{"text_format":"3","workbook":"xlsx","n_sheets":4,"sheets":["Table S1","Table S2","Table S3","Table S4"],"read":"whole","date_system":"1900"}

{"sheet":"Table S1","index":0,"n_rows":29,"n_cols":3,"rows_kept":29}
["Table S1 : Accession numbers of genomes used as references"]
["Bacterial species ","Number of genomes","Accession numbers "]
["Bacillus cereus",5,"AE016877; CP001177; AP023014; AP022964; CP053931"]
["Bacillus cytotoxicus",5,"CP024109; CP024096; CP024116; CP066179; CP000764"]
["Bacillus thuringiensis",5,"NC_005957; NZ_CP013275; NZ_CP004870; NZ_CP004858; NC_020238"]
["Brucella melitensis",5,"NC_003317; NZ_CP018512; NZ_CP022875; NZ_CP026337; NZ_CP098766"]
["Burkholderia mallei",4,"NC_006348; NC_008836; NZ_CP009727; NZ_CP009731"]
["Campylobacter jejuni",5,"NC_002163; NZ_LN831025; NZ_CP019838; NZ_CP012205; NZ_CP012237"]
["Citrobacter",5,"NZ_CP037864; NZ_CP038469; NZ_CP077262; NZ_CP082833; NZ_LR134485"]
["Clostridium botulinum",3,"CP013681; AM412317; CP063822; CP013296; CP022396"]
["Clostridium difficile",5,"NZ_CP076401; CP037839; CP049958; CP029154; AP025558"]
["Clostridium perfringens",5,"CP000246; CP000312; NC_003366; CP013101; CP010994"]
["Escherichia coli",5,"NC_000913; NC_002695; NZ_CP027599; NZ_CP033092; NZ_CP101292"]
["Klebsiella aerogenes",5,"NC_015663; NZ_CP011539; NZ_CP041925; NZ_CP077293; NZ_LR134254"]
["Leptospira interrogans",5,"NZ_JQPE01000001; NZ_JQPD01000001; NZ_JQOY01000001; NZ_JQPC01000001; NZ_JQPB01000001"]
["Listeria monocytogenes",6,"NC_003210; CP002002; HG813249; FM242711; CP002004; CP001175"]
["Mycobacterium bovis",5,"NZ_CP039850; NZ_CP013741; NZ_CP096844; NZ_CP027035; NZ_CP012095"]
["Mycobacterium tuberculosis ",5,"NC_000962; NZ_CP017597; NZ_CP046308; NZ_CP041827; NZ_CP072761"]
["Neisseria meningitidis",5,"NZ_CP020401; NZ_CP031334; NZ_CP021520; NZ_CP064367; NZ_LR134525"]
["Pseudomonas aeruginosa",5,"NC_002516; NC_004578; NC_008027; NC_021505; NZ_LS999205"]
["Ralstonia solanacearum",5,"CP085043; CP084738; NZ_AP024097; NZ_AP024157; NZ_CP076120"]
["Salmonella enterica",8,"CP025452; NC_011205; CP022504; NZ_CP011288; NC_003197; CP034697; CP045952; AE006468"]
["Staphylococcus argenteus",5,"; FR821777; CP086572; CP096114; CP083805; CP086570"]
["Staphylococcus aureus",6,"; NC_007795; AJ938182; AM990992; AP014653; AP014942; BA000018"]
["Taylorella equigenitalis",5,"CP021060; LR134346; CP021200; CP003264; CP002456"]
["Vibrio cholerae",5,"NZ_CP043554; NZ_CP046745; NZ_CP007634; NZ_CP072847; NZ_CP053810"]
["Vibrio parahaemolyticus",5,"NC_004603; NZ_CP083361; NZ_CP068633; NZ_CP064037; NZ_CP047985"]
["Xylella fastidiosa",6,"NZ_VDCM01000243; AE009442; CP006696; CP020870; NZ_CP047134; NZ_CP090316"]
["Yersinia enterocolitica",5,"NC_017564; NZ_CP011118; NZ_CP016937; NZ_LR134335; NZ_LR590469"]

{"sheet":"Table S2","index":1,"n_rows":25,"n_cols":9,"rows_kept":25}
["Table S2: Strain collection used for validation with real data "]
["Bacterial species ","Strain ID","Year of isolation","Country of isolation","DNA extraction protocol ","Depth repet. 1","Depth repet. 2","q30 rate repet. 1","q30 rate repet. 2"]
["Bacillus thuringiensis","18SBCL209A",2018,"France","KingFisher Cell and Tissue DNA kit, as described in Bonis et al. 2021","556x ","77x","0.932372","0.932679"]
["Bacillus thuringiensis","18SBCL421A",2018,"France","KingFisher Cell and Tissue DNA kit, as described in Bonis et al. 2021","488x","77x","0.931715","0.934793"]
["Bacillus thuringiensis","18SBCL483A",2018,"France","KingFisher Cell and Tissue DNA kit, as described in Bonis et al. 2021","634x","80x","0.933008","0.936177"]
["Bacillus thuringiensis","18SBCL487",2018,"France","KingFisher Cell and Tissue DNA kit, as described in Bonis et al. 2021","282x","138x","0.912914","0.911112"]
["Bacillus thuringiensis","18SBCL617",2018,"France","KingFisher Cell and Tissue DNA kit, as described in Bonis et al. 2021","240x","128x","0.906477","0.912554"]
["Listeria monocytogenes","16SEL760LM","NA","USA","Wizard® Genomic DNA Purification kit","154x","121x","0.978968","0.966905"]
["Listeria monocytogenes","18SEL530LM",2018,"France","Wizard® Genomic DNA Purification kit","152x","152x","0.947037","0.948551"]
["Listeria monocytogenes","21SEL419LM",2021,"France","Wizard® Genomic DNA Purification kit and KingFisher Cell and Tissue DNA kit","140x","148x","0.944642","0.942088"]
["Listeria monocytogenes","19SEL257LM",2019,"France","Wizard® Genomic DNA Purification kit and KingFisher Cell and Tissue DNA kit","184x","168x","0.95686","0.967414"]
["Salmonella enterica","02CEB7151SAL",2002,"France","Wizard® Genomic DNA Purification kit","136x","142x","0.881988","0.957886"]
["Salmonella enterica","03EB759SAL",2003,"France","Wizard® Genomic DNA Purification kit","50x","130x","0.891911","0.958901"]
["Salmonella enterica","2017LSAL00458",2017,"France","Wizard® Genomic DNA Purification kit","110x","134x","0.95991","0.960083"]
["Salmonella enterica","2017LSAL01908",2017,"France","Wizard® Genomic DNA Purification kit","138x","136x","0.964579","0.958412"]
["Salmonella enterica","2017LSAL03540",2017,"France","Wizard kit and KingFisher Cell and Tissue DNA kit","94x","96x","0.863075","0.891991"]
["Staphylococcus aureus","05CEB52STA",2005,"NA","Wizard® Genomic DNA Purification kit, as described in Merda et al. 2020","346x","605x","0.893892","0.922644"]
["Staphylococcus aureus","09CEB303STA",1997,"Japon","Wizard® Genomic DNA Purification kit, as described in Merda et al. 2020","830x","501x","0.918169","0.945106"]
["Staphylococcus aureus","46A",2001,"USA","Wizard® Genomic DNA Purification kit, as described in Merda et al. 2020","588x","653x","0.911464","0.951698"]
["Staphylococcus aureus","17SBCL09STA",2017,"France","Wizard® Genomic DNA Purification kit, as described in Merda et al. 2020","258x","679x","0.899181","0.865448"]
["Staphylococcus aureus","43A",2001,"NA","Wizard® Genomic DNA Purification kit, as described in Merda et al. 2020","732x","785x","0.912018","0.934343"]
["Xylella fastidiosa","LSV52.20",2020,"France","QuickPickTM SML Plant DNA kit (Bio-Nobile, Pargas, Finland) as described in Boutigny et al., 2023","72x","181x","0.909005","0.959063"]
["Xylella fastidiosa","LSV52.37",2020,"France","QuickPickTM SML Plant DNA kit (Bio-Nobile, Pargas, Finland) as described in Boutigny et al., 2023","75x","158x","0.909166","0.958913"]
["Xylella fastidiosa","LSV52.39",2020,"France","QuickPickTM SML Plant DNA kit (Bio-Nobile, Pargas, Finland) as described in Boutigny et al., 2023","68x","164x","0.907969","0.958132"]
["Xylella fastidiosa","LSV52.52",2020,"France","QuickPickTM SML Plant DNA kit (Bio-Nobile, Pargas, Finland) as described in Boutigny et al., 2023","60x","173x","0.908206","0.95913"]

{"sheet":"Table S3","index":2,"n_rows":25,"n_cols":3,"rows_kept":25}
["Table S3: Summary of cgMSLT schemes used for cgMLST analyses. Twenty-three species were analyzed; for 21 species, the scheme was publically available, and references are indicated in this table. For two species, Xylella fastidiosa and Taylorella equigenitalis, the scheme was an in-house scheme (Kozak et al. in preparation, and Merda et al. in preparation)."]
["Bacterial species ","Number of cgMLST genes","Scheme "]
["Bacillus cereus",1568,"Tourasse et al. 2023"]
["Bacillus cytotoxicus",1568,"Tourasse et al. 2023"]
["Bacillus thuringiensis",1568,"Tourasse et al. 2023"]
["Brucella melitensis",2704,"Janowicz et al. 2018"]
["Burkholderia mallei",3328,"Appelt et al. 2022"]
["Campylobacter spp.",1343,"Cody et al. 2017"]
["Clostridium perfringens",1431,"Abdel-Glil et al. 2021"]
["Escherichia coli",2513,"Zhou et al. 2020"]
["Klebsiella aerogenes",2358,"Weber et al. 2019"]
["Leptospira interrogans",874,"Guglielmini et al. 2019"]
["Listeria monocytogenes",1748,"Moura et al. 2017"]
["Mycobacterium bovis",2891,"Kohl et al. 2014"]
["Mycobacterium tuberculosis ",2891,"Kohl et al. 2014"]
["Neisseria meningitidis",1000," Bratcher et al. 2014"]
["Pseudomonas aeruginosa",3867,"Tönnies et al. 2021"]
["Salmonella enterica",3225,"Llarena et al. 2018"]
["Staphylococcus argenteus",1861,"Leopold et al. 2014"]
["Staphylococcus aureus",1861,"Leopold et al. 2014"]
["Taylorella equigenitalis",1669,"In-house"]
["Vibrio cholerae",1856,"Liang et al. 2020"]
["Vibrio parahaemolyticus",996,"Gonzalez-Escalona et al. 2017"]
["Xylella fastidiosa",1383,"In-house"]
["Yersinia enterocolitica",2406,"Savin et al. 2019"]

{"sheet":"Table S4","index":3,"n_rows":30,"n_cols":21,"rows_kept":30,"merged":[[1,1,1,5],[1,6,1,10],[1,11,1,15],[1,16,1,20]]}
["Table S4: p value obtained from Mann-Whitney test on parameter distributions obtained from 100x and other sequencing depths (25x, 50x, 75x, 100x, 150x)"]
[null,"Number of contigs",{"$nulls":4},"N50",{"$nulls":4},"% Misassemblies",{"$nulls":4},"% Largest contig"]
[null,"25x-100x","50x-100x","75x-100x","100x-100x","150x-100x","25x-100x","50x-100x","75x-100x","100x-100x","150x-100x","25x-100x","50x-100x","75x-100x","100x-100x","150x-100x","25x-100x","50x-100x","75x-100x","100x-100x","150x-100x"]
["Bacillus cereus","0.005","0.42","0.88",1,1,"0.004","0.79","0.83",1,1,"0.0000000000000000213","0.52","0.0000326*",1,1,"0.005","0.88","0.78",1,1]
["Bacillus cytotoxicus","0.03","0.56","0.59",1,1,"0.001","0.57","0.36",1,1,"1.32E-23","0.0004","0.005",1,1,"0.0008","0.79","0.84",1,1]
["Bacillus thuringiensis","0.31","0.43","0.85",1,1,"0.03","0.53","0.87",1,1,"4.42E-19","0.8","0.69",1,1,"0.68","0.96","0.83",1,1]
["Brucella melitensis","0.00000117","0.46","0.61",1,1,"0.0000626","0.7","0.92",1,1,"1.19E-21",1,1,1,1,"0.0000626","0.7","0.92",1,1]
["Burkholderia mallei","0.39","0.82","0.85",1,1,"0.72","0.83","0.62",1,1,"0.0000000409","0.37","0.35",1,1,"0.22","0.38","0.2",1,1]
["Campylobacter jejuni","0.77","0.92","0.98",1,1,"0.006","0.87","0.68",1,1,"0.00000000131","0.83","0.07",1,1,"0.16","0.88","0.84",1,1]
["Citrobacter","0.94","0.86","0.72",1,1,"0.03","0.82","0.67",1,1,"0.000000000000142","0.02","0.08",1,1,"0.04","0.74","0.69",1,1]
["Clostridium botulinum","0.06","0.64","0.92",1,1,"0.002","0.66","0.73",1,1,"0.000000000225","0.17","0.87",1,1,"0.005","0.59","0.99",1,1]
["Clostridium difficile","0.01","0.57","0.98",1,1,"0.0005","0.94","0.68",1,1,"2.64E-19","0.002","0.0004",1,1,"0.017","0.85","0.52",1,1]
["Clostridium perfringens","0.004","0.48","0.64",1,1,"0.02","0.7","0.79",1,1,"0.00000000014","0.01","0.48",1,1,"0.01","0.29","0.8",1,1]
["Escherichia coli","0.51","0.89","0.91",1,1,"0.09","0.87","0.99",1,1,"0.00000000000192","0.03","0.25",1,1,"0.56","0.95","0.99",1,1]
["Klebsiella aerogenes","0.015","0.65","0.96",1,1,"0.0000251","0.59","0.97",1,1,"0.00000000236","0.25","0.82",1,1,"0.0000515","0.23","0.14",1,1]
["Leptospira interrogans","0.0012","0.64","0.99",1,1,"0.00014","0.69","0.96",1,1,"0.002","0.29","0.43",1,1,"0.016","0.73","0.53",1,1]
["Listeria monocytogenes","0.15","0.69","0.67",1,1,"0.02","0.71","0.76",1,1,"0.27","0.58","0.08",1,1,"0.13","0.88","0.75",1,1]
["Mycobacterium bovis","0.89","0.36","0.22",1,1,"0.03","0.13","0.36",1,1,"0.00000000000381","0.007","0.001",1,1,"0.86","0.51","0.39",1,1]
["Mycobacterium tuberculosis ","0.22","0.43","0.63",1,1,"0.04","0.11","0.05",1,1,"0.00000322","0.04","0.84",1,1,"0.07","0.85","0.88",1,1]
["Neisseria meningitidis","0.002","0.05","0.08",1,1,"0.000000076","0.05","0.06",1,1,"0.21","0.44","0.05",1,1,"0.0008","0.39","0.68",1,1]
["Pseudomonas aeruginosa","0.54","0.91","0.92",1,1,"0.21","0.78",1,1,1,"0.000000000076","0.28","0.17",1,1,"0.34","0.95","0.9",1,1]
["Ralstonia solanacearum","0.16","0.65","0.65",1,1,"0.39","0.95","0.88",1,1,"0.000000000115","0.38","0.77",1,1,"0.02","0.92","0.95",1,1]
["Salmonella enterica","0.23","0.57","0.51",1,1,"0.0006","0.77","0.45",1,1,"0.0000000000205","0.69","0.22",1,1,"0.03","0.75","0.49",1,1]
["Staphylococcus argenteus","0.0000226","0.44","0.29",1,1,"0.0000279","0.1","0.39",1,1,"0.000000000000000161","0.52","0.41",1,1,"0.001","0.5","0.35",1,1]
["Staphylococcus aureus","0.0003","0.35","0.57",1,1,"0.0003","0.33","0.85",1,1,"0.000000000092","0.14","0.0000396",1,1,"0.0002","0.27","0.27",1,1]
["Taylorella equigenitalis","0.09","0.84","0.77",1,1,"0.01","0.92","0.82",1,1,"2.64E-19","0.002","0.08",1,1,"0.27","0.96","0.9",1,1]
["Vibrio cholerae","0.29","0.5","0.55",1,1,"0.0008","0.38","0.62",1,1,"0.000000988","0.04","0.02",1,1,"0.001","0.73","0.96",1,1]
["Vibrio parahaemolyticus","0.76","0.78","0.99",1,1,"0.64","0.8","0.95",1,1,"5.06E-24","0.000011","0.002",1,1,"0.32","0.84","0.74",1,1]
["Xylella fastidiosa","0.41","0.99","0.8",1,1,"0.36","0.61","0.62",1,1,"0.002","0.93","0.27",1,1,"0.14","0.52","0.97",1,1]
["Yersinia enterocolitica","0.25","0.92","0.76",1,1,"0.01","0.82","0.85",1,1,"0.0000268","0.28","0.27",1,1,"0.01","0.96","0.94",1,1]