Experiments

Dataset accession numbers

E.coli 100 (GenBank assembly accession number listed)

GCA_000005845.2_ASM584v2_genomic
GCA_000007445.1_ASM744v1_genomic
GCA_000008865.2_ASM886v2_genomic
GCA_000009565.2_ASM956v1_genomic
GCA_000010245.1_ASM1024v1_genomic
GCA_000010385.1_ASM1038v1_genomic
GCA_000010485.1_ASM1048v1_genomic
GCA_000010745.1_ASM1074v1_genomic
GCA_000010765.1_ASM1076v1_genomic
GCA_000013265.1_ASM1326v1_genomic
GCA_000013305.1_ASM1330v1_genomic
GCA_000014845.1_ASM1484v1_genomic
GCA_000017745.1_ASM1774v1_genomic
GCA_000017765.1_ASM1776v1_genomic
GCA_000017985.1_ASM1798v1_genomic
GCA_000019385.1_ASM1938v1_genomic
GCA_000019425.1_ASM1942v1_genomic
GCA_000019645.1_ASM1964v1_genomic
GCA_000021125.1_ASM2112v1_genomic
GCA_000022225.1_ASM2222v1_genomic
GCA_000022345.1_ASM2234v1_genomic
GCA_000022665.2_ASM2266v1_genomic
GCA_000023365.1_ASM2336v1_genomic
GCA_000023665.1_ASM2366v1_genomic
GCA_000025165.1_ASM2516v1_genomic
GCA_000025745.1_ASM2574v1_genomic
GCA_000026245.1_ASM2624v1_genomic
GCA_000026265.1_ASM2626v1_genomic
GCA_000026285.2_ASM2628v2_genomic
GCA_000026345.1_ASM2634v1_genomic
GCA_000026545.1_ASM2654v1_genomic
GCA_000027125.1_ASM2712v1_genomic
GCA_000091005.1_ASM9100v1_genomic
GCA_000148365.1_ASM14836v1_genomic
GCA_000148605.1_ASM14860v1_genomic
GCA_000167875.2_ASM16787v2_genomic
GCA_000183345.1_ASM18334v1_genomic
GCA_000184185.1_ASM18418v1_genomic
GCA_000210475.1_ASM21047v1_genomic
GCA_000212715.2_ASM21271v2_genomic
GCA_000219515.3_ASM21951v3_genomic
GCA_000227625.1_ASM22762v1_genomic
GCA_000233875.1_ASM23387v1_genomic
GCA_000233895.1_ASM23389v1_genomic
GCA_000245515.1_ASM24551v1_genomic
GCA_000257275.1_ASM25727v1_genomic
GCA_000258025.1_ASM25802v1_genomic
GCA_000258145.1_ASM25814v1_genomic
GCA_000262125.1_ASM26212v1_genomic
GCA_000270105.1_ASM27010v1_genomic
GCA_000284495.1_ASM28449v1_genomic
GCA_000285655.3_EC958.v1_genomic
GCA_000299255.1_ASM29925v1_genomic
GCA_000299455.1_ASM29945v1_genomic
GCA_000299475.1_ASM29947v1_genomic
GCA_000332755.1_ASM33275v1_genomic
GCA_000350185.1_ASM35018v1_genomic
GCA_000464955.2_ASM46495v2_genomic
GCA_000468515.1_ASM46851v1_genomic
GCA_000474035.1_ASM47403v1_genomic
GCA_000493755.1_ASM49375v1_genomic
GCA_000499485.1_MYMC4100_genomic
GCA_000520035.1_ASM52003v1_genomic
GCA_000520055.1_ASM52005v1_genomic
GCA_000597845.1_ASM59784v1_genomic
GCA_000599625.1_ASM59962v1_genomic
GCA_000599645.1_ASM59964v1_genomic
GCA_000599665.1_ASM59966v1_genomic
GCA_000599685.1_ASM59968v1_genomic
GCA_000599705.1_ASM59970v1_genomic
GCA_000618005.3_ASM61800v3_genomic
GCA_000618905.3_ASM61890v3_genomic
GCA_000662395.1_ASM66239v1_genomic
GCA_000671295.1_ASM67129v1_genomic
GCA_000714595.1_ASM71459v1_genomic
GCA_000725265.1_ASM72526v1_genomic
GCA_000725305.1_ASM72530v1_genomic
GCA_000730345.1_ASM73034v1_genomic
GCA_000732965.1_ASM73296v1_genomic
GCA_000743255.1_ASM74325v1_genomic
GCA_000750555.1_ASM75055v1_genomic
GCA_000784925.1_ASM78492v1_genomic
GCA_000800215.1_ASM80021v1_genomic
GCA_000800765.1_ASM80076v1_genomic
GCA_000800845.2_ASM80084v2_genomic
GCA_000801165.1_ASM80116v1_genomic
GCA_000801185.2_ASM80118v2_genomic
GCA_000801205.1_ASM80120v1_genomic
GCA_000803705.1_ASM80370v1_genomic
GCA_000813165.1_ASM81316v1_genomic
GCA_000814145.2_ASM81414v2_genomic
GCA_000819645.1_ASM81964v1_genomic
GCA_000827105.1_ASM82710v1_genomic
GCA_000829985.1_ASM82998v1_genomic
GCA_000830035.1_ASM83003v1_genomic
GCA_000831565.1_ASM83156v1_genomic
GCA_000833145.1_ASM83314v1_genomic
GCA_000833635.2_ASM83363v2_genomic
GCA_000931565.1_ASM93156v1_genomic
GCA_000952955.1_EcRV308Chr_genomic

E.coli 10 (GenBank assembly accession number)

GCA_000005845.2_ASM584v2_genomic
GCA_000007445.1_ASM744v1_genomic
GCA_000008865.2_ASM886v2_genomic
GCA_000009565.2_ASM956v1_genomic
GCA_000010245.1_ASM1024v1_genomic
GCA_000010385.1_ASM1038v1_genomic
GCA_000010485.1_ASM1048v1_genomic
GCA_000010745.1_ASM1074v1_genomic
GCA_000010765.1_ASM1076v1_genomic
GCA_000013265.1_ASM1326v1_genomic

Fungi 20 (RefSeq (release 97) assembly accession number listed)

GCF_000001985.1_JCVI-PMFA1-2.0_genomic
GCF_000002495.2_MG8_genomic
GCF_000002515.2_ASM251v1_genomic
GCF_000002525.2_ASM252v1_genomic
GCF_000002545.3_ASM254v2_genomic
GCF_000002655.1_ASM265v1_genomic
GCF_000002715.2_ASM271v1_genomic
GCF_000002855.3_ASM285v2_genomic
GCF_000002945.1_ASM294v2_genomic
GCF_000003125.1_JCVI-TSTA1-3.0_genomic
GCF_000003515.1_ASM351v2_genomic
GCF_000003525.1_BD_ER3_V1_genomic
GCF_000003835.1_ASM383v1_genomic
GCF_000003855.2_BD_SLH14081_V1_genomic
GCF_000004155.1_SCY4_genomic
GCF_000006335.3_ASM633v3_genomic
GCF_000006445.2_ASM644v2_genomic
GCF_000026365.1_ASM2636v1_genomic
GCF_000026945.1_ASM2694v1_genomic
GCF_000027005.1_ASM2700v1_genomic

Human gut microbiome 9 (ENA Project accession PRJEB33098 and study accession ERP115863) (ENA accession number listed)

ERR3450203
ERR3450229
ERR3450296
ERR3450606
ERR3451635
ERR3452318
ERR3452529
ERR3452574
ERR3452699

Human RNA-Seq 19 (SRA accession number listed)

SRR014494
SRR032276
SRR032278
SRR033725
SRR037696
SRR037697
SRR037698
SRR038298
SRR038301
SRR038446
SRR038450
SRR038996
SRR038998
SRR039000
SRR039190
SRR039191
SRR039193
SRR039628