Supplementary Table S1: Descriptive and diversity parameters of each simulated dataset. Page 2




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Supplementary Table S3: List of genomes and number of reads used in each simulated dataset.


Genome

Number of reads

All genomes




Elm mottle virus

2918

Agrotis segetum granulovirus

2845

Vibrio_Vibrio_cholerae_V52

2689

Streptococcus pneumoniae G54

2664

Mycobacterium phage Cali

2628

Simplexvirus_Human_herpesvirus_1

2511

Nairovirus_Crimean_Congo_hemorrhagic_fever_virus

2332

Fluviicola taffensis DSM 16823

2281

Fusobacterium_Fusobacterium_1_1_41FAA

2268

Enterovirus_Human_enterovirus_A

2261

Streptococcus mutans UA159

2207

Mycobacterium phage ScottMcG

2203

Begomovirus_Okra_leaf_curl_virus

2192

Lactobacillus gasseri ATCC 33323

2049

Tomato yellow leaf curl Mali virus associated DNA beta

1919

Iltovirus_Psittacid_herpesvirus_1

1782

Staphylococcus_Staphylococcus_aureus_TCH130

1781

Listeria_Listeria_monocytogenes_FSL_N3_165

1571

Chlorobium chlorochromatii CaD3

1561

Nitrosococcus halophilus Nc4

1544

Verrucomicrobiae bacterium DG1235

1518

Staphylococcus epidermidis RP62A

1504

Bacteroides phage B40 8

1408

Granulicatella_Granulicatella_adiacens_ATCC_49175

1316

Bromovirus_Broad_bean_mottle_virus

1304

Clostridium_Clostridium_leptum_DSM_753

1267

Anaeromyxobacter dehalogenans 2CP-C

1101

Parechovirus_Human_parechovirus

918

Shewanella_Shewanella_benthica_KT99

864

Aurantimonas_Aurantimonas_manganoxydans_SI85_9A1

731

Tomato leaf curl Sulawesi virus

581

Aeromicrobium_Aeromicrobium_marinum_DSM_15272

538

Candidatus Riesia pediculicola USDA

487

Bacillus_Bacillus_thuringiensis_serovar_tochigiensis_BGSC_4Y1

462

Acidimicrobium ferrooxidans DSM 10331

395

Haemophilus influenzae PittGG

319

Geobacter metallireducens GS-15

306

Alicycliphilus denitrificans K601

292

Begomovirus associated DNA II

217

Streptococcus pyogenes MGAS2096

163

Candidatus_Zinderia_Candidatus_Pelagibacter_ubique_HTCC1002

86

Enterococcus_Enterococcus_faecalis_X98

17

All genomes (dominant)




Staphylococcus phage EW

40523

Burkholderia ambifaria MC40-6

12180

Anaerofustis_Anaerofustis_stercorihominis_DSM_17244

6514

Foveavirus_Peach_chlorotic_mottle_virus

783

Bacterial genomes




Arthrobacter arilaitensis Re117

2981

Halorhabdus utahensis DSM 12940

2943

Candidatus Sulcia muelleri DMIN

2741

Mycoplasma leachii PG50

2661

Nitrosococcus oceani ATCC 19707

2383

Azorhizobium caulinodans ORS 571

2348

Caulobacter crescentus CB15

2295

Mycoplasma penetrans HF-2

2279

Methanoculleus marisnigri JR1

2216

Methanobrevibacter smithii ATCC 35061

2094

Granulibacter bethesdensis CGDNIH1

2025

Calditerrivibrio nitroreducens DSM 19672

2000

Serratia proteamaculans 568

1934

Burkholderia pseudomallei MSHR346

1868

Pseudomonas putida F1

1846

Desulfarculus baarsii DSM 2075

1820

Caldicellulosiruptor bescii DSM 6725

1810

Salinibacter ruber M8

1607

Akkermansia muciniphila ATCC BAA-835

1519

Bacteroides thetaiotaomicron VPI-5482

1412

Streptococcus pyogenes MGAS315

1383

Thermococcus barophilus MP

1369

Robiginitalea biformata HTCC2501

1291

Anaeromyxobacter dehalogenans 2CP-1

1264

Xylella fastidiosa Temecula1

1206

Macrococcus caseolyticus JCSC5402

1125

Rhodopseudomonas palustris CGA009

1119

Paenibacillus polymyxa SC2

1077

Burkholderia cenocepacia HI2424

1074

Dickeya dadantii Ech586

925

Helicobacter pylori G27

703

Pseudomonas aeruginosa PAO1

631

Leptothrix cholodnii SP-6

625

Leptotrichia buccalis C-1013-b

558

Helicobacter hepaticus ATCC 51449

460

Streptococcus pyogenes NZ131

397

Exiguobacterium sibiricum 255-15

381

Pelobacter propionicus DSM 2379

339

Colwellia psychrerythraea 34H

231

Borrelia duttonii Ly

217

Thermotoga naphthophila RKU-10

10

Nautilia profundicola AmH

3

Bact genomes (dominant)




Riemerella anatipestifer DSM 15868

32460

Thermoanaerobacterium thermosaccharolyticum DSM 571

27540

MetaSim 1




Catenulispora acidiphila DSM 44928

219

Solibacter usitatus Ellin6076

213

Streptosporangium roseum DSM 43021

210

Bradyrhizobium sp. BTAi1

208

Haliangium ochraceum DSM 14365

208

Streptomyces griseus subsp. griseus NBRC 13350

203

Myxococcus xanthus DK 1622 chromosome

191

Frankia alni ACN14a

185

Nostoc punctiforme PCC 73102

184

Chitinophaga pinensis DSM 2588

184

Rhodococcus jostii RHA1

181

Frankia sp. EAN1pec

180

Bacillus licheniformis ATCC 14580

178

Actinosynnema mirum DSM 43827

175

Saccharopolyspora erythraea NRRL 2338 chromosome

168

Conexibacter woesei DSM 14684

168

Gluconacetobacter diazotrophicus PAl 5

167

Hahella chejuensis KCTC 2396 chromosome

166

Bradyrhizobium japonicum USDA 110 chromosome

162

Trichodesmium erythraeum IMS101

159

Spirosoma linguale DSM 74

158

Kribbella flavida DSM 17836

155

Stackebrandtia nassauensis DSM 44728 chromosome

154

Pseudomonas fluorescens SBW25 chromosome

154

Bradyrhizobium sp. ORS278

153

Pseudomonas aeruginosa PAO1 chromosome

151

Mycobacterium smegmatis str. MC2 155

150

Mesorhizobium loti MAFF303099 chromosome

148

Nakamurella multipartita DSM 44233

148

Methylobacterium nodulans ORS 2060

147

Dyadobacter fermentans DSM 18053

145

Mycobacterium marinum M

145

Herpetosiphon aurantiacus ATCC 23779 chromosome

142

Pseudomonas aeruginosa PA7

141

Rhodopirellula baltica SH 1 chromosome

137

Desulfitobacterium hafniense Y51

137
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