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sample-08.vcf
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sample-08.vcf
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##fileformat=VCFv4.0
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20240114
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 5 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.0005 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512.2:1-7475 -o /data/jwd02f/main/066/348/66348163/tmp/lofreq2_call_parallelrrrw0nqf/0.vcf.gz reads.bam
##reference=reference.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Lofreq Allele Frequency; Fraction of variant-supporting bases with q > --min-bq among all bases at the site">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_67,Description="Minimum SNV Quality (Phred) 67">
##FILTER=<ID=min_indelqual_47,Description="Minimum Indel Quality (Phred) 47">
##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_indelqual_55,Description="Minimum Indel Quality (Phred) 55">
##contig=<ID=NC_045512.2>
##INFO=<ID=AmpliconBias,Number=0,Type=Flag,Description="Indicates that the AF value of the variant could not be corrected for potential amplicon bias.">
##bcftools_annotateVersion=1.10.2+htslib-1.10.2
##bcftools_annotateCommand=annotate --columns QUAL,INFO --annotations annotations.vcf.gz --mark-sites -AmpliconBias --output-type v --threads 1 input.vcf.gz; Date=Sun Jan 14 21:58:19 2024
##bcftools_annotateCommand=annotate --columns QUAL,INFO --annotations annotations.vcf.gz --mark-sites +AmpliconBias --output-type v --threads 1 input.vcf.gz; Date=Sun Jan 14 21:59:29 2024
##SnpEffVersion="4.5covid19 (build 2020-04-15 22:26), by Pablo Cingolani"
##SnpEffCmd="SnpEff -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-upstream -stats /data/jwd02f/main/066/348/66348343/outputs/dataset_70ba37f7-e7b2-499a-9e08-2aa221dd6c6f.dat NC_045512.2 /data/dnb09/galaxy_db/files/1/8/8/dataset_18889acb-965d-45b5-a945-557fd1ec5889.dat "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank | Genotype [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_045512.2 2832 . A G 16302.0 PASS DP=468;AF=0.938034;SB=0;DP4=0,1,215,251;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K856R|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K856R|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K38R|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K38R|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 4786 . T C 81.0 PASS DP=4423;AF=0.002261;SB=2;DP4=2206,2198,5,7;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1507|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L1507|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L689|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|ctT/ctC|L689|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5386 . T G 32232.0 PASS DP=960;AF=0.90625;SB=4;DP4=1,3,479,476;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A1707|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A1707|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A889|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcG|A889|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5743 . G C 107.0 PASS DP=1848;AF=0.005411;SB=0;DP4=919,918,5,6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1826D|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gaG/gaC|E1008D|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5744 . T C 150.0 PASS DP=1846;AF=0.007042;SB=3;DP4=911,915,10,7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1827H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y1009H|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 5924 . G A 35660.0 PASS DP=1094;AF=0.907678;SB=0;DP4=1,1,542,548;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1887I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gtt/Att|V1069I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 6512 . AGTT A 462.0 PASS DP=13;AF=1;SB=0;DP4=0,0,7,6;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL2083I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL2083I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL1265I|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||agttta/ata|SL1265I|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 8393 . G A 2955.0 PASS DP=88;AF=0.920455;SB=0;DP4=0,0,45,43;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A2710T|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009725299.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A1892T|1944|ORF1ab|protein_coding|CODING|YP_009742610.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10029 . C T 5734.0 PASS DP=184;AF=0.875;SB=0;DP4=0,0,92,91;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T492I|499|ORF1ab|protein_coding|CODING|YP_009725300.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T492I|499|ORF1ab|protein_coding|CODING|YP_009742611.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10449 . C A 2813.0 PASS DP=96;AF=0.864583;SB=0;DP4=0,0,50,46;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P132H|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P132H|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10484 . T G 346.0 PASS DP=64;AF=0.203125;SB=8;DP4=30,20,5,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S3407A|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Gca|S144A|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 10541 . C A 135.0 PASS DP=94;AF=0.06383;SB=0;DP4=46,42,3,3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H3426N|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009725301.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cac/Aac|H163N|305|ORF1ab|protein_coding|CODING|YP_009742612.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11282 . AGTTTGTCTG A 8666.0 PASS DP=252;AF=0.912698;SB=7;DP4=7,15,112,118;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF3674F|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF3674F|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|A|INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF105F|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttgtctggtttt/ttt|LSGF105F|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME)
NC_045512.2 11537 . A G 40888.0 PASS DP=1199;AF=0.924103;SB=2;DP4=2,1,595,600;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I3758V|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I3758V|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|G),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I189V|289|ORF1ab|protein_coding|CODING|YP_009725302.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Att/Gtt|I189V|289|ORF1ab|protein_coding|CODING|YP_009742613.1|1|G|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 11920 . TA T 58.0 PASS DP=36;AF=0.055556;SB=0;DP4=17,17,1,1;INDEL;HRUN=3;EFF=FRAME_SHIFT(HIGH||aaa/|K3886|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K3886|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|T|INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K27|82|ORF1ab|protein_coding|CODING|YP_009725303.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME),FRAME_SHIFT(HIGH||aaa/|K27|82|ORF1ab|protein_coding|CODING|YP_009742614.1|1|T|WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|28|0.14)
NC_045512.2 13195 . T C 17123.0 PASS DP=531;AF=0.896422;SB=0;DP4=0,0,241,287;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4310|7096|ORF1ab|protein_coding|CODING|GU280_gp01|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V4310|4405|ORF1ab|protein_coding|CODING|GU280_gp01.2|1|C),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|138|ORF1ab|protein_coding|CODING|YP_009725306.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON),SYNONYMOUS_CODING(LOW|SILENT|gtT/gtC|V57|138|ORF1ab|protein_coding|CODING|YP_009742617.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 14408 . C T 17844.0 PASS DP=509;AF=0.948919;SB=0;DP4=0,0,254,255;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4715L|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P323L|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 15240 . C T 28904.0 PASS DP=831;AF=0.925391;SB=0;DP4=0,0,401,428;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N4992|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|T),SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N600|931|ORF1ab|protein_coding|CODING|YP_009725307.1|2|T|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 17561 . G A 7777.0 PASS DP=3342;AF=0.103232;SB=0;DP4=1484,1483,184,185;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R5766Q|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|A),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cGg/cAg|R442Q|600|ORF1ab|protein_coding|CODING|YP_009725308.1|1|A|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 18966 . T C 6101.0 PASS DP=956;AF=0.232218;SB=0;DP4=363,338,130,117;EFF=SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C6234|7096|ORF1ab|protein_coding|CODING|GU280_gp01|2|C),SYNONYMOUS_CODING(LOW|SILENT|tgT/tgC|C309|526|ORF1ab|protein_coding|CODING|YP_009725309.1|1|C|WARNING_TRANSCRIPT_NO_START_CODON)
NC_045512.2 21762 . C T 49314.0 PASS DP=1712;AF=0.96028;SB=0;DP4=0,1,852,854;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A67V|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21764 . ATACATG A 49314.0 PASS DP=1616;AF=0.996287;SB=1;DP4=2,4,805,805;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||atacatgtc/atc|IHV68I|1273|S|protein_coding|CODING|GU280_gp02|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 21846 . C T 49314.0 PASS DP=1443;AF=0.957034;SB=0;DP4=0,0,703,736;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T95I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 21986 . GGTGTTTATT G 1449.0 PASS DP=46;AF=0.956522;SB=7;DP4=0,2,26,18;INDEL;HRUN=3;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtgtttattac/gac|GVYY142D|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 22193 . AATT A 2841.0 PASS DP=85;AF=0.976471;SB=6;DP4=3,8,41,42;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||aattta/ata|NL211I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22204 . T TGAGCCAGAA 2355.0 PASS DP=77;AF=0.844156;SB=1;DP4=6,8,31,34;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_INSERTION(MODERATE||gat/gaGCCAGAAGAt|D215EPED|1273|S|protein_coding|CODING|GU280_gp02|1|TGAGCCAGAA|INFO_REALIGN_3_PRIME)
NC_045512.2 22297 . T C 361.0 PASS DP=106;AF=0.132075;SB=0;DP4=45,44,8,9;EFF=SYNONYMOUS_CODING(LOW|SILENT|caT/caC|H245|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 22992 . G A 635.0 PASS DP=20;AF=0.9;SB=0;DP4=1,0,10,9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 22995 . C A 725.0 PASS DP=21;AF=0.952381;SB=0;DP4=0,0,11,10;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23013 . A C 1014.0 PASS DP=29;AF=0.931035;SB=0;DP4=1,0,14,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23040 . A G 1461.0 PASS DP=42;AF=0.952381;SB=0;DP4=0,0,22,20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23048 . G A 1758.0 PASS DP=46;AF=1;SB=0;DP4=0,0,24,22;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G496S|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23055 . A G 1694.0 PASS DP=50;AF=0.92;SB=0;DP4=0,0,26,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512.2 23063 . A T 1862.0 PASS DP=54;AF=0.944444;SB=0;DP4=0,0,28,26;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 23075 . T C 1828.0 PASS DP=50;AF=0.98;SB=0;DP4=0,0,26,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512.2 23202 . C A 1972.0 PASS DP=56;AF=0.928571;SB=0;DP4=0,0,27,28;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T547K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 23948 . G T 1073.0 PASS DP=32;AF=0.90625;SB=0;DP4=1,1,16,14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24130 . C A 1498.0 PASS DP=45;AF=0.911111;SB=0;DP4=0,1,21,23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N856K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24424 . A T 5012.0 PASS DP=142;AF=0.950704;SB=0;DP4=0,0,71,71;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 24469 . T A 49314.0 PASS DP=2281;AF=0.928979;SB=11;DP4=7,1,1199,1071;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512.2 24503 . C T 49314.0 PASS DP=2956;AF=0.936062;SB=0;DP4=2,1,1508,1437;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L981F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25000 . C T 306.0 PASS DP=8;AF=1;SB=0;DP4=0,0,4,4;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512.2 25584 . C T 15306.0 PASS DP=448;AF=0.912946;SB=0;DP4=0,0,222,223;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512.2 26248 . T C 4067.0 PASS DP=2716;AF=0.07106;SB=1;DP4=1203,1298,97,110;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y2H|75|E|protein_coding|CODING|GU280_gp04|1|C)
NC_045512.2 26270 . C T 49314.0 PASS DP=2176;AF=0.923713;SB=2;DP4=0,2,1015,1154;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512.2 26530 . A G 3232.0 PASS DP=92;AF=0.945652;SB=0;DP4=0,0,45,47;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D3G|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26577 . C G 1765.0 PASS DP=48;AF=0.958333;SB=0;DP4=0,0,24,24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512.2 26709 . G A 3564.0 PASS DP=106;AF=0.924528;SB=0;DP4=0,0,53,53;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512.2 27259 . A C 10290.0 PASS DP=295;AF=0.945763;SB=0;DP4=0,0,150,144;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512.2 27807 . C T 49314.0 PASS DP=3675;AF=0.948299;SB=0;DP4=1,0,1865,1801;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512.2 28254 . A C 111.0 PASS DP=5408;AF=0.002774;SB=1;DP4=2701,2671,9,11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Atc/Ctc|I121L|121|ORF8|protein_coding|CODING|GU280_gp09|1|C)
NC_045512.2 28271 . A T 49314.0 PASS DP=6657;AF=0.949677;SB=14;DP4=1,7,3326,3309
NC_045512.2 28292 . CA C 141.0 PASS DP=6848;AF=0.001752;SB=1;DP4=3360,3477,5,7;INDEL;HRUN=4;EFF=FRAME_SHIFT(HIGH||aat/|N8|419|N|protein_coding|CODING|GU280_gp10|1|C|INFO_REALIGN_3_PRIME)
NC_045512.2 28293 . A C 89.0 PASS DP=6848;AF=0.002629;SB=2;DP4=3344,3456,13,17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cCa|Q7P|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 28311 . C T 49314.0 PASS DP=6942;AF=0.876549;SB=21;DP4=2,13,3390,3510;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28361 . GGAGAACGCA G 49314.0 PASS DP=6081;AF=0.834402;SB=1;DP4=487,527,2473,2601;INDEL;HRUN=2;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
NC_045512.2 28363 . AGAACGCAGT A 281.0 PASS DP=5160;AF=0.005039;SB=54;DP4=2506,2638,24,2;INDEL;HRUN=1;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||gaacgcagtggg/ggg|ERSG31G|419|N|protein_coding|CODING|GU280_gp10|1|A|INFO_REALIGN_3_PRIME)
NC_045512.2 28484 . G T 3814.0 PASS DP=4197;AF=0.046938;SB=0;DP4=1967,2004,106,109;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggc/Tgc|G71C|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512.2 28881 . G A 49314.0 PASS DP=1478;AF=0.929635;SB=0;DP4=0,0,732,743;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28882 . G A 49270.0 PASS DP=1474;AF=0.901628;SB=0;DP4=1,2,728,730;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512.2 28883 . G C 49314.0 PASS DP=1474;AF=0.945726;SB=0;DP4=0,0,729,742;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512.2 29417 . T A 97.0 PASS DP=1186;AF=0.006745;SB=1;DP4=570,607,5,4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tta/Ata|L382I|419|N|protein_coding|CODING|GU280_gp10|1|A)