpos[0]); - - // Parse 'chr:start' - String posSplit[] = pos.split(":"); - String trChrName = posSplit[0]; - Chromosome trChr = chromo.getGenome().getOrCreateChromosome(trChrName); - int trStart = Gpr.parseIntSafe(posSplit[1]) - 1; - - VariantBnd var = new VariantBnd(chromo, start, ref, altBases, trChr, trStart, left, before); - list = new LinkedList<>(); - list.add(var); + list = variantsTranslocation(chromo, start, reference, alt, id); } else if (reference.length() == alt.length()) { - // Case: MNP (note that SNPs were covers at the beginning of this if/else clause) - // MNPs - // 20 3 . TC AT . PASS DP=100 - // Sometimes the first bases are the same and we can trim them - int startDiff = Integer.MAX_VALUE; - for (int i = 0; i < reference.length(); i++) - if (reference.charAt(i) != alt.charAt(i)) startDiff = Math.min(startDiff, i); - - // MNPs - // Sometimes the last bases are the same and we can trim them - int endDiff = 0; - for (int i = reference.length() - 1; i >= 0; i--) - if (reference.charAt(i) != alt.charAt(i)) endDiff = Math.max(endDiff, i); - - String newRef = reference.substring(startDiff, endDiff + 1); - String newAlt = alt.substring(startDiff, endDiff + 1); - list = Variant.factory(chromo, start + startDiff, newRef, newAlt, id, vcfFileIterator.isExpandIub()); + list = variantsMnp(chromo, start, reference, alt, id); } else { - // Short Insertions, Deletions or Mixed Variants (substitutions) - VcfRefAltAlign align = new VcfRefAltAlign(alt, reference); - align.align(); - int startDiff = align.getOffset(); + list = variantsInDelMixed(chromo, start, reference, alt, id); + } - switch (align.getVariantType()) { + if (list == null) list = new LinkedList<>(); + else { + // Assign the original 'ALT' to the genotype field, so we can trace it back even if we changed the 'ALT' when creating the variant + for (Variant variant : list) { + variant.setGenotype(alt); + } + } + return list; + } + + /** + * Create a list of Ins/Del/Mixed variants + */ + List variantsInDelMixed(Chromosome chromo, int start, String reference, String alt, String id) { + // Short Insertions, Deletions or Mixed Variants (substitutions) + VcfRefAltAlign align = new VcfRefAltAlign(alt, reference); + align.align(); + int startDiff = align.getOffset(); + + switch (align.getVariantType()) { case DEL: // Case: Deletion // 20 2 . TC T . PASS DP=100 @@ -1607,8 +1615,7 @@ List variants(Chromosome chromo, int start, String reference, String al String ref = ""; String ch = align.getAlignment(); if (!ch.startsWith("-")) throw new RuntimeException("Deletion '" + ch + "' does not start with '-'. This should never happen!"); - list = Variant.factory(chromo, start + startDiff, ref, ch, id, vcfFileIterator.isExpandIub()); - break; + return Variant.factory(chromo, start + startDiff, ref, ch, id, vcfFileIterator.isExpandIub()); case INS: // Case: Insertion of A { tC ; tCA } tC is the reference allele @@ -1616,28 +1623,160 @@ List variants(Chromosome chromo, int start, String reference, String al ch = align.getAlignment(); ref = ""; if (!ch.startsWith("+")) throw new RuntimeException("Insertion '" + ch + "' does not start with '+'. This should never happen!"); - list = Variant.factory(chromo, start + startDiff, ref, ch, id, vcfFileIterator.isExpandIub()); - break; + return Variant.factory(chromo, start + startDiff, ref, ch, id, vcfFileIterator.isExpandIub()); case MIXED: // Case: Mixed variant (substitution) reference = reference.substring(startDiff); alt = alt.substring(startDiff); - list = Variant.factory(chromo, start + startDiff, reference, alt, id, vcfFileIterator.isExpandIub()); - break; - + return Variant.factory(chromo, start + startDiff, reference, alt, id, vcfFileIterator.isExpandIub()); + default: - // Other change type? - throw new RuntimeException("Unsupported VCF change type '" + align.getVariantType() + "'\n\tRef: " + reference + "'\n\tAlt: '" + alt + "'\n\tVcfEntry: " + this); - } + throw new RuntimeException("Expecting either 'INS', 'DEL', or 'MIXED'. Unsupported type '" + align.getVariantType() + "'\n\tRef: " + reference + "'\n\tAlt: '" + alt + "'\n\tVcfEntry: " + this); } + } + + /** + * Create a list of MNP variants + * Example of VCF MNP entry: + * 20 3 . TC AT . PASS DP=100 + */ + List variantsMnp(Chromosome chromo, int start, String reference, String alt, String id) { + // Sometimes the first bases are the same and we can trim them + int startDiff = Integer.MAX_VALUE; + for (int i = 0; i < reference.length(); i++) + if (reference.charAt(i) != alt.charAt(i)) startDiff = Math.min(startDiff, i); + + // Sometimes the last bases are the same and we can trim them + int endDiff = 0; + for (int i = reference.length() - 1; i >= 0; i--) + if (reference.charAt(i) != alt.charAt(i)) endDiff = Math.max(endDiff, i); + + String newRef = reference.substring(startDiff, endDiff + 1); + String newAlt = alt.substring(startDiff, endDiff + 1); + List list = Variant.factory(chromo, start + startDiff, newRef, newAlt, id, vcfFileIterator.isExpandIub()); + return list; + } - //--- - // Add original 'ALT' field as genotype - //--- - if (list == null) list = new LinkedList<>(); - for (Variant variant : list) - variant.setGenotype(alt); + /** + * Create a list of structural variants + * See VCF specification sections 3 "INFO keys used for structural variants", and 4 "FORMAT keys used for structural variants" + * + * From section 3: + * ``` + * The following INFO keys are reserved for encoding structural variants. In general, when these keys are used by imprecise + * variants, the values should be best estimates + * + * ##INFO= + * Indicates that this record contains an imprecise structural variant ALT allele... + * + * ##INFO= + * END has been deprecated in favour of INFO SVLEN and FORMAT LEN. + * + * ##INFO= + * This field has been deprecated due to redundancy with ALT. Refer to section 1.4.5 for the set of + * valid ALT field symbolic structural variant alleles. + * + * ##INFO= + * SVLEN must be specified for symbolic structural variant alleles. SVLEN is defined for INS, DUP, INV, + * and DEL symbolic alleles as the number of the inserted, duplicated, inverted, and deleted bases + * respectively. SVLEN is defined for CNV symbolic alleles as the length of the segment over which the + * copy number variant is defined. + * For backwards compatibility, a missing SVLEN should be inferred from the END field. + * For backwards compatibility, the absolute value of SVLEN should be taken and a negative SVLEN should + * be treated as positive values. + * ``` + */ + List variantsStructural(Chromosome chromo, int start, String reference, String alt, String id) { + List list = null; + + // Structural variants + if (alt.startsWith(" variants + * 2 321682 . T 6 PASS IMPRECISE;SVTYPE=DEL;END=321887;SVLEN=-105;CIPOS=-56,20;CIEND=-10,62 + */ + List variantsStructuralDel(Chromosome chromo, int start, String reference, String alt, String id) { + String refVariant = ref; + + if (end > start) { + int svlen = end - start + 1; + refVariant = padNs(ref, svlen); + } + return Variant.factory(chromo, start, refVariant, "", id, false); + } + + /** + * Create a list of variants + */ + List variantsStructuralDup(Chromosome chromo, int start, String reference, String alt, String id) { + // VCF Specification (version 4.5) FORMAT keys used for structural variants + int svlen = end - start + 1; + var altDup = padNs(ref + ref, svlen); + Variant var = new Variant(chromo, start, ref, altDup, id); + var.setVariantType(VariantType.DUP); + List list = new LinkedList<>(); + list.add(var); + return list; + } + + /** + * Create a list of variants + */ + List variantsStructuralInv(Chromosome chromo, int start, String reference, String alt, String id) { + // Inversion + var altInv = new StringBuffer(ref).reverse().toString(); + int svlen = end - start + 1; + altInv = padNs(altInv, svlen); + Variant var = new Variant(chromo, start, reference, altInv, id); + var.setVariantType(VariantType.INV); + List list = new LinkedList<>(); + list.add(var); + return list; + } + + /** + * Create a list of translocation variants + */ + List variantsTranslocation(Chromosome chromo, int start, String reference, String alt, String id) { + List list = null; + + // Parse ALT string + boolean left = alt.indexOf(']') >= 0; + String sep = (left ? "\\]" : "\\["); + String tpos[] = alt.split(sep); + String pos = tpos[1]; + boolean before = (alt.indexOf(']') == 0) || (alt.indexOf('[') == 0); + String altBases = (before ? tpos[2] : tpos[0]); + + // Parse 'chr:start' + String posSplit[] = pos.split(":"); + String trChrName = posSplit[0]; + Chromosome trChr = chromo.getGenome().getOrCreateChromosome(trChrName); + int trStart = Gpr.parseIntSafe(posSplit[1]) - 1; + + VariantBnd var = new VariantBnd(chromo, start, ref, altBases, trChr, trStart, left, before); + list = new LinkedList<>(); + list.add(var); return list; } diff --git a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationDup.java b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationDup.java index b50895b5..d5d84052 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationDup.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/integration/TestCasesIntegrationDup.java @@ -21,10 +21,9 @@ public TestCasesIntegrationDup() { super(); } - /** - */ @Test public void test_01_dup() { + verbose = true; Log.debug("Test"); String genome = "testHg19Chr8"; @@ -38,6 +37,7 @@ public void test_01_dup() { snpeff.setVerbose(verbose); snpeff.setSupressOutput(!verbose); snpeff.setFormatVersion(EffFormatVersion.FORMAT_ANN_1); + snpeff.setTesting(true); // The problem appears when splice site is large (in this example) snpeff.setUpDownStreamLength(0); diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 4cf6e8df..78095f57 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -37,7 +37,6 @@ public TestCasesVcf() { */ @Test public void test_00() { - Log.debug("Test"); String fileName = path("1kg_head.vcf"); VcfFileIterator vcf = new VcfFileIterator(fileName); @@ -51,7 +50,6 @@ public void test_00() { */ @Test public void test_01() { - Log.debug("Test"); String fileName = path("vcf.vcf"); VcfFileIterator vcf = new VcfFileIterator(fileName); vcf.setCreateChromos(true); @@ -69,7 +67,6 @@ public void test_01() { */ @Test public void test_04_del() { - Log.debug("Test"); String fileName = path("vcf_04_del.vcf"); VcfFileIterator vcf = new VcfFileIterator(fileName); vcf.setCreateChromos(true); @@ -86,7 +83,6 @@ public void test_04_del() { */ @Test public void test_05_choking_on_dot_slash_dot() { - Log.debug("Test"); String fileName = path("choking_on_dot_slash_dot.vcf"); VcfFileIterator vcf = new VcfFileIterator(fileName); vcf.setCreateChromos(true); @@ -118,7 +114,6 @@ public void test_05_choking_on_dot_slash_dot() { @Test public void test_06_mixed_change() { // WARNING: This test is expected to fail, because this functionality is unimplemented - Log.debug("Test"); String file = path("array_out_of_bounds.vcf"); VcfFileIterator vcf = new VcfFileIterator(file); @@ -140,7 +135,6 @@ public void test_06_mixed_change() { */ @Test public void test_07_long_lines() { - Log.debug("Test"); String file = path("long.vcf"); @@ -166,7 +160,6 @@ public void test_07_long_lines() { */ @Test public void test_08_alt_del() { - Log.debug("Test"); String file = path("alt_del.vcf"); @@ -192,7 +185,6 @@ public void test_08_alt_del() { */ @Test public void test_09_empty_ALT() { - Log.debug("Test"); String file = path("empty.vcf"); VcfFileIterator vcf = new VcfFileIterator(file); @@ -207,7 +199,6 @@ public void test_09_empty_ALT() { */ @Test public void test_10_empty_QUAL() { - Log.debug("Test"); String file = path("empty.vcf"); VcfFileIterator vcf = new VcfFileIterator(file); @@ -222,7 +213,6 @@ public void test_10_empty_QUAL() { */ @Test public void test_11_empty() { - Log.debug("Test"); String file = path("empty.vcf"); VcfFileIterator vcf = new VcfFileIterator(file); @@ -234,7 +224,6 @@ public void test_11_empty() { @Test public void test_12_readHeader() { - Log.debug("Test"); String file = path("test.chr1.1line.vcf"); VcfFileIterator vcfFile = new VcfFileIterator(file); @@ -254,7 +243,6 @@ public void test_12_readHeader() { */ @Test public void test_12_readHeader_NL() { - Log.debug("Test"); String file = path("test.chr1.1line.vcf"); VcfFileIterator vcfFile = new VcfFileIterator(file); @@ -265,7 +253,6 @@ public void test_12_readHeader_NL() { @Test public void test_13_chrOri() { - Log.debug("Test"); String file = path("test.chr1.1line.vcf"); VcfFileIterator vcfFile = new VcfFileIterator(file); @@ -280,7 +267,6 @@ public void test_13_chrOri() { @Test public void test_14_VcfInfoKey() { - Log.debug("Test"); new VcfOutputFormatter((List) null); String testIn[] = {"Hi ", "Hi how;", "Hi how;are|", "Hi how;are|you,", "Hi how;are|you,doing=", "Hi how;are|you,doing=today(.)", ".ann"}; String testOut[] = {"Hi_", "Hi_how_", "Hi_how_are_", "Hi_how_are_you_", "Hi_how_are_you_doing_", "Hi_how_are_you_doing_today_._", "_.ann"}; @@ -293,7 +279,6 @@ public void test_14_VcfInfoKey() { @Test public void test_14_VcfInfoValue() { - Log.debug("Test"); new VcfOutputFormatter((List) null); String testIn[] = {"Hi ", "Hi how;", "Hi how;are|", "Hi how;are|you,", "Hi how;are|you,doing=", "Hi how;are|you,doing=today(.)"}; String testOut[] = {"Hi_", "Hi_how_", "Hi_how_are_", "Hi_how_are_you_", "Hi_how_are_you_doing_", "Hi_how_are_you_doing_today_._"}; @@ -306,7 +291,6 @@ public void test_14_VcfInfoValue() { @Test public void test_15_Eff_format_version_guess() { - Log.debug("Test"); String vcfFileName = path("test.EFF_V2.vcf"); EffFormatVersion formatVersion = formatVersion(vcfFileName); assertEquals(EffFormatVersion.FORMAT_EFF_2, formatVersion); @@ -318,7 +302,6 @@ public void test_15_Eff_format_version_guess() { @Test public void test_16_indels() { - Log.debug("Test"); String vcfFile = path("1kg.indels.vcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFile); @@ -345,7 +328,6 @@ public void test_16_indels() { @Test public void test_18_vcf_tabix() { - Log.debug("Test"); VcfFileIterator vcf = new VcfFileIterator(path("test_tabix.vcf.gz")); String chrpos = ""; @@ -360,7 +342,6 @@ public void test_18_vcf_tabix() { @Test public void test_22_huge_headers() { - Log.debug("Test"); String vcfFile = path("huge_header_slow.vcf.gz"); Timer timer = new Timer(); @@ -376,7 +357,6 @@ public void test_22_huge_headers() { @Test public void test_23_VcfUnsorted() { - Log.debug("Test"); String vcfFile = path("out_of_order.vcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFile); @@ -424,6 +404,7 @@ public void test_24_VcfEffect_parse_SO() { */ @Test public void test_25_Genomic_VCF() { + verbose = true; String vcfFileName = path("genomic_vcf.gvcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFileName); @@ -444,7 +425,8 @@ public void test_25_Genomic_VCF() { } if (!ok) throw new RuntimeException("Variant type should be '" + ve.getInfo("Type") + "'\n" + ve); - start += ve.size(); + System.out.println("START: " + start + "\tve.START: " + ve.getStart() + "\tEND:" + ve.getEnd() + "\tSIZE: " + ve.size()); + start = ve.getEnd() + 1; } } @@ -453,7 +435,6 @@ public void test_25_Genomic_VCF() { */ @Test public void test_26_vcfInfoHeaderAdd() { - Log.debug("Test"); String vcfFileName = path("example_42.vcf"); // Create a new INFO field @@ -486,7 +467,6 @@ public void test_26_vcfInfoHeaderAdd() { */ @Test public void test_27_vcfInfoHeaderReplace() { - Log.debug("Test"); String infoFieldName = "NEW_INFO"; String vcfFileName = path("example_42.vcf"); @@ -530,7 +510,6 @@ public void test_27_vcfInfoHeaderReplace() { */ @Test public void test_28_vcfInfoReplace() { - Log.debug("Test"); String vcfFileName = path("example_42.vcf"); @@ -565,7 +544,6 @@ public void test_28_vcfInfoReplace() { */ @Test public void test_29() { - Log.debug("Test"); String fileName = path("test_vcf_ann_plus_sign.vcf"); VcfFileIterator vcf = new VcfFileIterator(fileName); @@ -587,7 +565,6 @@ public void test_29() { */ @Test public void test_30_gVCF_NON_REF() { - Log.debug("Test"); String vcfFileName = path("test_gVCF_NON_REF.vcf"); @@ -649,7 +626,6 @@ public void test_32_VcfInfoKeyNames() { @Test public void test_33_translocations() { - Log.debug("Test"); String vcfFile = path("vcf_translocation.vcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFile); @@ -677,7 +653,6 @@ public void test_34_vcfInfoEncoding() { @Test public void test_35_translocations_parsing() { - Log.debug("Test"); String vcfFile = path("vcf_translocation_parsing.vcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFile); @@ -700,7 +675,6 @@ public void test_35_translocations_parsing() { @Test public void test_36_cleanupUnderscores() { - Log.debug("Test"); verbose = true; debug = true; assertEquals("", VcfEntry.cleanUnderscores("")); @@ -717,7 +691,6 @@ public void test_36_cleanupUnderscores() { @Test public void test_37_inversions_parsing() { - Log.debug("Test"); String vcfFile = path("test_inv.vcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFile); @@ -755,5 +728,80 @@ public void test_37_inversions_parsing() { assertEquals(startExpected, inv.getStart()); assertEquals(endExpected, inv.getEnd()); } + + @Test + public void test_38_DEL_01() { + String vcfContent = "2\t321682\t.\tT\t\t6\tPASS\tIMPRECISE;SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("2", ve.getChromosomeName()); + assertEquals(321682, ve.getStart()); + assertEquals(321887 - 1, ve.getEnd()); + assertEquals(321887 - 321682, Math.abs(ve.getInfoInt("SVLEN"))); + Variant var = ve.variants().get(0); + assertEquals(VariantType.DEL, var.getVariantType()); + } + + @Test + public void test_39_DEL_02() { + String vcfContent = "chrA\t2\t.\tT\t\t.\t.\tSVLEN=2;SVCLAIM=DJ;EVENT=DEL_symbolic"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("A", ve.getChromosomeName()); + assertEquals(2, ve.getStart()); + assertEquals(3, ve.getEnd()); + assertEquals(2, Math.abs(ve.getInfoInt("SVLEN"))); + Variant var = ve.variants().get(0); + assertEquals(VariantType.DEL, var.getVariantType()); + } + + @Test + public void test_40_DUP() { + String vcfContent = "chrA\t5\t.\tG\t\t.\t.\tSVLEN=3;CIPOS=0,5;EVENT=homology_dup"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("A", ve.getChromosomeName()); + assertEquals(5, ve.getStart()); + assertEquals(7, ve.getEnd()); + assertEquals(3, Math.abs(ve.getInfoInt("SVLEN"))); + Variant var = ve.variants().get(0); + assertEquals(VariantType.DUP, var.getVariantType()); + } + + // @Test + // public void test_41_INS() { + // String vcfContent = "chrA\t14\t.\tT\t\t.\t.\tIMPRECISE;SVLEN=100;CILEN=-50,50;CIPOS=-10,10"; + // VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + // VcfEntry ve = vi.next(); + + // // Check VCF entry + // assertEquals("A", ve.getChromosomeName()); + // assertEquals(14, ve.getStart()); + // assertEquals(113, ve.getEnd()); + // assertEquals(100, Math.abs(ve.getInfoInt("SVLEN"))); + // Variant var = ve.variants().get(0); + // assertEquals(VariantType.INS, var.getVariantType()); + // } + + @Test + public void test_42_INV() { + String vcfContent = "chrA\t14\t.\tT\t\t.\t.\tIMPRECISE;SVLEN=100;CILEN=-50,50;CIPOS=-10,10"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("A", ve.getChromosomeName()); + assertEquals(14, ve.getStart()); + assertEquals(113, ve.getEnd()); + assertEquals(100, Math.abs(ve.getInfoInt("SVLEN"))); + Variant var = ve.variants().get(0); + assertEquals(VariantType.INV, var.getVariantType()); + } } diff --git a/test_04_TestCasesEff.csv b/test_04_TestCasesEff.csv index 8497dcb5..baad014d 100644 --- a/test_04_TestCasesEff.csv +++ b/test_04_TestCasesEff.csv @@ -3,8 +3,8 @@ Name , Value Genome , testHg3770Chr22 -Date , 2024-04-09 11:48 -SnpEff_version , SnpEff 5.2c (build 2024-04-09 11:45), by Pablo Cingolani +Date , 2024-09-13 08:41 +SnpEff_version , SnpEff 5.2c (build 2024-09-13 04:51), by Pablo Cingolani Command_line_arguments , SnpEff -csvStats test_04_TestCasesEff.csv testHg3770Chr22 tests/integration/eff/eff_sort.vcf Warnings , 1096 Number_of_lines_in_input_file, 1205 From 37f72e10583f54c08bc8d86fdc5644f468c8aaa3 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sat, 21 Sep 2024 13:05:02 +0200 Subject: [PATCH 13/21] Split tests --- src/main/java/org/snpeff/vcf/VcfEntry.java | 232 ++++++++---------- .../testCases/unity/TestCasesVcf.java | 24 +- tests/unity/vcf/test_inv.vcf | 1 - tests/unity/vcf/test_inv_2.vcf | 2 + 4 files changed, 120 insertions(+), 139 deletions(-) create mode 100644 tests/unity/vcf/test_inv_2.vcf diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index e829dfec..03f94f94 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -41,10 +41,8 @@ public enum AlleleFrequencyType { public static final String[] EMPTY_STRING_ARRAY = new String[0]; public static final double ALLELE_FEQUENCY_COMMON = 0.05; public static final double ALLELE_FEQUENCY_LOW = 0.01; + public static final Pattern INFO_KEY_PATTERN = Pattern.compile("[\\p{Alpha}_][\\p{Alnum}._]*"); - public static final String VCF_INFO_END = "END"; // Imprecise variants. Deprecated: "END has been deprecated in favour of INFO SVLEN and FORMAT LEN." - public static final String VCF_INFO_SVLEN = "SVLEN"; // "SVLEN must be specified for symbolic structural variant alleles" - public static final String VCF_INFO_IMPRECISE = "IMPRECISE"; // IMPRECISE must be specified for imprecise structural variant alleles // In order to report sequencing data evidence for both variant and non-variant positions in the genome, the VCF // specification allows to represent blocks of reference-only calls in a single record using the END INFO tag, an idea @@ -55,18 +53,39 @@ public enum AlleleFrequencyType { public static final String VCF_ALT_NON_REF = "<*>"; // See VCF 4.2 section "5.5 Representing unspecified alleles and REF-only blocks (gVCF)" public static final String VCF_ALT_NON_REF_OLD = ""; // NON_REF tag for ALT field (only in gVCF fields (olf version of '<*>') public static final String VCF_ALT_MISSING_REF = "*"; // The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion (see VCF 4.3 spec., ALT definition) + public static final String VCF_ALT_INV = ""; // Inversion + public static final String[] VCF_ALT_A_ARRAY = { "A" }; + public static final String[] VCF_ALT_C_ARRAY = { "C" }; + public static final String[] VCF_ALT_G_ARRAY = { "G" }; + public static final String[] VCF_ALT_T_ARRAY = { "T" }; + public static final String[] VCF_ALT_N_ARRAY = { "A", "C", "G", "T" }; // aNy base + public static final String[] VCF_ALT_B_ARRAY = { "C", "G", "T" }; // B: Not 'A' + public static final String[] VCF_ALT_D_ARRAY = { "A", "G", "T" }; // D: not 'C' + public static final String[] VCF_ALT_H_ARRAY = { "A", "C", "T" }; // H: No 'G' + public static final String[] VCF_ALT_V_ARRAY = { "A", "C", "G" }; // V: Not 'T' + public static final String[] VCF_ALT_M_ARRAY = { "A", "C" }; + public static final String[] VCF_ALT_R_ARRAY = { "A", "G" }; + public static final String[] VCF_ALT_W_ARRAY = { "A", "T" }; // Weak + public static final String[] VCF_ALT_S_ARRAY = { "C", "G" }; // Strong + public static final String[] VCF_ALT_Y_ARRAY = { "C", "T" }; + public static final String[] VCF_ALT_K_ARRAY = { "G", "T" }; + public static final String[] VCF_ALT_ASTERISK_ARRAY = { "*" }; + public static final String[] VCF_ALT_MISSING_ARRAY = { "." }; + public static final String[] VCF_ALT_NON_REF_OLD_ARRAY = { VCF_ALT_NON_REF_OLD }; public static final String[] VCF_ALT_NON_REF_ARRAY = { VCF_ALT_NON_REF }; - public static final String[] VCF_ALT_MISSING_REF_ARRAY = { VCF_ALT_MISSING_REF }; + // public static final String[] VCF_ALT_MISSING_REF_ARRAY = { VCF_ALT_MISSING_REF }; public static final String[] VCF_ALT_INV_ARRAY = { VCF_ALT_INV }; + public static final String VCF_INFO_END = "END"; // Imprecise variants. Deprecated: "END has been deprecated in favour of INFO SVLEN and FORMAT LEN." + public static final String VCF_INFO_SVLEN = "SVLEN"; // "SVLEN must be specified for symbolic structural variant alleles" + public static final String VCF_INFO_IMPRECISE = "IMPRECISE"; // IMPRECISE must be specified for imprecise structural variant alleles public static final String VCF_INFO_HOMS = "HO"; public static final String VCF_INFO_HETS = "HE"; public static final String VCF_INFO_NAS = "NA"; - - public static final String VCF_INFO_PRIVATE = "Private"; + public static final String VCF_INFO_PRIVATE = "Private"; // Private variant private static final Map INFO_VALUE_ENCODE; @@ -242,7 +261,7 @@ public VcfEntry(VcfFileIterator vcfFileIterator, Marker parent, String chromosom this.infoStr = infoStr; parseInfo(); this.format = format; - parseEnd(); + this.end = parseEnd(); } /** @@ -866,7 +885,7 @@ public boolean isAltNonRef(String alt) { */ public boolean isBiAllelic() { if (alts == null) return false; - return alts.length == 1; // Only one ALT option? => homozygous + return alts.length == 1; // Only one ALT option? } /** @@ -886,7 +905,7 @@ public boolean isFilterPass() { */ public boolean isMultiallelic() { if (alts == null) return false; - return alts.length > 1; // More than one ALT option? => not homozygous + return alts.length > 1; // More than one ALT option? } @Override @@ -1023,8 +1042,6 @@ public void parse() { parent = chromo; vcfFileIterator.sanityCheckChromo(chromosomeName, chromo); // Sanity check - // Start - start = vcfFileIterator.parsePosition(vcfFileIterator.readField(fields, 1)); // ID (e.g. might indicate dbSnp) id = vcfFileIterator.readField(fields, 2); @@ -1050,7 +1067,9 @@ public void parse() { info = null; // Start & End coordinates are anchored to the reference genome, thus based on REF field (ALT is not taken into account) - parseEnd(); + // But INFO fields can affect Start & End coordinates, for example in cases of imprecise variants + this.start = parseStart(vcfFileIterator.readField(fields, 1)); + this.end = parseEnd(); // Genotype format format = null; @@ -1065,8 +1084,11 @@ public void parse() { * Parse ALT field */ String[] parseAlts(String altsStr) { - if (altsStr.length() == 1 || altsStr.indexOf(',') < 0) { - // SNP or single field (no commas) + if (altsStr.length() == 1) { + // Probably a SNP (single character) + return parseAltSingleChar(altsStr); + } else if (altsStr.indexOf(',') < 0) { + // Single field (no commas) alts = parseAltSingle(altsStr); return alts != null ? alts : new String[0]; } else { @@ -1090,130 +1112,85 @@ String[] parseAlts(String altsStr) { } /** - * Parse single ALT record, return parsed ALTS + * Parse single ALT record which is NOT a SNP, return parsed ALTS + * Return null if it is not a variant */ String[] parseAltSingle(String altsStr) { - if (altsStr.length() != 1 // Not a SNP? Do not expand - || !isVariant(altsStr) // Not a variant? Do not expand - || !vcfFileIterator.isExpandIub() // Do not expand IUB option? - ) { - String alts[] = { altsStr }; - return alts; + if (altsStr.length() == 1) return parseAltSingleChar(altsStr); + // // TODO: Remove? + // // Not a variant? + // if (altsStr.equals(VCF_ALT_NON_REF)) return VCF_ALT_NON_REF_ARRAY; + // if (altsStr.equals(VCF_ALT_NON_REF_OLD)) return VCF_ALT_NON_REF_OLD_ARRAY; + // if (altsStr.equals(VCF_ALT_INV)) return VCF_ALT_INV_ARRAY; + + // Other cases + return new String[] { altsStr }; + } + + /** + * Parse single ALT record which is a SNP, expand IUB codes + * Return parsed ALTS + */ + String[] parseAltSingleChar(String altsStr) { + // Standard SNPs, no IUB expansion + switch (altsStr) { + case "A": return VCF_ALT_A_ARRAY; + case "C": return VCF_ALT_C_ARRAY; + case "G": return VCF_ALT_G_ARRAY; + case "T": return VCF_ALT_T_ARRAY; + case "*": return VCF_ALT_ASTERISK_ARRAY; + case ".": return VCF_ALT_MISSING_ARRAY; } - // Not a variant? - if (altsStr.equals(VCF_ALT_NON_REF)) { return VCF_ALT_NON_REF_ARRAY; } - if (altsStr.equals(VCF_ALT_MISSING_REF)) { return VCF_ALT_MISSING_REF_ARRAY; } - if (altsStr.equals(VCF_ALT_NON_REF_OLD)) { return VCF_ALT_NON_REF_OLD_ARRAY; } - if (altsStr.equals(VCF_ALT_INV)) { return VCF_ALT_INV_ARRAY; } + // Is IUB expantion enabled? + if(!vcfFileIterator.isExpandIub() ) return new String[] { altsStr }; // SNP IUB conversion table - String alts[]; switch (altsStr) { - case "A": - case "C": - case "G": - case "T": - case "*": - case ".": - alts = new String[1]; - alts[0] = altsStr; - break; - - case "N": // aNy base - alts = new String[4]; - alts[0] = "A"; - alts[1] = "C"; - alts[2] = "G"; - alts[3] = "T"; - break; - - case "B": // B: not A - alts = new String[3]; - alts[0] = "C"; - alts[1] = "G"; - alts[2] = "T"; - break; - - case "D": // D: not C - alts = new String[3]; - alts[0] = "A"; - alts[1] = "G"; - alts[2] = "T"; - break; - - case "H": // H: not G - alts = new String[3]; - alts[0] = "A"; - alts[1] = "C"; - alts[2] = "T"; - break; - - case "V": // V: not T - alts = new String[3]; - alts[0] = "A"; - alts[1] = "C"; - alts[2] = "G"; - break; - - case "M": - alts = new String[2]; - alts[0] = "A"; - alts[1] = "C"; - break; - - case "R": - alts = new String[2]; - alts[0] = "A"; - alts[1] = "G"; - break; - - case "W": // Weak - alts = new String[2]; - alts[0] = "A"; - alts[1] = "T"; - break; - - case "S": // Strong - alts = new String[2]; - alts[0] = "C"; - alts[1] = "G"; - break; - - case "Y": - alts = new String[2]; - alts[0] = "C"; - alts[1] = "T"; - break; - - case "K": - alts = new String[2]; - alts[0] = "G"; - alts[1] = "T"; - break; - - default: - throw new RuntimeException("WARNING: Unkown IUB code for SNP '" + altsStr + "'"); + case "N": return VCF_ALT_N_ARRAY; + case "B": return VCF_ALT_B_ARRAY; + case "D": return VCF_ALT_D_ARRAY; + case "H": return VCF_ALT_H_ARRAY; + case "V": return VCF_ALT_V_ARRAY; + case "M": return VCF_ALT_M_ARRAY; + case "R": return VCF_ALT_R_ARRAY; + case "W": return VCF_ALT_W_ARRAY; + case "S": return VCF_ALT_S_ARRAY; + case "Y": return VCF_ALT_Y_ARRAY; + case "K": return VCF_ALT_K_ARRAY; + default: + throw new RuntimeException("WARNING: Unkown IUB code for SNP '" + altsStr + "'"); } + } - return alts; + /** + * Parse 'start' coordinate + */ + int parseStart(String startStr) { + int start = vcfFileIterator.parsePosition(startStr); + + // In some cases we need to adjust the start possition + // In "non-ref" (i.e. '<*>' or ) cases, we don't need to adjust the start position + // Imprecise variants are indicated by an angle brackets '<...>', for example + // when we have , , , , or similar, we need to adjust the 'start'possition + // From VCF specification: + // ```Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant.``` + if (altStr.indexOf('<') >= 0 && !hasAltNonRef() ) { + start++; + } + + return start; } /** * Parse 'end' coordinate */ - void parseEnd() { + int parseEnd() { + // SNP or single char variant? + if( altStr.length() == 1 ) return start; + // Imprecise variants are indicated by an angle brackets '<...>' if (altStr.indexOf('<') >= 0 ) { - !!!!!!!! MOVE TO PARSE START - if( hasAltNonRef() ) { - // Non-ref alt: '<*>' or - } else { - // , , , , or similar - // "Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant." - start++; - } - if ( hasInfo(VCF_INFO_SVLEN) ) { // From VCF specification: // ``` @@ -1227,19 +1204,22 @@ void parseEnd() { // "For backwards compatibility, the absolute value of SVLEN should be taken and a negative SVLEN // should be treated as positive values." if (svlen < 0) svlen = -svlen; - end = start + svlen - 1; + return start + svlen - 1; } else if ( hasInfo(VCF_INFO_END) ) { // "For backwards compatibility, a missing SVLEN should be inferred from the END field." // Get 'END' field and do some sanity check end = (int) getInfoInt(VCF_INFO_END) - 1; if (end < start) { throw new RuntimeException("INFO field 'END' is before varaint's 'POS'\n\tEND : " + end + "\n\tPOS : " + start); } + return end; } else { // If no SVLEN or END field is present, we can't infer the end position, we'll use 'ref' length - end = start + ref.length() - 1; + return start + ref.length() - 1; } - } else { - end = start + ref.length() - 1; } + + // Normal variants (i.e. not imprecise) + // We use 'ref' length to calculate 'end' position + return start + ref.length() - 1; } /** diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 78095f57..060562d8 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -404,7 +404,6 @@ public void test_24_VcfEffect_parse_SO() { */ @Test public void test_25_Genomic_VCF() { - verbose = true; String vcfFileName = path("genomic_vcf.gvcf"); VcfFileIterator vcf = new VcfFileIterator(vcfFileName); @@ -425,7 +424,6 @@ public void test_25_Genomic_VCF() { } if (!ok) throw new RuntimeException("Variant type should be '" + ve.getInfo("Type") + "'\n" + ve); - System.out.println("START: " + start + "\tve.START: " + ve.getStart() + "\tEND:" + ve.getEnd() + "\tSIZE: " + ve.size()); start = ve.getEnd() + 1; } } @@ -675,7 +673,6 @@ public void test_35_translocations_parsing() { @Test public void test_36_cleanupUnderscores() { - verbose = true; debug = true; assertEquals("", VcfEntry.cleanUnderscores("")); assertEquals("", VcfEntry.cleanUnderscores("_")); @@ -710,17 +707,20 @@ public void test_37_inversions_parsing() { assertEquals(altExpected, inv.getAlt()); assertEquals(startExpected, inv.getStart()); assertEquals(endExpected, inv.getEnd()); + } - - // Read the second entry - ve = vcf.next(); + @Test + public void test_37_inversions_parsing_2() { + String vcfFile = path("test_inv_2.vcf"); + VcfFileIterator vcf = new VcfFileIterator(vcfFile); + VcfEntry ve = vcf.next(); if (verbose) Log.info(ve); - vars = ve.variants(); - inv = (Variant) vars.get(0); - refExpected = "CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; - altExpected = new StringBuilder(refExpected).reverse().toString(); - startExpected = 37973491; - endExpected = startExpected + refExpected.length() - 1; + var vars = ve.variants(); + var inv = (Variant) vars.get(0); + var refExpected = "CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; + var altExpected = new StringBuilder(refExpected).reverse().toString(); + var startExpected = 37973491; + var endExpected = startExpected + refExpected.length() - 1; assertEquals(1, vars.size()); assertEquals(VariantType.INV, inv.getVariantType()); assertEquals(refExpected, inv.getReference()); diff --git a/tests/unity/vcf/test_inv.vcf b/tests/unity/vcf/test_inv.vcf index c32afb6d..9d367f62 100644 --- a/tests/unity/vcf/test_inv.vcf +++ b/tests/unity/vcf/test_inv.vcf @@ -1,3 +1,2 @@ #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B_1_Lymphoma chr1 27360853 DRAGEN:INV:962:0:0:1:15:0 GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC . MinSomaticScore END=27360932;SVTYPE=INV;SVLEN=-79;CIGAR=1M79I79D;CONTIG=CACTATGTTCTTGTGGCGCAGGCGTCTGTGAAGAGCGATCTCTTCATGCAGGGGCTGAGAGAACCTGAGGGGAGGTAAGGGAGAGAGGAAAGGGACCGAGGTGGGCAGAGAAGCCCCGCCCATCCCACGCCAGCCTGGCCCCGCCCCAAGGACCCGCCCCGCCCACAAGCCCTCTCCGACCTTCCCCACCCTTACTACCCTGCCCACAGGACCCTCCAGACCTCAATCCCGCCCGCACGGTCCTGGCTGTTCCGCCCACGGGCCCAGTCCACAGGGCTCGAACTCTCAGGTCCTACGAGCCCGCCCACTAGGCCCCGCCCACAGGAGCCGCTCCGCTCGTGGCCCGGCTCACTCGGCCCTCGCGAGCCCTCAGCCCCACCCGCGCTGCCACGCACCGCACCTGCTGTCCCGCTCCGGGATCTCCTTGATGGCGATGCGCACCCTCGTGTGGCGATCGCGGCCCGCGTACACCACCCCATACGTGCCCTTGCCCAGCACCAGCCGCTCGCCCGTCTCCGTGTACTCATAATCAAACTGCCGGGCGCGGGGGAGATGTTGGAGGTGAGGACGCGGGACTGGGAGCTCGCGGAGGGCGAGGGGCCGCGGGCCCTGCTGAACTCCCATCTCACCCCGCGCCCTCCGCCTCCTCCGCGGGCGCCGTGGAATCCGGGTTCGTCACCCAGGCCTGGATCAGGCCGCAGAACCTGAAGGTGGGGGAGGTCAGACCCGCGGGAGGGGCATCTTGGTCCCCACCTAAGCCGGAGCATCCAACGGACGTCGTCCCTTTCTTTCCCCCACTCCCCCCCGGGCATCCTGGCCCTCAGAGTACCCCGACCATGAAAGGCTGCGCACCACTGGCAGTGCCCTACGCTGGGGAAGCACAGCTGGACGTCCTGAGCCGGGGGGAGTGCATAGAGGAAGCAGCAGCGCTCGTCGCGCTTTGAGGCG;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 1272,0:4027,3:3624,3 -chr22 37973492 DRAGEN:INV:49554:0:0:0:16:0 CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT . MinSomaticScore END=37973553;SVTYPE=INV;SVLEN=-61;CIGAR=1M61I61D;CONTIG=AACCTCCTTCTCCTCTGTCCAGCCTGTTCTCCTGGGGCTTTGCTGCTGGAGCCTGGATGGGGCGGGTGGGTCATCAGGGCAGTGAGCCAGACAGAAAGCCCCCCGACCTGTCAGCCTCTTCAGCCTCCTCAGCCTCCTCCACTGCCACCACCAGGCCTGAGGTGGGCAAGGAACAGGGCACACAGGCTGGGGGCAGGGGCTGGGCGGGGGGTGGTGGCGACAGGGCCCCAGTCCCACAGCCCCACACACTGGGAGCAGCCAGTATATACGACACTGTCCCGGCCCTAAAGGGGGCCCTGAGGGGCTGGGGTCAGAGATGGCCGTGTAGAGGGGCCGCTGCGAGGGCCCCATATAGGAGAAGGCCGAGTAGAGGCCAGAGGCCTGGCCCGAGTGGCCATAATAGGGTCCTGAGGGCTGATGGTCAGAGTAGTCAAACTGGGGGCGGGAGATGGAGGGGAAGGCTGAGCCATAGTGGGGCAGGCTGAGGGAGGTGTAGGCGATCTGTGAGGTGGATGGCTGGTCGGTGTAGTGTGGGGGCCCCTGGGGCCCCGCGGTCTCTGTCTTCACCTGGGCTTTGGCATCCACACCAGGTGGTGAGACCGTGGGCAGAGCCACGCCTGGTGGCTTGGAGATCCAGGCGGAGTGTCCACTGGCCACGGCCAGGGCACTGCCCAGCCCATAGCCGGCTGCTGAGTAGCTGCTCACATGGCCTGGGTGCCCATTGGGCGGCAGGTACTGGTCCAACTCAGCCACATCAAAGGTCTCCATGTTGGACATTACCTCGTGGCTGATCTCACCAATGTCCACGTTGCCGAAGTCGATGTGAGGCTTCCCGCCCTCCCCCATGGAGCGCCCGTCCCGCTTCGGGTCTGCCTTGCCCGACTGCAGCTCTGTCTTCGGGGTGGTTGGAGGGGTGGGTGGGCCATGGCTCTGGCCTGGGTAGAAGGGAGACAGAGAGAGAGAGCGCAAGGGGGAAGCAGGTTAGAGGCAGGTGGGCGCACGTGAACTTCCATGGTTCACCTTCAGGCAGCGGGTGCCTCTGGGAAAACCTTGTAAGTTTCACATTTTGGCAGCATGAGTCGGGTTTTTTTTTGTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGACTGGAGTGCAGTGGCGCCATCTCGGCTCACTGCA;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 705,0:2396,2:2155,2 diff --git a/tests/unity/vcf/test_inv_2.vcf b/tests/unity/vcf/test_inv_2.vcf new file mode 100644 index 00000000..562bc801 --- /dev/null +++ b/tests/unity/vcf/test_inv_2.vcf @@ -0,0 +1,2 @@ +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT B_1_Lymphoma +chr22 37973492 DRAGEN:INV:49554:0:0:0:16:0 CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT . MinSomaticScore END=37973553;SVTYPE=INV;SVLEN=-61;CIGAR=1M61I61D;CONTIG=AACCTCCTTCTCCTCTGTCCAGCCTGTTCTCCTGGGGCTTTGCTGCTGGAGCCTGGATGGGGCGGGTGGGTCATCAGGGCAGTGAGCCAGACAGAAAGCCCCCCGACCTGTCAGCCTCTTCAGCCTCCTCAGCCTCCTCCACTGCCACCACCAGGCCTGAGGTGGGCAAGGAACAGGGCACACAGGCTGGGGGCAGGGGCTGGGCGGGGGGTGGTGGCGACAGGGCCCCAGTCCCACAGCCCCACACACTGGGAGCAGCCAGTATATACGACACTGTCCCGGCCCTAAAGGGGGCCCTGAGGGGCTGGGGTCAGAGATGGCCGTGTAGAGGGGCCGCTGCGAGGGCCCCATATAGGAGAAGGCCGAGTAGAGGCCAGAGGCCTGGCCCGAGTGGCCATAATAGGGTCCTGAGGGCTGATGGTCAGAGTAGTCAAACTGGGGGCGGGAGATGGAGGGGAAGGCTGAGCCATAGTGGGGCAGGCTGAGGGAGGTGTAGGCGATCTGTGAGGTGGATGGCTGGTCGGTGTAGTGTGGGGGCCCCTGGGGCCCCGCGGTCTCTGTCTTCACCTGGGCTTTGGCATCCACACCAGGTGGTGAGACCGTGGGCAGAGCCACGCCTGGTGGCTTGGAGATCCAGGCGGAGTGTCCACTGGCCACGGCCAGGGCACTGCCCAGCCCATAGCCGGCTGCTGAGTAGCTGCTCACATGGCCTGGGTGCCCATTGGGCGGCAGGTACTGGTCCAACTCAGCCACATCAAAGGTCTCCATGTTGGACATTACCTCGTGGCTGATCTCACCAATGTCCACGTTGCCGAAGTCGATGTGAGGCTTCCCGCCCTCCCCCATGGAGCGCCCGTCCCGCTTCGGGTCTGCCTTGCCCGACTGCAGCTCTGTCTTCGGGGTGGTTGGAGGGGTGGGTGGGCCATGGCTCTGGCCTGGGTAGAAGGGAGACAGAGAGAGAGAGCGCAAGGGGGAAGCAGGTTAGAGGCAGGTGGGCGCACGTGAACTTCCATGGTTCACCTTCAGGCAGCGGGTGCCTCTGGGAAAACCTTGTAAGTTTCACATTTTGGCAGCATGAGTCGGGTTTTTTTTTGTTTTTTTTTTTTGAGATGGAGTTTCGCTCTTGTTGCCCAGACTGGAGTGCAGTGGCGCCATCTCGGCTCACTGCA;SOMATIC;SOMATICSCORE=0.00;SOMATIC_EVENT=1 PR:SR:VF 705,0:2396,2:2155,2 From ef42fddaaf26a80713eea1f5a63a2b10621e643e Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sat, 21 Sep 2024 14:45:47 +0200 Subject: [PATCH 14/21] Project updated --- src/main/java/org/snpeff/vcf/VcfEntry.java | 63 +++++++++++++------ .../testCases/unity/TestCasesVcf.java | 8 +-- 2 files changed, 47 insertions(+), 24 deletions(-) diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index 03f94f94..9a7391cb 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -1042,6 +1042,8 @@ public void parse() { parent = chromo; vcfFileIterator.sanityCheckChromo(chromosomeName, chromo); // Sanity check + // Start + start = vcfFileIterator.parsePosition(vcfFileIterator.readField(fields, 1)); // ID (e.g. might indicate dbSnp) id = vcfFileIterator.readField(fields, 2); @@ -1068,7 +1070,6 @@ public void parse() { // Start & End coordinates are anchored to the reference genome, thus based on REF field (ALT is not taken into account) // But INFO fields can affect Start & End coordinates, for example in cases of imprecise variants - this.start = parseStart(vcfFileIterator.readField(fields, 1)); this.end = parseEnd(); // Genotype format @@ -1163,24 +1164,24 @@ String[] parseAltSingleChar(String altsStr) { } } - /** - * Parse 'start' coordinate - */ - int parseStart(String startStr) { - int start = vcfFileIterator.parsePosition(startStr); + // /** + // * Parse 'start' coordinate + // */ + // int parseStart(String startStr) { + // int start = vcfFileIterator.parsePosition(startStr); - // In some cases we need to adjust the start possition - // In "non-ref" (i.e. '<*>' or ) cases, we don't need to adjust the start position - // Imprecise variants are indicated by an angle brackets '<...>', for example - // when we have , , , , or similar, we need to adjust the 'start'possition - // From VCF specification: - // ```Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant.``` - if (altStr.indexOf('<') >= 0 && !hasAltNonRef() ) { - start++; - } + // // In some cases we need to adjust the start possition + // // In "non-ref" (i.e. '<*>' or ) cases, we don't need to adjust the start position + // // Imprecise variants are indicated by an angle brackets '<...>', for example + // // when we have , , , , or similar, we need to adjust the 'start'possition + // // From VCF specification: + // // ```Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant.``` + // if (altStr.indexOf('<') >= 0 && !hasAltNonRef() ) { + // start++; + // } - return start; - } + // return start; + // } /** * Parse 'end' coordinate @@ -1712,8 +1713,12 @@ List variantsStructuralDup(Chromosome chromo, int start, String referen // VCF Specification (version 4.5) FORMAT keys used for structural variants int svlen = end - start + 1; var altDup = padNs(ref + ref, svlen); + + // Create the variant and set the type Variant var = new Variant(chromo, start, ref, altDup, id); var.setVariantType(VariantType.DUP); + + // Create a list of varinats List list = new LinkedList<>(); list.add(var); return list; @@ -1723,12 +1728,30 @@ List variantsStructuralDup(Chromosome chromo, int start, String referen * Create a list of variants */ List variantsStructuralInv(Chromosome chromo, int start, String reference, String alt, String id) { - // Inversion - var altInv = new StringBuffer(ref).reverse().toString(); + // In some cases we need to adjust the start possition + // In "non-ref" (i.e. '<*>' or ) cases, we don't need to adjust the start position + // Imprecise variants are indicated by an angle brackets '<...>', for example + // when we have , , , , or similar, we need to adjust the 'start'possition + // From VCF specification: + // ```Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant.``` + start++; + + // Calculate the 'ALT' sequence + // If 'REF' is more than a single character, then 'ALT' is 'REF' reversed + var altInv = alt; int svlen = end - start + 1; - altInv = padNs(altInv, svlen); + if(reference.length() > 1 ) { + reference = reference.substring(1); // Remove the first base + altInv = (new StringBuffer(reference)).reverse().toString(); + // Check that the length of the inverted sequence is the same as the reference + if( svlen > altInv.length() ) altInv = padNs(altInv, svlen); // Pad with Ns if necessary + } + + // Create the variant and set the type Variant var = new Variant(chromo, start, reference, altInv, id); var.setVariantType(VariantType.INV); + + // Create a list of varinats List list = new LinkedList<>(); list.add(var); return list; diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 060562d8..398f250f 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -697,8 +697,8 @@ public void test_37_inversions_parsing() { var vars = ve.variants(); var inv = (Variant) vars.get(0); if (verbose) Log.info(inv); - var refExpected = "GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC"; - var startExpected = 27360852; + var refExpected = "TGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC"; // In VCF the first base on an is not included + var startExpected = 27360853; var endExpected = startExpected + refExpected.length() - 1; var altExpected = new StringBuilder(refExpected).reverse().toString(); assertEquals(1, vars.size()); @@ -717,9 +717,9 @@ public void test_37_inversions_parsing_2() { if (verbose) Log.info(ve); var vars = ve.variants(); var inv = (Variant) vars.get(0); - var refExpected = "CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; + var refExpected = "CTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; // In VCF the first base on an is not included var altExpected = new StringBuilder(refExpected).reverse().toString(); - var startExpected = 37973491; + var startExpected = 37973492; var endExpected = startExpected + refExpected.length() - 1; assertEquals(1, vars.size()); assertEquals(VariantType.INV, inv.getVariantType()); From e43748836811a14555c207ce8a35def4dbccfe6f Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sun, 22 Sep 2024 16:07:00 +0200 Subject: [PATCH 15/21] VCF Test cases improved --- papers/VCFv4.5.pdf | Bin 896346 -> 905918 bytes .../java/org/snpeff/interval/Variant.java | 10 +- src/main/java/org/snpeff/vcf/VcfEntry.java | 188 +++++++++------- .../testCases/unity/TestCasesVcf.java | 206 ++++++++++++++---- tests/unity/vcf/1kg.indels.20240922.vcf.gz | Bin 0 -> 207878 bytes tests/unity/vcf/1kg.indels.vcf.gz | Bin 209130 -> 207879 bytes 6 files changed, 278 insertions(+), 126 deletions(-) create mode 100644 tests/unity/vcf/1kg.indels.20240922.vcf.gz diff --git a/papers/VCFv4.5.pdf b/papers/VCFv4.5.pdf index abc64247bd0126d0b9200483380c20fe25c79a69..fdb8c46b7ac9e0c0ec8611151e7acee164cf4d4a 100644 GIT binary patch delta 9492 zcmeHNe{dAl9S5l(t5K$cPC@E|1QLdFx3{}*_bdZFNP^TvAVdjDq?gwv)3KfTpP-$(c6e`GcKjC{{b;^!wiX?(MtVz4Q{D z=|BDB-reo(e!t)M{qgz!cz5(6gyZbR?)FK^+O|NKoeld*cg)%Us|KQqC7_ z(HRKmFZe>3O6K(if;%I)GlDxKxHAL48_svsoWV9KsRnM;Fl_D=2JX~gJC#)v8JNhx zM1m#~G?Ac*1WhDpqUKDbXCl2Y(hDO!h#BULVVe`oQ>|25n1y{+3z6svGf52>YF1vYZh!`aZ z#!$v97zZa=LvYd%oQeua{Xb_m32qZS0RhbsP(uLoaWLS=oly{wp_W%bhI;j~hG1uF z9Q{g5Gz9`8K$avRf~O!LgGJjbA;ND_m5Cb5&wLt3++61CR%0BEZ80nujQI$}y}ZG92{^jPR=={Avbw4nF~HPcczoV-DH5 zDCt(E28RnlK!)RvfP!ly&IcN7p}4_7^kGp7%3-PynfoR$4RZ+BhTWsmO5=Ga=U_VG zkZ(w0PI3j(UDyTG<=U`m#ilzTDVBPu4IdUIXhZiPsjg5j_L#y3=G`<}&e2)e zxj&5S3gP+R&oe!anIG#q$M2F%p?lz4XT>CF!_F_ebu2o2B@okNi2^wqvYoP9XK3%S zkE~+``2x*@1u`>_&1!y~r4~QttiJLsMs&;|g725&m{@%~z5(@*&gy7~d9DM}F%RgN zWppgVb<8B)n#jKx(Xn!O&=$79{ZH6KF6Zl5);p4dpe(&Og1Ts?V`A_%(SOkr)IUPq zUFO(J2+UbJ^I>ja z?({>=0<}Z^pI6l9N@bfh&n|aNnId-@st$LNmFVqoi(p28zjfm1Cf8qY;It*cH8rr{7WWnyIxL%wrm!IT_kmSVr zs}zSOd>Z3sIjnO05R_muR9rq)r}*m_PS66jGk&;23PQVBWakGq!RE;gCc^ScuK(z< z2V;72425F(1{1;5<)a9j58X&!YRTn5f;oubXsO$r=ZioRagq}{RDt@a{@rmP@uVHX zW>Y>EqQfhgU432)*&_48AqipW#bMrK3t@lOt%YnHgc2NO`IrbT#D-&zEP|`DacQp= z;g^32DeR+&L8k%~iKl}kMLI~5>ma=iBq^0S@D}~g(?JpjZa!+~V@H4I?*Vhzc+UTDaw({trE7<| z3kf*->^T(3gik|r*iH2W^(XkQcVsCO9F>X!(U5lp68s>{XQ;h$LR&;F*ALj-Sv-{> zY$WM0ceN4bq0$>|uwkd|o|70(nc<@i1M3x68%EGy8wMVz_-Vt3gY6TOg(a~Ot|66YsQ0}CFJd6Avt$xw+q=Nq^ASyoZz-ktl7F=V5g zDTe>f`NnOS&J|_uH0e%{Zsd(I1hwOtR*!bhH*ObW?ipDa{>7Yu$7P04)CrI%x)(&R zr%9pnC&|DgHYZaW&dk9t60oQf{2^}?E@;J>U;81fP`A7#^NcIfkUiI^n??oV0MGwHV0I6M)^ zeKMV5YI?gBkF=y)6LC3&hb68;Oop?LOhB)S9=ldl-5m;s;N&6{Qi4GeR38im#{}V3 z3CF&f^uk0^u7HmX$!L4K6_W!s(Y6#FPBv6Gj<3nIwKYfMaVsfxP1{@+ynSv(gViY4 zwl1;cP*4d6s;uVLXnbzhQ=7|%-WF(RO}7C$f{WeX0bWrmxD}r14_W5#V<#%7{_^9l% z{cz<MrtP^}g@4kD4?g{KkO$zd38|(5na9 z0=q{)vFG-oPhHwLt>gSXV?UeokNF#3)L$OBa?p@7`$s*0`mWXYP2IR|&qtFxQ%7E( z^U$Q#>-1~CpLF!(SKnH?q;m1T zcc#dazyA20NbUQdtvm7f-wyuq!?i=++f=@#Jl1%i?b`L5*6csk)%WKEZyn2`!f|6B z#Q(R*|I#8htF-bh(pYcJmjlz{F^m2wg#MdEk?CJJV1*(|k?BD*tdPZFh5Q98;5Dq! zlftSi609(DgB9w0SfSviD}9z8SkTp^D?AH_RdjF;D?mG4=>v3p3oA6R3QR~1`WbpD zSYd2O*DzfnxD}YQuoY?-_zYtbSQ#|}|ImQX(2v7P>AGD3j@`v6T{~l^LvzjRF5sQ6z)yfM##F&R7~u2Q+zv0R0tMo8+!K7qkcu7^*=f>;==jOPcG_|zdxg5RQm3%kJF?izPy`P&s=yKJ8N z_rIoW9o+uGGvz<{BsSz?-;SfzwQsdQyJ5`S>UaCUF`^^#_3?M^pEfP?$_Md3o!jxN z70S5<+jgg4-MBvf&VZ(cQ=g#)5&|&)7m+Nb(vS+4K^Bq1K{)3jQh9mx^y_M*{{X^_ BmMQ=M delta 35 qcmdnD)cn>hvxXMN7N!>F7M2#)7Pc1l7LFFq7OocV7M?A factory(Chromosome chromo, int start, String ref, St // Add each alt for (String alt : alts) { - // Note: We use 'hasIUBMax()' instead of 'hasIUB()' because large InDels may - // have tons of 'N' bases. In such cases, it is impractical (and useless) to - // produce all possible combinations boolean refIub, altIub; if (!expand) { // Non-IUB expansion needed Variant var = new Variant(chromo, start, ref, alt, id); list.add(var); } else { + // Note: We use 'hasIUBMax()' instead of 'hasIUB()' because large InDels may + // have tons of 'N' bases. In such cases, it is impractical (and useless) to + // produce all possible combinations refIub = IubString.hasIUBMax(ref); altIub = IubString.hasIUBMax(alt); @@ -494,9 +494,9 @@ public enum VariantType { , MIXED // A mixture of insertion, deletions, SNPs and or MNPs (a.k.a. substitution) , INV // Inversion (structural variant) , DUP // Duplication (structural variant) + , CNV // Copy number variation , BND // Break-ends (rearrangement) - , INTERVAL - // Just analyze interval hits. Not a variant (e.g. BED input format) + , INTERVAL // Just analyze interval hits. Not a variant (e.g. BED input format) } } diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index 9a7391cb..cbc67432 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -1,6 +1,7 @@ package org.snpeff.vcf; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; import java.util.Iterator; import java.util.LinkedList; @@ -27,6 +28,11 @@ * A VCF entry is a line in a VCF file * A VCF line can have multiple variants, and multiple genotypes * + * The VcfEntry represents the VCF line, NOT the variant itself. for example, if the `START` field + * in the VCF line may differ from the `start` possition of the variant because the first base of + * the `REF` field is used as an "anchor". + * + * * @author pablocingolani */ public class VcfEntry extends Marker implements Iterable { @@ -41,6 +47,7 @@ public enum AlleleFrequencyType { public static final String[] EMPTY_STRING_ARRAY = new String[0]; public static final double ALLELE_FEQUENCY_COMMON = 0.05; public static final double ALLELE_FEQUENCY_LOW = 0.01; + public static final int MAX_PADN = 1000; public static final Pattern INFO_KEY_PATTERN = Pattern.compile("[\\p{Alpha}_][\\p{Alnum}._]*"); @@ -50,6 +57,9 @@ public enum AlleleFrequencyType { // likelihoods against an unknown alternate allele. Think of this as the likelihood for reference as compared to any // other possible alternate allele (both SNP, indel, or otherwise). A symbolic alternate allele <*> is used to represent // this unspecified alternate allele + // + // From the VCF Spec: "To retain backwards compatibility with with gVCF, the symbolic allele should be treated as an alias of <*>" + // public static final String VCF_ALT_NON_REF = "<*>"; // See VCF 4.2 section "5.5 Representing unspecified alleles and REF-only blocks (gVCF)" public static final String VCF_ALT_NON_REF_OLD = ""; // NON_REF tag for ALT field (only in gVCF fields (olf version of '<*>') public static final String VCF_ALT_MISSING_REF = "*"; // The '*' allele is reserved to indicate that the allele is missing due to a upstream deletion (see VCF 4.3 spec., ALT definition) @@ -191,10 +201,19 @@ public static boolean isValidInfoValue(String value) { * Pad with 'N' characters up length 'len' */ String padNs(String ref, int len) { - if( ref.length() <= len ) return ref; - char[] bases = new char[len]; - for( int i = 0; i < len; i++ ) bases[i] = (i < ref.length() ? ref.charAt(i) : 'N'); - return new String(bases); + if(len > MAX_PADN) len = MAX_PADN; + if(ref == null || ref.isEmpty()) { + // No reference, create a string of 'N' characters + char[] bases = new char[len]; + Arrays.fill(bases, 'N'); + return new String(bases); + } else { + // Extend reference + if( ref.length() >= len ) return ref; + char[] bases = new char[len]; + for( int i = 0; i < len; i++ ) bases[i] = (i < ref.length() ? ref.charAt(i) : 'N'); + return new String(bases); + } } /** @@ -1099,6 +1118,7 @@ String[] parseAlts(String altsStr) { // Parse each one String altsSplit[] = altsStr.split(","); for (String altSingle : altsSplit) { + // Each `altSingle` can be expanded into multiple ALTs because of IUB codes String altsTmp[] = parseAltSingle(altSingle); // Append all to list @@ -1118,13 +1138,7 @@ String[] parseAlts(String altsStr) { */ String[] parseAltSingle(String altsStr) { if (altsStr.length() == 1) return parseAltSingleChar(altsStr); - // // TODO: Remove? - // // Not a variant? - // if (altsStr.equals(VCF_ALT_NON_REF)) return VCF_ALT_NON_REF_ARRAY; - // if (altsStr.equals(VCF_ALT_NON_REF_OLD)) return VCF_ALT_NON_REF_OLD_ARRAY; - // if (altsStr.equals(VCF_ALT_INV)) return VCF_ALT_INV_ARRAY; - - // Other cases + // All other cases return new String[] { altsStr }; } @@ -1164,25 +1178,6 @@ String[] parseAltSingleChar(String altsStr) { } } - // /** - // * Parse 'start' coordinate - // */ - // int parseStart(String startStr) { - // int start = vcfFileIterator.parsePosition(startStr); - - // // In some cases we need to adjust the start possition - // // In "non-ref" (i.e. '<*>' or ) cases, we don't need to adjust the start position - // // Imprecise variants are indicated by an angle brackets '<...>', for example - // // when we have , , , , or similar, we need to adjust the 'start'possition - // // From VCF specification: - // // ```Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant.``` - // if (altStr.indexOf('<') >= 0 && !hasAltNonRef() ) { - // start++; - // } - - // return start; - // } - /** * Parse 'end' coordinate */ @@ -1192,7 +1187,27 @@ int parseEnd() { // Imprecise variants are indicated by an angle brackets '<...>' if (altStr.indexOf('<') >= 0 ) { - if ( hasInfo(VCF_INFO_SVLEN) ) { + if( altStr.indexOf("= 0 ) return start; // Insertions happen at one position (right after POS) + + // For other imprecise variants, we need to check INFO fields + if ( hasInfo(VCF_INFO_END) ) { + // From VCF specification: + // ``` + // For backwards compatibility, a missing SVLEN should be inferred from the END field. + // ... + // This is a computed field that, when present, must be set to the maximum end reference position (1-based) of: + // the position of the final base of the REF allele, + // the end position corresponding to the SVLEN of a symbolic SV allele, + // and the end positions calculated from FORMAT LEN for the <*> symbolic allele. + // ``` + // This means that the END possition includes the last base of the REF allele, i.e. `[start, end]` is a + // closed interval (not half-open as in BED format). + + // Get 'END' field and do some sanity check + end = (int) getInfoInt(VCF_INFO_END) - 1; // END is closed 1-based (includes the last base from REF) + if (end < start) throw new RuntimeException("INFO field 'END' is before varaint's 'POS'\n\tEND : " + end + "\n\tPOS : " + start); + return end; + } else if ( hasInfo(VCF_INFO_SVLEN) ) { // From VCF specification: // ``` // SVLEN must be specified for symbolic structural variant alleles. SVLEN is defined for INS, DUP, @@ -1205,15 +1220,9 @@ int parseEnd() { // "For backwards compatibility, the absolute value of SVLEN should be taken and a negative SVLEN // should be treated as positive values." if (svlen < 0) svlen = -svlen; - return start + svlen - 1; - } else if ( hasInfo(VCF_INFO_END) ) { - // "For backwards compatibility, a missing SVLEN should be inferred from the END field." - // Get 'END' field and do some sanity check - end = (int) getInfoInt(VCF_INFO_END) - 1; - if (end < start) { throw new RuntimeException("INFO field 'END' is before varaint's 'POS'\n\tEND : " + end + "\n\tPOS : " + start); } - return end; + return start + (svlen - 1); // END is closed interval (i.e. the last base from REF is included) } else { - // If no SVLEN or END field is present, we can't infer the end position, we'll use 'ref' length + // If neither SVLEN nor END fields are present, we can't infer the end position, we'll use 'ref' length return start + ref.length() - 1; } } @@ -1671,48 +1680,81 @@ List variantsMnp(Chromosome chromo, int start, String reference, String List variantsStructural(Chromosome chromo, int start, String reference, String alt, String id) { List list = null; + // Update start position + // from VCF spec.: "Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant." + var startVariant = Math.min(start + 1, end); + + // Variant's reference + var refVariant = reference; + // If the reference allele is longer than the variant, pad with Ns + int svlen = (end >= startVariant ? end - startVariant + 1 : 0); + // Variant's reference: Remove anchor base ("... POS corresponds to the base immediately preceding the variant") + if( refVariant.length() > 1 ) { + refVariant = reference.substring(1); // Remove the first base + refVariant = padNs(refVariant, svlen); // Pad with Ns if necessary + } else { + // If it's one base, we need to remove the anchor base and pad with Ns, which is the same as creating a new string with Ns + refVariant = padNs(null, svlen); + } + // Structural variants + VariantType vaType = null; + boolean hasImprecise = hasInfo(VCF_INFO_IMPRECISE); if (alt.startsWith(" happens right after the anchor base + list = variantsStructuralIns(chromo, start, alt, id); + vaType = VariantType.INS; } else { // Unknown structural variants? throw new RuntimeException("Unsupported structural variant type '" + alt + "'"); } - // Assign 'imprecise' flag - if (hasInfo(VCF_INFO_IMPRECISE)) { - for (Variant var : list) - var.setImprecise(true); + // Adjust variants: Set variant type, adjust 'end' coordinate, set 'imprecise' flag + for (Variant var : list) { + // Set variant type + var.setVariantType(vaType); + // Make sure the `end` coordinate is correct + // Why is this necessary? + // When padding with Ns, `padNs` function will add at most `MAX_PADNS` Ns, since the `end` coordinate + // is based on the length of the reference allele, we may need to adjust it + var.setEnd(end); + // Set 'imprecise' flag if INFO field 'IMPRECISE' is present + if( hasImprecise ) var.setImprecise(true); } return list; } - /** - * Create a list of variants - * 2 321682 . T 6 PASS IMPRECISE;SVTYPE=DEL;END=321887;SVLEN=-105;CIPOS=-56,20;CIEND=-10,62 - */ - List variantsStructuralDel(Chromosome chromo, int start, String reference, String alt, String id) { - String refVariant = ref; + List variantsStructuralCnv(Chromosome chromo, int start, String reference, String alt, String id) { + // Create the variant and set the type + Variant var = new Variant(chromo, start, end, id); + var.setVariantType(VariantType.CNV); - if (end > start) { - int svlen = end - start + 1; - refVariant = padNs(ref, svlen); - } - return Variant.factory(chromo, start, refVariant, "", id, false); + // Create a list of varinats + List list = new LinkedList<>(); + list.add(var); + return list; } /** * Create a list of variants + * VCF Specification (version 4.5) FORMAT keys used for structural variants */ List variantsStructuralDup(Chromosome chromo, int start, String reference, String alt, String id) { - // VCF Specification (version 4.5) FORMAT keys used for structural variants int svlen = end - start + 1; - var altDup = padNs(ref + ref, svlen); + var altDup = padNs(reference + reference, svlen); // Create the variant and set the type Variant var = new Variant(chromo, start, ref, altDup, id); @@ -1724,32 +1766,32 @@ List variantsStructuralDup(Chromosome chromo, int start, String referen return list; } + List variantsStructuralIns(Chromosome chromo, int start, String alt, String id) { + // Create the variant and set the type + Variant var = new Variant(chromo, start, "", alt, id); + var.setVariantType(VariantType.INS); + + // Create a list of varinats + List list = new LinkedList<>(); + list.add(var); + return list; + } + /** * Create a list of variants */ List variantsStructuralInv(Chromosome chromo, int start, String reference, String alt, String id) { - // In some cases we need to adjust the start possition - // In "non-ref" (i.e. '<*>' or ) cases, we don't need to adjust the start position - // Imprecise variants are indicated by an angle brackets '<...>', for example - // when we have , , , , or similar, we need to adjust the 'start'possition - // From VCF specification: - // ```Note that for structural variant symbolic alleles, POS corresponds to the base immediately preceding the variant.``` - start++; - // Calculate the 'ALT' sequence - // If 'REF' is more than a single character, then 'ALT' is 'REF' reversed + // If 'REF' is more than a single character, then 'ALT' is 'REF' reversed var altInv = alt; - int svlen = end - start + 1; if(reference.length() > 1 ) { - reference = reference.substring(1); // Remove the first base altInv = (new StringBuffer(reference)).reverse().toString(); - // Check that the length of the inverted sequence is the same as the reference - if( svlen > altInv.length() ) altInv = padNs(altInv, svlen); // Pad with Ns if necessary + int svlen = end - start + 1; + altInv = padNs(altInv, svlen); // Pad with Ns if necessary } // Create the variant and set the type Variant var = new Variant(chromo, start, reference, altInv, id); - var.setVariantType(VariantType.INV); // Create a list of varinats List list = new LinkedList<>(); diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 398f250f..5be6eee8 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -12,6 +12,8 @@ import org.snpeff.vcf.*; import org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber; +import htsjdk.variant.variantcontext.Allele; + import java.util.List; import static org.junit.jupiter.api.Assertions.*; @@ -687,76 +689,167 @@ public void test_36_cleanupUnderscores() { } @Test - public void test_37_inversions_parsing() { + public void test_37_INV() { String vcfFile = path("test_inv.vcf"); - VcfFileIterator vcf = new VcfFileIterator(vcfFile); + // Parameters as in the VCF file + var ref = "GTGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC"; + var start = 27360853; + var end = 27360932; + var svlen = 79; + // Read the first entry + VcfFileIterator vcf = new VcfFileIterator(vcfFile); VcfEntry ve = vcf.next(); - if (verbose) Log.info(ve); + + // Check VCF entry + assertEquals(start - 1, ve.getStart()); + assertEquals(end - 1, ve.getEnd()); + assertEquals(ref, ve.getRef()); + assertEquals(svlen, Math.abs(ve.getInfoInt("SVLEN"))); + assertEquals("", ve.getAltsStr()); + // Check variant var vars = ve.variants(); var inv = (Variant) vars.get(0); - if (verbose) Log.info(inv); - var refExpected = "TGAGATGGGAGTTCAGCAGGGCCCGCGGCCCCTCGCCCTCCGCGAGCTCCCAGTCCCGCGTCCTCACCTCCAACATCTC"; // In VCF the first base on an is not included - var startExpected = 27360853; - var endExpected = startExpected + refExpected.length() - 1; - var altExpected = new StringBuilder(refExpected).reverse().toString(); assertEquals(1, vars.size()); assertEquals(VariantType.INV, inv.getVariantType()); - assertEquals(refExpected, inv.getReference()); - assertEquals(altExpected, inv.getAlt()); - assertEquals(startExpected, inv.getStart()); - assertEquals(endExpected, inv.getEnd()); + assertEquals(ref.substring(1), inv.getReference()); + var altVariant = new StringBuilder(ref.substring(1)).reverse().toString(); + assertEquals(altVariant, inv.getAlt()); + assertEquals(start + 1 - 1, inv.getStart()); // In VCF the first base on an is not included, so we add 1. It's zero-based, so we substract 1 + assertEquals(end - 1, inv.getEnd()); } @Test - public void test_37_inversions_parsing_2() { + public void test_37_INV_2() { String vcfFile = path("test_inv_2.vcf"); + + // Parameters as in the VCF file + var ref = "CCTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; + var start = 37973492; + var end = start + (ref.length() - 1); + + // Read the first entry VcfFileIterator vcf = new VcfFileIterator(vcfFile); VcfEntry ve = vcf.next(); - if (verbose) Log.info(ve); + + // Check VCF entry + assertEquals(start - 1, ve.getStart()); + assertEquals(end - 1, ve.getEnd()); + assertEquals(ref, ve.getRef()); + assertEquals("", ve.getAltsStr()); + // Check variant var vars = ve.variants(); var inv = (Variant) vars.get(0); - var refExpected = "CTTTAGGGCCGGGACAGTGTCGTATATACTGGCTGCTCCCAGTGTGTGGGGCTGTGGGACT"; // In VCF the first base on an is not included + var refExpected = ref.substring(1); // In VCF the first base on an is not included var altExpected = new StringBuilder(refExpected).reverse().toString(); - var startExpected = 37973492; - var endExpected = startExpected + refExpected.length() - 1; assertEquals(1, vars.size()); assertEquals(VariantType.INV, inv.getVariantType()); assertEquals(refExpected, inv.getReference()); assertEquals(altExpected, inv.getAlt()); - assertEquals(startExpected, inv.getStart()); - assertEquals(endExpected, inv.getEnd()); + assertEquals(start + 1 - 1, inv.getStart()); // In VCF the first base on an is not included, so we add 1. It's zero-based, so we substract 1 + assertEquals(end - 1, inv.getEnd()); + } + + @Test + public void test_37_INV_3() { + String vcfContent = "chrA\t14\t.\tT\t\t.\t.\tIMPRECISE;SVLEN=100"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("A", ve.getChromosomeName()); + assertEquals(14 - 1, ve.getStart()); + assertEquals(14 + (100 - 1) - 1, ve.getEnd()); + assertEquals(100, Math.abs(ve.getInfoInt("SVLEN"))); + Variant var = ve.variants().get(0); + assertEquals(VariantType.INV, var.getVariantType()); + assertEquals(14, var.getStart()); + assertEquals(14 + (100 - 1) - 1, var.getEnd()); } - + @Test public void test_38_DEL_01() { - String vcfContent = "2\t321682\t.\tT\t\t6\tPASS\tIMPRECISE;SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62"; + // In this case we have both 'END' and 'SVLEN' fields + String vcfContent = "2\t321682\t.\tT\t\t6\tPASS\tIMPRECISE;SVTYPE=DEL;END=321887;SVLEN=-206"; VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); VcfEntry ve = vi.next(); // Check VCF entry assertEquals("2", ve.getChromosomeName()); - assertEquals(321682, ve.getStart()); + assertEquals(321682 - 1, ve.getStart()); assertEquals(321887 - 1, ve.getEnd()); - assertEquals(321887 - 321682, Math.abs(ve.getInfoInt("SVLEN"))); + assertEquals(321887 - 321682 + 1, Math.abs(ve.getInfoInt("SVLEN"))); // SVLEN is the number of bases in the REF field, including the first and last base + // Check variant Variant var = ve.variants().get(0); assertEquals(VariantType.DEL, var.getVariantType()); + assertEquals(321682, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(321887 - 1, var.getEnd()); + assertTrue(var.getReference().startsWith("NNNNNNNNNNN")); // Ref was padded with Ns + assertEquals("", var.getAlt()); } @Test public void test_39_DEL_02() { - String vcfContent = "chrA\t2\t.\tT\t\t.\t.\tSVLEN=2;SVCLAIM=DJ;EVENT=DEL_symbolic"; + // In this case we have 'SVLEN', but not 'END' + String vcfContent = "chrA\t2\t.\tT\t\t.\t.\tSVLEN=2"; VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); VcfEntry ve = vi.next(); // Check VCF entry assertEquals("A", ve.getChromosomeName()); - assertEquals(2, ve.getStart()); - assertEquals(3, ve.getEnd()); + assertEquals(2 - 1, ve.getStart()); + assertEquals(3 - 1, ve.getEnd()); // END = start + (SVLEN - 1) = 2 + (2 - 1) = 3. To zero-base index => 3 - 1 assertEquals(2, Math.abs(ve.getInfoInt("SVLEN"))); + // Check variant + Variant var = ve.variants().get(0); + assertEquals(VariantType.DEL, var.getVariantType()); + assertEquals(2, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(2, var.getEnd()); + assertTrue(var.getReference().startsWith("N")); // Ref was padded with Ns (first base in REF is not included in the variant) + assertEquals("", var.getAlt()); + } + + @Test + public void test_39_DEL_03() { + // In this case we have 'END', but not 'SVLEN' + String vcfContent = "chrA\t2\t.\tT\t\t.\t.\tEND=3"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("A", ve.getChromosomeName()); + assertEquals(2 - 1, ve.getStart()); + assertEquals(3 - 1, ve.getEnd()); // END = start + (SVLEN - 1) = 2 + (2 - 1) = 3. To zero-base index => 3 - 1 + // Check variant + Variant var = ve.variants().get(0); + assertEquals(VariantType.DEL, var.getVariantType()); + assertEquals(2, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(2, var.getEnd()); + assertTrue(var.getReference().startsWith("N")); // Ref was padded with Ns (first base in REF is not included in the variant) + assertEquals("", var.getAlt()); + } + + @Test + public void test_39_DEL_04() { + // Long SVLEN (i.e. more than MAX_PADN bases). This tests for maximum 'padNs' when padding the REF field in the variant + String vcfContent = "2\t321682\t.\tT\t\t6\tPASS\tIMPRECISE;SVTYPE=DEL;END=323687;SVLEN=-2006;CIPOS=-56,20;CIEND=-10,62"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("2", ve.getChromosomeName()); + assertEquals(321681, ve.getStart()); + assertEquals(323687 - 1, ve.getEnd()); + assertEquals(2006, Math.abs(ve.getInfoInt("SVLEN"))); + // Check variant Variant var = ve.variants().get(0); assertEquals(VariantType.DEL, var.getVariantType()); + assertEquals(321682, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(323687 - 1, var.getEnd()); + assertTrue(var.getReference().startsWith("N")); // Ref was padded with Ns (first base in REF is not included in the variant) + assertTrue(var.getReference().length() >= VcfEntry.MAX_PADN); // Ref was padded with Ns (first base in REF is not included in the variant) + assertEquals("", var.getAlt()); } @Test @@ -767,41 +860,58 @@ public void test_40_DUP() { // Check VCF entry assertEquals("A", ve.getChromosomeName()); - assertEquals(5, ve.getStart()); - assertEquals(7, ve.getEnd()); + assertEquals(5 - 1, ve.getStart()); + assertEquals(7 - 1, ve.getEnd()); assertEquals(3, Math.abs(ve.getInfoInt("SVLEN"))); Variant var = ve.variants().get(0); assertEquals(VariantType.DUP, var.getVariantType()); + assertEquals(5 - 1 + 1, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(7 - 1, var.getEnd()); + assertEquals("G", var.getReference()); // Ref was padded with Ns (first base in REF is not included in the variant) + assertEquals("NNNN", var.getAlt()); } - // @Test - // public void test_41_INS() { - // String vcfContent = "chrA\t14\t.\tT\t\t.\t.\tIMPRECISE;SVLEN=100;CILEN=-50,50;CIPOS=-10,10"; - // VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); - // VcfEntry ve = vi.next(); - - // // Check VCF entry - // assertEquals("A", ve.getChromosomeName()); - // assertEquals(14, ve.getStart()); - // assertEquals(113, ve.getEnd()); - // assertEquals(100, Math.abs(ve.getInfoInt("SVLEN"))); - // Variant var = ve.variants().get(0); - // assertEquals(VariantType.INS, var.getVariantType()); - // } - @Test - public void test_42_INV() { - String vcfContent = "chrA\t14\t.\tT\t\t.\t.\tIMPRECISE;SVLEN=100;CILEN=-50,50;CIPOS=-10,10"; + public void test_41_INS() { + String vcfContent = "chrA\t14\t.\tT\t\t.\t.\tIMPRECISE;SVLEN=100;CILEN=-50,50;CIPOS=-10,10"; VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); VcfEntry ve = vi.next(); // Check VCF entry assertEquals("A", ve.getChromosomeName()); - assertEquals(14, ve.getStart()); - assertEquals(113, ve.getEnd()); + assertEquals(14 - 1, ve.getStart()); + assertEquals(14 - 1, ve.getEnd()); assertEquals(100, Math.abs(ve.getInfoInt("SVLEN"))); + // Check variant Variant var = ve.variants().get(0); - assertEquals(VariantType.INV, var.getVariantType()); + assertEquals(VariantType.INS, var.getVariantType()); + assertEquals(14 - 1, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(14 - 1, var.getEnd()); + assertEquals("", var.getReference()); + assertEquals("", var.getAlt()); + } + + @Test + public void test_43_CNV_01() { + // From the VCF Spec: + // For example, a region on chr1 from position 101 to 130 (both inclusive) with allele-specific copy numbers of 1 and 2 can be represented as follows: + // chr1 100 . T , . . SVLEN=30,30;CN=1,2 GT:CN 1/2:3 + String vcfContent = "chr1\t100\t.\tT\t\t.\t.\tSVLEN=30"; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check VCF entry + assertEquals("1", ve.getChromosomeName()); + assertEquals(100 - 1, ve.getStart()); + assertEquals(100 + (30 -1) - 1, ve.getEnd()); + assertEquals(30, Math.abs(ve.getInfoInt("SVLEN"))); // SVLEN is the number of bases in the REF field, including the first and last base + // Check variant + Variant var = ve.variants().get(0); + assertEquals(VariantType.CNV, var.getVariantType()); + assertEquals(100, var.getStart()); // The first base in VCF's REF is not included in the + assertEquals(100 + (30 -1) - 1, var.getEnd()); + assertEquals(var.getReference(), ""); + assertEquals(var.getAlt(), ""); } } diff --git a/tests/unity/vcf/1kg.indels.20240922.vcf.gz b/tests/unity/vcf/1kg.indels.20240922.vcf.gz new file mode 100644 index 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zzTkQ@@`hy{{~qhV74dvo@IV9Lrex-uyD$$Q(fMf`?VK_9_n~c^WKPPXecP#1!snb3 z?FtbvSt!#bO7Y(As@e9Q*gmxaSK74P&;S3Pfy(DM+0P%%PD^8O^U=QIvm}b@sVNAp zMxr>4Gs2U9-xapK?wP$g3E@aZKC6nXuM)Ma_K70M?U^3Zt$vRmt0bU{iZ6aeIr4h&dh!312sS>V@n0)b2DN#yy?= zo>Y{sjzCjP*82Zha^10l1xfW4##Lj09i|jJ$=l>BD-dkW#?kK|`cr}%J@n0ftdNjL z`91|iQ-py#_BMYZMhyiQ01|vj`qWY^ejRGM-j+$=BVT(eaHCt)gk?lZltUj{>}T9m z`=kdG&6cMe7*{Q44`I6eV79vn(_15N_agrzlm>sOY=6r5>_*k}MtX3+x%Vgif(l-i zE{|g*Zwm2fEP#D3lgQ>f3pAN%a3C{U6#R0@c%&|Gg>Du&qDvSPnDu6smQyuXl>-*nBoa4Qd+1=;Ngm zf+HVg8c*SgDMvLZ)}<6~*nH*;+h)_=I-{;F?#y~APD~%v=0WvQvcr&;xRF>VL7iPe zMo}r#Q;f*ndOyP8OaPlNGv1Tjh)wM9vq~5BH^QGGh zBqx?yAN-0}u3`JJb`h4CI8Z@jC0GmYP;H*Q=EfiT(SQR&bUdZo)Y(&HB-?8NN2!m6 W^kVGl+ZV6`xTGRG$OgNA$NvC9E Date: Sun, 22 Sep 2024 16:20:52 +0200 Subject: [PATCH 16/21] Project updated --- test_04_TestCasesEff.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test_04_TestCasesEff.csv b/test_04_TestCasesEff.csv index baad014d..f518ddac 100644 --- a/test_04_TestCasesEff.csv +++ b/test_04_TestCasesEff.csv @@ -3,8 +3,8 @@ Name , Value Genome , testHg3770Chr22 -Date , 2024-09-13 08:41 -SnpEff_version , SnpEff 5.2c (build 2024-09-13 04:51), by Pablo Cingolani +Date , 2024-09-22 16:14 +SnpEff_version , SnpEff 5.2c (build 2024-09-21 11:42), by Pablo Cingolani Command_line_arguments , SnpEff -csvStats test_04_TestCasesEff.csv testHg3770Chr22 tests/integration/eff/eff_sort.vcf Warnings , 1096 Number_of_lines_in_input_file, 1205 From fe0ef946b981c48bc1836dd5640c6fac7ea703b8 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sun, 22 Sep 2024 16:28:11 +0200 Subject: [PATCH 17/21] Removed comments from tests --- .../snpeff/snpEffect/testCases/unity/TestCasesAlign.java | 1 - .../snpEffect/testCases/unity/TestCasesDnaOverlap.java | 3 --- .../snpEffect/testCases/unity/TestCasesReactome.java | 9 --------- .../testCases/unity/TestCasesSeekableReader.java | 4 ---- 4 files changed, 17 deletions(-) diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesAlign.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesAlign.java index 2f1cba23..711aae91 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesAlign.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesAlign.java @@ -103,7 +103,6 @@ public void test_StringDiff_06() { var s2 = "XcgtactgatagtcagtcatgctagtcagX"; StringDiff sd = new StringDiff(s1, "Sequence 1", s2, "Name2"); var sdToStr = "Sequence 1 : " + s1 + "\n diff : " + di + "\n Name2 : " + s2 + "\n"; - Log.debug("\n" + sd); assertEquals(3, sd.count(), "Mismatches count error"); assertEquals(sdToStr, sd.toString(), "Mismatches count error"); } diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java index c0247622..c9b6ee31 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesDnaOverlap.java @@ -442,9 +442,7 @@ public void test_16_DnaCoder_copy_2() { int numTests = 100000; int maxLen, minLen = 10; - System.err.print("\nDnaCoder.copyBases test:"); for (int numWords = 1; numWords < 10; numWords++) { - System.err.print("\n\tMax words: " + numWords + "\t"); for (int i = 1; i < numTests; i++) { maxLen = 32 * numWords; int seqlensrc = Math.max(rand.nextInt(maxLen), minLen); @@ -454,7 +452,6 @@ public void test_16_DnaCoder_copy_2() { Gpr.showMarkStderr(i, 10000); } } - System.err.print("\nDone.\n"); } @Test diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesReactome.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesReactome.java index 22e8d514..88f1cd29 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesReactome.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesReactome.java @@ -45,7 +45,6 @@ public void test_01() { Entity.BETA = 3.0; double out = r.calc(); - Log.debug("Out: " + out); assertEquals(0.9051482536448667, out); } @@ -72,12 +71,10 @@ public void test_02() { Entity.TRANSFER_FUNCTION = TransferFunction.SIGM_PLUS_MINUS; double out = r.calc(); - Log.debug("Out: " + out); assertEquals(-0.8192933610763514, out); cat.setWeight(0.5); out = r.calc(); - Log.debug("Out: " + out); assertEquals(2.1152011710898737, out); } @@ -102,12 +99,10 @@ public void test_03() { reg.setFixedOutput(-1.0); double out = r.calc(); - Log.debug("Out: " + out); assertEquals(0.86631007995171, out); reg.setFixedOutput(0.37); out = r.calc(); - Log.debug("Out: " + out); assertEquals(2.1219547901144384, out); } @@ -132,12 +127,10 @@ public void test_04() { reg.setFixedOutput(-1.0); double out = r.calc(); - Log.debug("Out: " + out); assertEquals(0.6973026352658382, out); reg.setFixedOutput(0.37); out = r.calc(); - Log.debug("Out: " + out); assertEquals(-0.5583420748968899, out); } @@ -162,12 +155,10 @@ public void test_05() { reg.setFixedOutput(-1.0); double out = r.calc(); - Log.debug("Out: " + out); assertEquals(-0.9154962776570641, out); reg.setFixedOutput(0.37); out = r.calc(); - Log.debug("Out: " + out); assertEquals(0.34014843250566407, out); } diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSeekableReader.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSeekableReader.java index 15492568..547205aa 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSeekableReader.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesSeekableReader.java @@ -32,7 +32,6 @@ long calcHash(String fileName) throws IOException { while ((line = sbr.readLine()) != null) { hash += line.hashCode(); } - sbr.close(); return hash; } @@ -61,8 +60,6 @@ public void test_00() throws IOException { String fileName = path("testLukas.vcf"); long hashExp = calcHashBufferedReader(fileName); long hash = calcHash(fileName); - System.out.println(String.format("%016x\t%016x\t%s", hashExp, hash, fileName)); - assertEquals(hashExp, hash); } @@ -75,7 +72,6 @@ public void test_01() throws IOException { String fileName = path("testLukas.vcf"); long hashExp = calcHashBufferedReader(fileName); long hash = calcHash(fileName); - System.out.printf("%016x\t%016x\t%s%n", hashExp, hash, fileName); assertEquals(hashExp, hash); } } From e2092a7e9f6626a0a8050032954f1180bda999bd Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sun, 22 Sep 2024 17:48:39 +0200 Subject: [PATCH 18/21] Version bumped up to 5.2d --- src/main/java/org/snpeff/SnpEff.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/snpeff/SnpEff.java b/src/main/java/org/snpeff/SnpEff.java index 2b663cc4..1ceec7ec 100644 --- a/src/main/java/org/snpeff/SnpEff.java +++ b/src/main/java/org/snpeff/SnpEff.java @@ -94,7 +94,7 @@ public enum OutputFormat { // Version info public static final String SOFTWARE_NAME = "SnpEff"; - public static final String REVISION = "c"; + public static final String REVISION = "d"; public static final String BUILD = Gpr.compileTimeStamp(SnpEff.class); public static final String BUILD_DATE = Gpr.compileDate(SnpEff.class); public static final String VERSION_MAJOR = "5.2"; From 2add8265669b307ce9bafb40725b4ba4a53dcde5 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sun, 22 Sep 2024 18:27:26 +0200 Subject: [PATCH 19/21] Added VCF deletion test --- src/main/java/org/snpeff/vcf/VcfEntry.java | 2 +- .../testCases/unity/TestCasesVcf.java | 25 +++++++++++++++++-- 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/src/main/java/org/snpeff/vcf/VcfEntry.java b/src/main/java/org/snpeff/vcf/VcfEntry.java index cbc67432..f9d3232e 100644 --- a/src/main/java/org/snpeff/vcf/VcfEntry.java +++ b/src/main/java/org/snpeff/vcf/VcfEntry.java @@ -1183,7 +1183,7 @@ String[] parseAltSingleChar(String altsStr) { */ int parseEnd() { // SNP or single char variant? - if( altStr.length() == 1 ) return start; + if( ref.length() == 1 && altStr.length() == 1 ) return start; // Imprecise variants are indicated by an angle brackets '<...>' if (altStr.indexOf('<') >= 0 ) { diff --git a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java index 5be6eee8..ed6755ca 100644 --- a/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java +++ b/src/test/java/org/snpeff/snpEffect/testCases/unity/TestCasesVcf.java @@ -12,8 +12,6 @@ import org.snpeff.vcf.*; import org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber; -import htsjdk.variant.variantcontext.Allele; - import java.util.List; import static org.junit.jupiter.api.Assertions.*; @@ -914,4 +912,27 @@ public void test_43_CNV_01() { assertEquals(var.getAlt(), ""); } + @Test + public void test_44_deletion() { + String vcfContent = "chr11\t66326794\t.\tAGAGC\tA\t.\t.\t."; + VcfFileIterator vi = VcfFileIterator.fromString(vcfContent); + VcfEntry ve = vi.next(); + + // Check coordinates + assertEquals("11", ve.getChromosomeName()); + assertEquals(66326794 - 1, ve.getStart()); + assertEquals(66326794 + 4 - 1, ve.getEnd()); + assertEquals(5, ve.getRef().length()); + assertEquals(1, ve.getAltsStr().length()); + // Check variant + Variant var = ve.variants().get(0); + assertEquals(VariantType.DEL, var.getVariantType()); + assertEquals(66326794, var.getStart()); + assertEquals(66326794 + 4 - 1, var.getEnd()); + assertEquals("GAGC", var.getReference()); + assertEquals("", var.getAlt()); + } + + + } From 4aae378cd3e7dfb5fbd084eeda77d556fa8ac444 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sun, 22 Sep 2024 21:49:41 +0200 Subject: [PATCH 20/21] Project updated --- galaxy/tool-data/snpEff_genomes.loc | 1 + galaxy/tool-data/snpEff_genomes.loc.sample | 1 + 2 files changed, 2 insertions(+) diff --git a/galaxy/tool-data/snpEff_genomes.loc b/galaxy/tool-data/snpEff_genomes.loc index 9f417ef7..caa9e84a 100644 --- a/galaxy/tool-data/snpEff_genomes.loc +++ b/galaxy/tool-data/snpEff_genomes.loc @@ -24841,6 +24841,7 @@ test_GRCh38.mane.1.0.ensembl.chr19 GRCh38 test_GRCh38.mane.1.0.ensembl.chr19 test_GRCh38.mane.1.0.ensembl.chr21 GRCh38 test_GRCh38.mane.1.0.ensembl.chr21 test_GRCh38.mane.1.0.refseq.chr19 GRCh38 test_GRCh38.mane.1.0.refseq.chr19 test_GRCh38.mane.1.0.refseq.chr21 GRCh38 test_GRCh38.mane.1.0.refseq.chr21 +test_GRCh38.mane.1.2.ensembl.chr1 GRCh38 test_GRCh38.mane.1.2.ensembl.chr1 GRCh38.86 GRCh38.86 GRCh38.86 gadMor1.75 Gadus_morhua gadMor1.75 gadMor1.99 Gadus_morhua gadMor1.99 diff --git a/galaxy/tool-data/snpEff_genomes.loc.sample b/galaxy/tool-data/snpEff_genomes.loc.sample index 9f417ef7..caa9e84a 100644 --- a/galaxy/tool-data/snpEff_genomes.loc.sample +++ b/galaxy/tool-data/snpEff_genomes.loc.sample @@ -24841,6 +24841,7 @@ test_GRCh38.mane.1.0.ensembl.chr19 GRCh38 test_GRCh38.mane.1.0.ensembl.chr19 test_GRCh38.mane.1.0.ensembl.chr21 GRCh38 test_GRCh38.mane.1.0.ensembl.chr21 test_GRCh38.mane.1.0.refseq.chr19 GRCh38 test_GRCh38.mane.1.0.refseq.chr19 test_GRCh38.mane.1.0.refseq.chr21 GRCh38 test_GRCh38.mane.1.0.refseq.chr21 +test_GRCh38.mane.1.2.ensembl.chr1 GRCh38 test_GRCh38.mane.1.2.ensembl.chr1 GRCh38.86 GRCh38.86 GRCh38.86 gadMor1.75 Gadus_morhua gadMor1.75 gadMor1.99 Gadus_morhua gadMor1.99 From 4d8c9fe7b1f022053d446247609ea70b3180a076 Mon Sep 17 00:00:00 2001 From: Pablo Cingolani Date: Sat, 28 Sep 2024 05:50:26 -0400 Subject: [PATCH 21/21] Project updated --- docs/versions.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/versions.txt b/docs/versions.txt index 0f0978ce..411f3f40 100644 --- a/docs/versions.txt +++ b/docs/versions.txt @@ -1 +1 @@ -SNPEFF 5.2C 2024-04-09 https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip +SNPEFF 5.2D 2024-09-23 https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip

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