{"text_format":"3","workbook":"xlsx","n_sheets":14,"sheets":["sup1","sup2","sup3","sup4","sup5","sup6","sup7","sup8","sup9a","sup9b","sup10","sup11","sup12a","sup12b"],"not_rendered":{"defined_names":1},"read":"whole","date_system":"1900"}

{"sheet":"sup1","index":0,"n_rows":29,"n_cols":6,"rows_kept":29,"merged":[[0,0,0,5],[28,0,28,5]]}
["Supplementary Table 1. Primers used in this study."]
["Amplicon name","Primer","Sequence (5´-3´)","Melting temperature (°C)","Amplicon length in base pairs1","References"]
["F1.1","CMVF1","AAGGACACGGCCAAACCAT","59.85"]
[null,"CMVR1.1","TCCAGAACGTGGCGCTTATT","60.04",7832,"this study"]
["F1.2","CMVF1","AAGGACACGGCCAAACCAT","59.85"]
[null,"CMVR1.2","ACTGGGCCTGAACCAACG","59.89",13846,"this study"]
["F1.3","CMVF1","AAGGACACGGCCAAACCAT","59.85"]
[null,"CMVR1.3","GCAGTCCACCCCAGGTTC","59.97",18055,"this study"]
["F2.1","CMVF2","TGATGACGTAGCGAGCGAAG","60.25"]
[null,"CMVR2.1","CTCCAACGCCAAAAACGTC","57.84",8322,"this study"]
["F2.2","CMVF2","TGATGACGTAGCGAGCGAAG","60.25"]
[null,"CMVR2.2","GCTCCCGTTTTCAGCGATTC","59.90",13374,"this study"]
["F2.3","CMVF2","TGATGACGTAGCGAGCGAAG","60.25"]
[null,"CMVR2.3","CCTTCTCTCGGGTGTAACGC","60.46",17917,"this study"]
["F3","CMVF3","GATCAGGCCTCGCTGGTG","60.20"]
[null,"CMVR3.1","GGTTGCGTGTACAACCCCC","61.26",7772,"this study"]
["F4","CMVF4","ACACTACGTCGTAAATGCGTTGTTC","62.28"]
[null,"CMVR4","GTGGCCCTGGCAAACATATAT","58.40",6671,"this study"]
["gN","gNADMErTowF","GGCGGTGGTGTGATGGAG","58.00"]
[null,"gNADMerTowR","AGTTCTGGAAA/GCAGCAATGTCG","55.00",391,"adapted2"]
["UL146","UL146 first forward","TAGACACTACGTCGTAAATG","57.50"]
[null,"UL146 first reverse","TGTAGAATTAGTCTAGATTCCTGA","59.30",1031]
["UL146nested","UL146 second forward","GCTTGCGCGTTAGGATTGAGACAC","68.90"]
[null,"UL146 second reverse","ATACCGGATATTACGAATT","54.00",771,"adapted3"]
["gOAd-like","gOMerlinADFw","TACCTGGTTAACGCCATGAG","58.65"]
[null,"gOAD169Rv","GTGGCCATAATGGACTTCATA","57.44   ",299,"adapted2"]
["gOMer-like","gOMerlinADFw","TACCTGGTTAACGCCATGAG","58.65"]
[null,"gOMerlinRv","GGCCATAATGGATTTCATAAAGTT","59.53",297,"adapted2"]
["1) Amplicon lenght according to Merlin (Acc.Nr. AY446894.2) except for gOAd-like (AD169, AC146999); 2) Goerzer et al., 2010; doi: 10.1128/JVI.00475-10; 3) Bradley et al., 2008; doi:10.1002/jmv.21241."]

{"sheet":"sup2","index":1,"n_rows":5,"n_cols":7,"rows_kept":5,"merged":[[0,0,0,6]]}
["Supplementary Table 2. Main characteristics of PCR Kits used for evaluation."]
["Long-Range PCR Enzymes","Company","Catalog number","Amplicon size (kilobases)","Fidelity","For GC-rich templates","Proof reading ability (5‘-3‘ exonuclease activity) "]
["TaKaRa LA Taq® DNA Polymerase Hot-Start Version","TaKaRa","RR042A",">20","6.5x higher than Taq DNA polymerase ","GC buffer can be acquired"]
["QIAGEN LongRange PCR Kit","Qiagen",206401,"20-40","5x higher than Taq DNA polymerase","✓","✓"]
["GoTaq Long PCR Master Mix","Promega","PAM4021",30,"Not described ",null,"✓"]

{"sheet":"sup3","index":2,"n_rows":7,"n_cols":14,"rows_kept":7,"merged":[[0,0,0,13],[5,0,5,13],[6,0,6,13]]}
["Supplementary Table 3. Outcome and quality of PacBio sequencing runs."]
["Template HCMV DNA","Input DNA","productive ZMWs","% Productivity","total reads","reads with full passes","%","bp %","Passes median","q75","assigned ZMWs *","%*","SRA BioSample accession numbers","Experimental set-up"]
["Merlin + TB40-BAC4-luc","non-enriched",603773,"59.5",600909,384599,64,94,2,10,450606,"74.6","SAMN17705239 \nSAMN17705240 \nSAMN17705241 ","Estimation of PCR and sequencing error rate "]
["Merlin + TB40-BAC4-luc","F1.1+F3 amplicons",721812,"71.1",718386,287484,40,85,0,3,345895,"47.9","SAMN17705242\nSAMN17705243","Estimation of PCR and sequencing error rate "]
["BAL-derived","F3+F4 amplicons",675633,"66.7",670211,360229,54,94,1,6,456488," 67.6","SAMN17705245\nSAMN17705246\nSAMN17705247","Haplotype determination"]
["ZMW, zero mode waveguides;  Productive ZMWs, ZMWs with (only) one polymerase; % productivity, functional ZMWs with one polymerase / all ZMWs (with none or more than 1 pol) *100; %, reads (full pass) / total reads *100; bp %, how many bp of all reads are included in the full passes; assigned ZMWs, barcode assigned ZMWs; %*, barcode assigned reads of total reads; SRA, sequence read archive. "]
["  "]

{"sheet":"sup4","index":3,"n_rows":8,"n_cols":9,"rows_kept":8,"merged":[[0,0,0,8],[7,0,7,8]]}
["Supplementary Table 4. Outcome and quality of Illumina sequencing runs."]
["Template HCMV DNA","Input DNA","Total reads1","Cluster PF %","PF reads","% Reads Identified (PF)","% ≥Q30","SRA BioSample accession numbers","Experimental set-up"]
["Merlin + TB40-BAC4-luc","non-enriched","24,842,431","87.90 ±1.94","21,838,712","90.60","90.31","SAMN17705202\nSAMN17705203\nSAMN17705204","Estimation of PCR and sequencing error rate "]
["Merlin + TB40-BAC4-luc","F1.1+F3 amplicons","42,231,684","81.96 ±2.52","34,624,162","94.43","76.33","SAMN17705199 \nSAMN17705200 \nSAMN17705201","Estimation of PCR and sequencing error rate "]
["Merlin + TB40-BAC4-luc","F1.1+F3 amplicons","41,761,670","77.38 ±3.70","32,345,822","95.25","73.88","SAMN17705219\nSAMN17705220 \nSAMN17705221\nSAMN17705222 \nSAMN17705223\nSAMN17705224 \nSAMN17705225\nSAMN17705226 \nSAMN17705227\nSAMN17705228","Ratio estimation"]
["Merlin + TB40-BAC4-luc","F3 amplicons","34,996,908","88.98 ±1.50","31,151,874","96.70","79.85","SAMN17705229\nSAMN17705230 \nSAMN17705231\nSAMN17705232 \nSAMN17705233\nSAMN17705234 \nSAMN17705235\nSAMN17705236 \nSAMN17705237\nSAMN17705238","Ratio estimation of dilution series"]
["BAL-derived","gN, gO, UL146 amplicons",{"v":40936250,"d":"40,936,250"},"84.36 ±1.45",{"v":34532786,"d":"34,532,786"},"92.68","90.32","SAMN17705205\nSAMN17705206 \nSAMN17705207\nSAMN17705208\nSAMN17705209 \nSAMN17705210 ","Screening for mixed-genotype infections"]
["1) reads that are not performed for this study are also included; PF, passed filters; SRA, sequence read archive."]

{"sheet":"sup5","index":4,"n_rows":20,"n_cols":11,"rows_kept":20,"merged":[[0,0,0,10],[1,4,1,10],[19,0,19,10]]}
["Supplementary Table 5. Trimming, filtering, and mapping of Illumina-derived reads for error estimation with a base-calling error probability of 0.01 and 0.001."]
["pError","HCMV strain","Input DNA","Reference length in kb","Sequencing reads"]
[{"$nulls":5},"raw reads","after qtrim 0.01","after hu removal","% HCMV mapping","map to reference","average coverage"]
["0.01","Merlin","PCR enriched","F1.1 + F3 target regions","number",3011938,2139250,972371,{"v":0.9982,"d":"99.82%"},970643,12355]
[{"$nulls":4},"length",170,192,199]
[null,"TB40-BAC4","PCR enriched","F1.1 + F3 target regions","number",1627226,1291065,1046869,{"v":0.9995,"d":"99.95%"},1046385,13727]
[{"$nulls":4},"length",196,201,204]
[null,"Merlin","non-enriched","whole genome","number",2297022,1519562,63568,{"v":0.9547,"d":"95.47%"},60686,37]
[{"$nulls":4},"length",123,139,140]
[null,"TB40-BAC4","non-enriched","whole genome","number",2675272,1632173,255406,{"v":0.9831,"d":"98.31%"},251083,147]
[{"$nulls":4},"length",118,138,138]
["0.001","Merlin","PCR enriched","F1.1 + F3 target regions","number",3011938,1626872,640715,{"v":0.9983,"d":"99.83%"},639632,7742]
[{"$nulls":4},"length",170,182,189]
[null,"TB40-BAC4","PCR enriched","F1.1 + F3 target regions","number",1627226,916954,646783,{"v":0.9996,"d":"99.96%"},646530,7914]
[{"$nulls":4},"length",196,185,191]
[null,"Merlin","non-enriched","whole genome","number",2297022,1195595,48974,{"v":0.9711,"d":"97.11%"},47558,28]
[{"$nulls":4},"length",123,136,137]
[null,"TB40-BAC4","non-enriched","whole genome","number",2675272,1296467,202401,{"v":0.9832,"d":"98.32%"},198993,114]
[{"$nulls":4},"length",118,135,136]
["kb, kilobases; qtrim, quality trim; hu, human DNA-specific reads; ltrim, length trim; Mer, Merlin; TB, TB-BAC4-luc."]

{"sheet":"sup6","index":5,"n_rows":34,"n_cols":4,"rows_kept":34,"merged":[[0,0,0,3]]}
["Supplementary Table 6. References used for genotype determination. "]
["Name","Size","Accession number","Sequence"]
["Merlin_gN4d",208,"AY446894.2","ATGGAGTGGAACACACTAGTATTAGGTCTTTTGGTTTTATCGGTAGTGGCAAGTTCCAACAATACGTCGACTGCTAGCACACCGCGTCCCTCTAGTTCTACTCACGCCTCAACAACCGTGAAGGCAACGACTGTTGCGACAACTAGTACAACTACGGCGACAAGTACTTCATCGACGACTAGTGCCAAACCTGGTTCCACTACTCACG"]
["Toledo_gN4c",208,"GU937742.1","ATGGAGTGGAACACACTAGTACTAGGTCTTTTGGTTTTATCGGTAGCGGCAAGTTCCAACAATACGTCGACTGCTAGCACACCGAGTCCTTCTAGCTCTACTCGCACCTCAACAACCGTGAAGTCAACGGCTGTTGCGACAACTAGTACAACTACGGCGACAAGTACTTCATCGACGACTAGTGCCAAACCCGGTTCCACCACTCACG"]
["HAN2_gN2",205,"JX512200.1","ATGGAGTGCAAAACACTGGTGCTAGGCCTTTTGATTATATCGGCGGTAACAGGGAGCTCTAGCAGCAACTCGTCCACGTCAACGTCTTCAACTACACCAAGTCCTTCTAGTGTGTCGACGAGTAAACCAACTACGAGCGTAACAACCTCCACGACAACTACAACTACATCAACAACTAGCACTAGGCTCAGTTCCACTACCCACG"]
["BE/35/2011_gN3a",217,"KP745713.1","ATGGAGTGGAAAACAGTGATACTAGGTCTTTTTGTTTTATCGGTGGCAGCGGGGAGTTCTGGTAACAGCTCATCCACGTCAACCTCCGCAACTACGTTAAAATCGTCCAGTTCTAGCGTGTCAACAAGCAAATTGACGACAACTGCAACAACTACGACAACTACGATGAGTACGACCTCATCGACAACTACGACTAAACCGAGTTCCACCACTCACG"]
["BE/29/2010_gN4a",211,"KP745714.1","ATGGAGTGGAACACACTAGTACTGGGTCTTTTGGTTTTATCGGTAGCGGCGAGTTCCAACAATACGTCGACTGTTAGCACACCGAGTCCCTCTAGCTCTACTCGCACCTTAACAACCGTGAAGGCAACCACAACTGCAACAACTTCTACAACAACTACGAGGAGCACGACCTCATCGACAACTAGTACTAAACTCAGTTCCACCACCCACG"]
["AD169_gN1",217,"FJ527563.1","ATGGAGTGGAACACACTAGTATTAGGTCTTTTAGTTTTATCGGTAGTGGCAGAGAGTTCTGGTAACAATTCATCCACGTCAACCTCTGCAACTACATCAAAGTCTTCTGCTAGCGTATCAACTACCAAACTAACAACAGTTGCAACAACTTCTGCAACAACTACGACGACTACGACCTTATCGACAACTAGCACTAAACTCAGTTCTACCACCCACG"]
["Towne_gN4b",211,"FJ616285.1","ATGGAGTGGAACACACTAGTACTAGGTCTTTTGGTTTTATCGGTAGCGGCAAGTTCCAACCATACGTCGACTGCTAGCACACCGAGTCCCTCTAGCTCTACTCACACCTCAACGACCGTGAAGGCAACGACTACTGCGACAACTAGTACAACTACGGTGACAAGTACGACTTCATCAACGACTAGTACCAAACCCGGTTCCACCACTCACG"]
["Davis_gN3b",217,"JX512198.1","ATGGAGTGGAAAACACGAGTACTAAGTTTTTTGGTTTTATCGGTGGCGGTAGGGAGTTATGGTAACAGCTCATCTACGTCAACCTCTGCAAGTACACCGAGTCCTCCTAGTTCTAGTGTATCAACGGTAAAATCGACTACCAGCGTAACAACCTCCACAACACCTACGACGACCACAACCACATTAACGAGTACTAAACCAGGTTCTACCACTCACA"]
["Merlin_gO5",680,"AY446894.2","ATGGGGAAAAAAGAGATGATAATGGTGAAAGGCATTCCTAAAATTATGCTCCTGATCTCTATAACGTTCTTGCTCCTTTCCCTCATAAATTGTAATGTATTGGTAAACTCCAGAGGAACAAGACGTTCCTGGCCGTATACCGTGCTATCTTATCGAGGTAAAGAGATTCTGAAGAAACAGAAGGAAGATATCTTAAAACGATTGATGTCTACATCATCTGACGGATACCGGTTTTTAATGTACCCCAGTCAGCAAAAATTTCATGCCATCGTTATTAGCATGGATAAATTTCCTCAAGACTACATTTTAGCGGGTCCCATTAGAAATGATAGCATTACCCATATGTGGTTTGACTTTTACAGTACTCAACTCCGAAAACCAGCCAAGTACGTATATTCCGAATATAATCACACGGCCCACAAAATAACGTTACGACCCCCACCTTGCGGCACAGTGCCTTCTATGAACTGCCTATCCGAAATGTTAAATGTTTCCAAACGCAATGATACCGGCGAAAAAGGTTGCGGTAATTTCACCACGTTTAATCCTATGTTTTTCAACGTACCACGTTGGAACACAAAACTGTACATAGGTTCCAACAAAGTCAACGTGGATAGTCAGACAATCTACTTTTTGGGCCTAACCGCCCTACTTTTACGATACGCGCAACGTAACTGCAC"]
["BE/3/2011_gO3",665,"KP745659.1","ATGGGGAGAAAAGGAGAGATGAGAGGTGTTTTTAACTTATTGTTTCTTATATCGTTAACTTTTCTGCTATTTTCTCTTTTGAACTGTAAGAGCGCCGCAAGAGTTTTCAGACCACCGTTTCCCTATGGCAGGGTATTATCAAAAAATGGCAGGCTAGCTGAAATAAAGTGGAAACAAGAACTGTTAAAGCAGATAGGTGCGAGCCAGGATTACTATAAATTTTTTACCATTCCTACTAAACAAGGACTAAACGCTGTTGTAACAATGGAACGGTTTCCCGATAACTATATCTTGGCTGGTCCTATTCAAAATGATAGTATTACCTATATGTGGTTCGATTTCTATAGTACCCAACTGCGAAAACCGGCCAAGTACGTTTACTCAGAGTATAATCAAACAGGCCGAAAGATGAGGTTTAGACCTCCATCTTGTGGCACTGTGCCATCTATGGGTTGTCTATCTGAGATGTTGAACGTATCCTTTCGTAACAACACCGGAGAAGAAAGCTGTGTTAATTTGACCACGTTTAATCCTATGTTTTTTAACGTACCACGTTGGAACACTAAACTGTACGTTGGTTCCACTAAAGTCAATGTGGATAGTCAGACGATCTACTTTTTAGGCCTAGCCGCCCTGCTTCTACGTTACGCGCAACGTAACTGCAC"]
["Toledo_gO1c",656,"GU937742.1","ATGGGGAGAAAAGGAGACATGAGAAGCATTTCTAAATTATTCTTTATTATATCACTGACTGTCCTGTTATTTTCTATAATAAACTGTAAGGTCGTCAGACCACCGGGACGTTACTGGTTAGGTACAGTACTTTCTACGATAGGCAAGCAAAAACTAGATAAATTCAAGTTAGAGATTTTAAAACAATTAGAAAGGGAACCTTATACAAAATACTTCAATATGACTAGACAACACGTTAAAAATCTTACTATGAATATGACCCAGTTTCCACAATACTACATTCTAGCAGGTCCCATTCGAAACGATAGTATAACCTATCTGTGGTTCGATTTTTATAGTACCCAGCTTAGAAAACCCGCCAAATACGTCTACTCACAGTACAATCATACGGCTAAAACGATAACATTCAGACCCCCATCTTGTGGTACAGTGCCTTCAATGACTTGTCTTTCCGAAATGTTAAACGTTTCCAAACGTAATGATACTGGCGAACAAGGCTGCGGTAATTTTACCACGTTCAACCCCATGTTTTTCAATGTACCACGTTGGAATACCAAATTGTACGTGGGTCCGACTAAAGTTAACGTAGATAGTCAAACGATTTATTTTTTGGGTTTAACCGCCCTACTTCTACGTTACGCACAACGCAACTGCAC"]
["BE/12/2011_gO2a",653,"KP745683.1","ATGTGGGGAAAAGGAGAGATGAGAGGTGTTAACTTATTGTTTCTTATATGGTTAACTTTCCTGTTGTTCTTTTTCATAAACTGTAAGGGTGCGCGATCACAACGAGCACCATTTCGTCCTAGGATATGGCACCCCACGGTATTAAAAAAGCTAAAGCAATTAAAATTAGAAATTTTAAGACAACTAGAACCTATTCCTTACATAAAGTACCCACAAATCAATACGACTCGAGTTCAAAGTCTTACTGTTAATATGACCGAGTTTCCTTATTATTATATTTTAGCAGGTCCTATTCGCAACGAAAGTGTAACTCATTTGTGGTATGATTTCTATAGCACACAGCTTAGGAAACCAGCCAAATATGTATACTCTATGTATAATCACACGGCCCGAAAAATAACGTTCAAACCCCCGTCGTGTGGCGCAGTGCCTTCCATGACTTGTCTTTCTGAAATGCTAAACGTTTCCAAGCGTAATGATACCGGCGAAGAAGGCTGCGGTAACTTCACCACGTTCAATCCTATGTTTTTCAATGTACCGCGTTGGAACACCAAATTGTACGTGGGTCCGACTAAAGTTAACGTAGATAGTCAAACGATTTATTTTTTAGGTTTAACCGCCCTGCTTCTACGTTACGCGCAACGCAACTGCAC"]
["BE/19/2011_gO2b",659,"KP745654.1","ATGGGGAAAAAAGAAATACTGGTGAGAGGCGTTTTTAGGATATTTATGGTATATACATTCCTGCTTATTTTTCTCATAAACTGTAAAGGTGCGTTAAACGTACCCCGAGGACGTCCCTGGATAGGTAAAGTACCCTCTCTAAAATGGAAACTTAAAGAACAACAATTGAAGATTGAAATTTTAAAGCAATTACAGAGCGACATATACACAAAATATCCCCAGATCACCAAAAATTACACTCAGTTTATTACTACAGAGCTTAAAAAATTTCCACTGTACTATATCCTAGCGGGTCCTATTCGAAACGAAAGTGTAACTCATTTGTGGTTTGATTTTTATAGCACTCAACTTCGAAAACCTGCCAAATATGTTTACTCTATGTATAATCAAACGGCTCAGAAAATCACGTTTAGGCCCCCGCCTTGCGGTACAGTGCCTTCTATGAATTGTTTATCCGAGATGTTAAACGTTTCCAAGCGTAATGATACCGGCGAAGAAGGCTGTGGTAACTTCACCACGTTCAATCCTATGTTTTTCAATGTACCGCGTTGGAACACCAAATTGTACGTGGGTCCGACTAAAGTTAACGTAGATAGTCAAACCATTTATTTTCTAGGTTTAGCCGCCCTGCTTTTACGTTACGCGCAACGCAACTGCAC"]
["CZ/1/2013_gO1b",662,"KP745691.1","ATGGGGAGAAAAGGAGAGATGAGAGATGTTTTTAATTTATTCTTCCTTATGTCGCTAACTTTCCTGCTATTCTCTTTCATAAACTGTAGGGCTGCGGTAAGATTATCCGTAGGACGTCACTGGTCAGGTAAAGTACTGTCTACGATAGGCAAGCAAAGACTAGACAAGTTCAAATTAGAGATTTTGAAACAACTAGAAAAGGATATCTATACAAAATACTTTAATATGACCAGACAACACATTAAAAATCTGACTATGAACATGACCGAGTTTCCACGGTATTACATTTTAGCGGGACCCATTCAAAATAACAGTGTTACCTATCTTTGGTTCGATTTTTATAGCACTCAGCTTCGAAAACCGGCTAAGTACGTTTTCTCAGAATACAATCATACGGCTAAAACAATAACATTCAGACCCCCATCTTGCGGTACGGTGCCTTCCATGACTTGTCTTTCCGAAATGCTAAACGTTTCCAAACGTAATGATACTGGCGAACAAGGCTGCGGCAATTTCACCACGTTCAACCCCATGTTTTTCAATGTGCCACGTTGGAACACGAAGTTATATGTAGGTTCCAAGAAAGTAAACGTGGATAGTCAAACGATCTACTTTTTAGGCCTAACCGCCTTGCTTCTACGTTACGCGCAACGCAACTGTAC"]
["AD169_gO1a",662,"FJ527563.1","ATGGGGAGAAAAGAGATGATGGTGAGAGACGTCCCTAAGATGGTGTTTCTAATATCTATATCTTTCTTGCTTGTTTCTTTCATAAACTGTAAAGTTATGTCAAAAGCGCTTTATAATCGTCCTTGGAGGGGCTTGGTACTGTCTAAGATAGGCAAATATAAATTAGATCAGCTTAAGTTAGAAATTTTGAGACAACTAGAAACGACTATTTCTACAAAATACAATGTAAGTAAACAACCGGTTAAAAATCTCACTATGAACATGACAGAGTTTCCACAATACTACATTTTAGCGGGCCCCATTCAGAATTATAGTATAACCTATCTGTGGTTTGATTTTTATAGTACCCAGCTTAGAAAACCCGCAAAATACGTTTACTCACAGTACAATCATACGGCTAAAACGATAACATTCAGACCCCCACCTTGTGGTACTGTGCCTTCCATGACTTGTCTTTCCGAAATGCTAAACGTTTCCAAACGTAATGATACTGGCGAACAAGGTTGCGGTAATTTCACCACGTTCAACCCCATGTTTTTCAATGTACCGCGTTGGAACACCAAATTGTACGTGGGTCCGACTAAGGTTAACGTAGATAGTCAAACGATTTATTTTCTAGGTTTAACCGCCCTGCTTTTACGTTACGCACAACGCAACTGTAC"]
["Towne_gO4",650,"FJ616285.1","ATGGGGAGAAAGGGAGAGATGAGAGGTGTTTTTAATTTATTTTTCCTTATGTCGCTAACTTTCCTGCTATTCTCTTTCATAAACTGTAAGATCGCGGTAGCGCGTTTTCGAGTAAAGAGTCAGAAAGCAAAAGAGGAAGAGAGGCAACTAAAATTACGTATACTGCAAGAACTAGCGTCAAAAACAGGTGATTATTACAAGTTTTTCACATTTCCTAGTCAGCAAAAGTTGTATAACATAACTGTAGAAATGAAACAGTTTCCCCCGAATTCCATTTTAGCAGGACCTATTCGTAATCATAGCATTACCCACCTCTGGTTCGATTTTCACACGACCCAACTCCGTAAACCGGCCAAATATGTGTATTCGGAATATAATCATACAGGGCAAAAAATAACATTTCGACCCCCATCCTGTGGTACGATACCTTCCATGACTTGCCTTTCTGAAATGCTAAATGTATCCCGGCGTAACAACACCGGGGAGGAAAACTGTGGCAATTTTACCACATTTAATCCTATGTTTTTTAACGTACCACGTTGGAACACCAAACTGTACGTGGGTCCGAGTAAAGTCAATGTGGATAGCCAAACAATTTATTTTTTAGGTTTAGCCGCCCTGCTTCTACGTTACGCGCAACGTAACTGTAC"]
["Merlin_Ul146-2",360,"AY446894.2","ATGCGATTAATTTTTGGTGCGTTGATTATTTCTTTAACGTATATGTATTATTATGAAGTGCATGGAACGGAATTACGCTGCAAATGTCTTGATGGTAAAAAACTGCCGCCCAAAACAATTATGTTGGGTAATTTTTGGTTTCATCGCGAATCTGGTGGTCCCAGATGCAATAACAATGAATATTTCTTGTATCTAGGCGGAGGAAAAAAACATGGACCTGGAGTATGTTTATCGCCCCATCACCCTTTTTCAAAATGGCTAGACAAACGCAACGATAACAGGTGGTATAATGTTAATGTAACAAGACAACCGGAACGAGGGCCGGGAAAAATAACTGTAACCCTAGTAGGTCTGAAGGAA"]
["BE/33/2010_Ul146-3",375,"KP745661.1","ATGCGATTTATTTTCGGTTTGTTAATTATTTTTTTAGCATATATGTATTATTATGAGGTAAATGGAACGGAATTACGCTGCAAATGTCCCGGTGATAAAAAATTACCGCGTACAAGAATTATGTTGGGTGATTTTTGGACTCATCGCGAATCCGGTGGTCCCGGGTGCAATGGGTATCAATACTTATTATATTTTAATAACGGCGGAAAACATGGACGTGGGGTATGTCTAGCTCCCGATCATCACATTTCAAAATGGTTGGATACACATAACGATGGCAGGTGGTATAATGTTAATATAACGAAACAACCAGGACGACGAACGGGGGGACGAGGCCCGGGACAAGTAAATATAACCTTAATAGCTGTCAAACAA"]
["Toledo_UL146-1",351,"GU937742.1","ATGCGATTAATTTTTGGTGCGTTGATTATTTTTTTAGCATATGTGTATCATTATGAGGTGAATGGAACAGAATTACGCTGCAGATGTCTTCATAGAAAATGGCCGCCTAATAAAATTATATTGGGTAATTATTGGCTTCATCGCGATCCCAGAGGGCCCGGATGCGATAAAAATGAACATTTATTGTATCCAGACGGAAGGAAACCGCCTGGACCTGGAGTATGTTTATCGCCCGATCACCTCTTCTCAAAATGGTTAGACAAACACAACGATAATAGGTGGTATAATGTTAACATAACGAAATCACCAGGACCGAGACGAATAAATATAACCTTGATAGGTGTTAGAGGA"]
["BE/49/2011_UL146-10",345,"KP745725.1","ATGCGATTAATTTTCGGTCCGTTGATTAGCATTTTGATCGTGTGCTATTATGGGGTCGAAAGTGTGGAACTGCGTTGTCCATGTGGGAGTAATAGTGTAAATAAGCCCGTAAGTGGTGTATTTCTCATTGGTCGTGACCCTCCAAACCCTCCTGGTTGTAATAGATTCCAATATTATTTGGCGCCTCCTCACGGTAAACCTGTATGTTTGGATTCCGAACATCATATATCTAAATGGCTGGATGGTCAAAATAGTAATTCATGGTATAAAGTTATAATAAAAAACGGAGATAATAAACCAAAAGTAGAAAAAAGGACTGAAATTAAAAAGCGCTTCAAATGGAAT"]
["Towne_UL146-7",354,"FJ616285.1","ATGCGATTAATTTTTGGTTCGCTGATTAGTCTTTTGATGGCATTTATGTATTACCATGGGGTTCACAGTAGAGAATTGCGTTGTCCGTGTACCCACAAAGCTTTACATCATCCTATAGGTGGCTTATTTTGGGTTGGTCGTGACCCTCCCAATCCTCCTGAGTGTGACAAACCTCAACATTATCTATTGCCTCCTCGAGGTAAACCTGTATGTTTAGCTCCCGATCATCATTTGTCCAAATGGCTGGATGGTAAAAAAGACAACTCATGGCACAGAGTATTGGTAAAAGTAAAGGATAGTAATGGACCGCATGTAGAAGAAAACGCTGTCACTAACAAACGTCCGCGTTGGAAA"]
["BE/1/2010_UL146-6",351,"KP745677.1","ATGCGATTTATCTTTGGTTTATTGATCTCCCTTATGGTTGCACATACATGTAACGCCGGTTTAGGCAGTGAAGGTAACGGACGTTGTACGTGCGTGGGGTATCATCGATTTGACAAACAACTACCTCGTGGAACGATTTGGCTAGGACATCGACCCCCAGGTCCACATTGTCCAAGAGGAGACGTTTTGATGAAATTAGGTGAACAGCCAACTGTATGCTTATCTGATCACCATCCTTTATCTAAGTGGATGTATAGACATCATGGATCAGATACAGAAATATGGTTTCAAATAGAATTTAAGGGCCCACAAAATACCAAGGTAGTATCAAAATCGTTTACTCCACCAAGT"]
["BE/14/2011_UL146-12",354,"KP745671.1","ATGCGATTTATTTTCGGCCTGTTAGTTAGTCTTGTTATCGTGTATACGTATTATTATGAAGTACAGAGCGTAGAATTACGTTGCCCGTGTACTGATGGTTTCCGCAATCCTTTATTCGGTCTATTTCTTATTGGTCATGATCCTCCACATCCTCCCGTTTGTGAGAGAGATCAATTTTTTTTGAAACCTCCCCAAGGCAAGACCGTATGCTTGGGTCCAGAACATCACTTATCATCATGGCTCAAAGGTCAAAATAGTAGTTTATGGCACAAAGTACTGGTGACAAAAAAAGGCGATGAACCACAAGTACATAAGAGAGGTGAGTATCCTAAGAACCGAGCACGTATAATTGTT"]
["AD169_UL146-9",354,"FJ527563.1","ATGCGATTTATTTTTAGTCTGTTTGGTCTTTTGATCGCGTTGTACTATAAAGTTGAGAGTGTGGAGTTACGTTGCCCTTGTGGTAGTAATGGTTTAAGCTATCCAATAGGTGGCTTTTTTTGGATTGGATATAATCCCCCAGATCCTCCTAAATGTGAAAAGCCGCAACATTTTTTATTGCCTCCTAAAGGTAAACCTGTGTGTTTGTCTCCTGATCATGTGTTATCTAAATGGCTTCATGGCAAATCAAGTAACACATGGCACAAAGTGTTATTAAGAACAAAAGGTGGTGGTGGACCGCACGTAGAGGAAAGAACTGCTAGTAACGGACGTCCGCCTTGGAAACTAAAATTT"]
["HAN8_UL146-13",357,"JX512202.1","ATGCGGTTTATTTTCGGTTTGCTGATTGGTCTTGTAATCGTGTATACGTATTATTATGAAGTACAAAGTACGGAACTACGTTGCCCATGCACTGGTGGTTTACACGATCCTTTATATGGCATATTTTATGCTGGTCGTGACCCTCCACGTCCTCCCGGTTGTGAAAAAGATCAATATTATTTAAAACCTCCCAAAGGTAAAGCTGTATGCTTAGGTCCACAACATCATTTATCAATATGGCTCAATGGTCAAAATAGTAGTTTATGGCACAGAGTGCTGGTGACGGGAAAAAACGGTAATGGACCACACGTAACTAAGAAAGGTGACTTTCCTAGAGGTCGAAAAAATATAATGATT"]
["BE/29/2011_UL146-4",369,"KP745672.1","ATGCGATTAATTTTTGGTCCATTCATTGGTCTTTTGATTGCGTGTATGTGTTACTACGTTTGGAGCACAGAATTACGTTGTAAATGTGCAGGAGGACAGAGTTGGCATCCTAGAGGAAAATGGCCTACAAAACATCATTGGTTAGAATGCTATCCACCTTCAGGCAATTGTCCAGCTGGAGAGTTGCTAATATATTTTGAAGAACATAATTGGAGTCCTAAGTGTGTGCATGTTCATAATCCTTTTGGTCAAAAATTTATGTCAAAATGTGACAAACATGAATGGTTTGAAGTTACTTTTAACAGCACAAGAAAATATCCAATGATTACACGTAAAGGAAGTACTAAGCCTACCTTTTCTAGTGGAAAA"]
["HAN22_UL146-8",342,"JX512206.1","ATGCGATTTATTTTTAGTCTGTTTGGTCTTTTGATCGCGTTGTGCTATAAGGTGGAAAGTGTGGAACTACGTTGTCGGTGTAGCAATGGTTCAAATCATCCCGTATTCGGCGTTTTTTGGGTCGGCTATAAACCTCCAGATCCTACATGCGACAAAACGCAACACTTTTTATTACCTCCCCGACAAACACCTGTATGTTTGTCTCCTGATCATTATCTATCGAAATGGGTTGATGGCAAACGAAGTAACTGGTGGCATAAAGTGTTTATAAAGAAAAACTCTGATAATGGACCACATATAGAAGACAAAAGTGACACCAATAGACACCCGCCTTGGCGACTA"]
["Davis_UL146-5",348,"JX512198.1","ATGCGTTTAATTTTTGGTTTATTGATCATTTTTATTGTTACAGATACATGTAACGGCGGTTTTGGCACTGAAGGTAATGGTCGTTGTACATGCATAGGGTATCATCGACTTTTAGGACAATTGCCTCGTGGAACTTTCTGGTTAGGACATTTACCACCAGGCTCACATTGCCCAAAGGGACAAGTCATGATAAAGATAGGCCAAGGACCGATCGTCTGTTTATCCGATTATCATCCTTTATCTAAGTGGATGTATGGAAATCATAAATCTGGTTCGGAAACATGGCTTCAGATAAAAATGGAAGGTCCAAGAAATGCTACAGTAGTACAAAGATCGAATACTCGCCCA"]
["PAV20_UL146-11",345,"KJ872541.1","ATGCGATTAATTTTTGGTTCGTTGATTAGTATTTTGATTGTGTGCTATTATGGAGTCGAAAGCGTAGAATTGCGTTGTCCATGCGGTAGTAATGGTTTACGCGATCCTCTCAGCGGTGTATTTCTGGTTGGTCGTGATCCACCCCGTCCTCCCGGTTGTACCAAACATCAACATTATTTGGTGCCTCCCAATGGTAGACGTGCATGTTTGAATCCCGATCACCATTTATCAAAATGGTTGGATGCTCAAAATAGTAACTCATGGTACAAAGTTGTGGTAACAACGGGAGGTGGTGGTGGACCGCATGTAGACAAAAAAGCTGAAATTAAGAAACGGTTGAGTTAA"]
["JER2282_UL146-14",357,"KR534202.1","ATGCGATTAATTTTTGGCTTGTTGATTTTTTTTATGGTGGCGTATATGTGTTATGAGGTTCAAAGCGTAGAATTACGTTGTCCATGTACCCATAATGTTTTAAATCGTCCCATAGGTGGTGTATTTTGGATTGGTCGTGACCCACCAAAGCCTCCTGAATGTGACAAACCTCAACATTTTTTATTGACTTCGCAAGGTAAAACTGTATGTTTGGGCCAGACCACCATATAACAAAATGGCTTGATGGACAAAACAGCAACTCGTGGTACAAAGTGTTCATAACGACAAACGGTAATAATGGACCACAAATACATAAAAGGGCTGAACATAATAAACGTCCAAAATGGAAATTATAA"]
["TB40_gH1",180,"KF297339.1","ATGCGGCCCGGCCTCCCCTTCTACCTCACCGTCTTCGCCGTCTACCTCCTTAGTCACCTACCTTCGCAACGATATGGCGCAGACGCCGCATCCGAAGCGCTGGACCCTCACGCGTTTCACCTACTACTCAACACCTATGGGAGACCCATCCGTTTCCTGCGTGAAAACACCACCCAGTGC"]
["Merlin_gH2",177,"AY446894.2","ATGCGGCCAGGCCTCCCCTCCTACCTCATCATCCTCGCCGTCTGTCTCTTCAGCCACCTACTTTCGTCACGATATGGCGCAGAAGCCGTATCCGAACCGCTGGACAAAGCGTTTCACCTACTGCTCAACACCTACGGGAGACCCATCCGCTTCCTGCGTGAAAATACCACCCAGTGT"]

{"sheet":"sup7","index":6,"n_rows":238,"n_cols":3,"rows_kept":238,"merged":[[0,0,0,2]]}
["Supplementary Table 7. HCMV full genome references used for haplotype assessment."]
["Accession number","Description","Size"]
["AC146904.1","Human Herpesvirus 5 PH-BAC isolate, complete sequence",229700]
["AY446894.2","Human herpesvirus 5 strain Merlin, complete genome",235646]
["FJ527563.1","Human herpesvirus 5 strain AD169, complete genome",231781]
["FJ616285.1","Human herpesvirus 5 strain Towne, complete genome",235147]
["GQ221973.1","Human herpesvirus 5 strain HAN13, complete genome",236219]
["GQ221975.1","Human herpesvirus 5 strain JP, complete genome",236375]
["GQ221974.1","Human herpesvirus 5 strain 3157, complete genome",235154]
["GQ396662.1","Human herpesvirus 5 strain HAN38, complete genome",236112]
["GQ396663.1","Human herpesvirus 5 strain HAN20, complete genome",235728]
["GQ466044.1","Human herpesvirus 5 strain 3301, complete genome",235703]
["GU179288.1","Human herpesvirus 5 strain U8, complete genome",235709]
["GU179289.1","Human herpesvirus 5 strain VR1814, complete genome",235233]
["GU179290.1","Human herpesvirus 5 strain U11, complete genome",234732]
["GU179291.1","Human herpesvirus 5 strain AF1, complete genome",235937]
["GU980198.1","Human herpesvirus 5 transgenic strain CINCY+Towne, complete genome",228624]
["HQ380895.1","Human herpesvirus 5 strain JHC, complete genome",235476]
["JX512197.1","Human herpesvirus 5 strain 6397, complete genome",235870]
["JX512198.1","Human herpesvirus 5 strain Davis, complete genome",229768]
["JX512199.1","Human herpesvirus 5 strain HAN1, complete genome",235006]
["JX512200.1","Human herpesvirus 5 strain HAN2, complete genome",232940]
["JX512201.1","Human herpesvirus 5 strain HAN3, complete genome",235703]
["JX512202.1","Human herpesvirus 5 strain HAN8, complete genome",234951]
["JX512203.1","Human herpesvirus 5 strain HAN12, complete genome",236006]
["JX512204.1","Human herpesvirus 5 strain HAN16, complete genome",235112]
["JX512205.1","Human herpesvirus 5 strain HAN19, complete genome",235810]
["JX512206.1","Human herpesvirus 5 strain HAN22, complete genome",236379]
["JX512207.1","Human herpesvirus 5 strain HAN28, complete genome",236017]
["JX512208.1","Human herpesvirus 5 strain HAN31, complete genome",235720]
["KF021605.1","Human herpesvirus 5 strain TR, complete genome",235681]
["KF297339.1","Human herpesvirus 5 strain TB40/E clone Lisa, complete genome",237683]
["KC519319.1","Human herpesvirus 5 strain BE/9/2010, complete genome",235631]
["KC519320.1","Human herpesvirus 5 strain BE/10/2010, complete genome",235215]
["KC519321.1","Human herpesvirus 5 strain BE/11/2010, complete genome",235061]
["KC519322.1","Human herpesvirus 5 strain BE/21/2010, complete genome",235722]
["KC519323.1","Human herpesvirus 5 strain BE/27/2010, complete genome",234810]
["KJ361946.1","Human herpesvirus 5 strain 2CEN2, complete genome",235360]
["KJ361947.1","Human herpesvirus 5 strain 2CEN5, complete genome",235567]
["KJ361948.1","Human herpesvirus 5 strain 2CEN15, complete genome",234949]
["KJ361949.1","Human herpesvirus 5 strain 2CEN30, complete genome",236168]
["KJ361950.1","Human herpesvirus 5 strain HAN11, complete genome",235276]
["KJ361951.1","Human herpesvirus 5 strain HAN21, complete genome",235834]
["KJ361952.1","Human herpesvirus 5 strain HAN27, complete genome",235861]
["KJ361953.1","Human herpesvirus 5 strain HAN30, complete genome",235483]
["KJ361954.1","Human herpesvirus 5 strain HAN32, complete genome",235458]
["KJ361955.1","Human herpesvirus 5 strain HAN33, complete genome",235512]
["KJ361956.1","Human herpesvirus 5 strain HAN36, complete genome",234844]
["KJ361957.1","Human herpesvirus 5 strain HAN39, complete genome",235056]
["KJ361958.1","Human herpesvirus 5 strain HAN40, complete genome",235763]
["KJ361959.1","Human herpesvirus 5 strain PAV1, complete genome",235815]
["KJ361960.1","Human herpesvirus 5 strain PAV4, complete genome",235272]
["KJ361961.1","Human herpesvirus 5 strain PAV5, complete genome",235485]
["KJ361962.1","Human herpesvirus 5 strain PAV6, complete genome",235432]
["KJ361963.1","Human herpesvirus 5 strain PAV7, complete genome",235142]
["KJ361964.1","Human herpesvirus 5 strain PAV8, complete genome",235432]
["KJ361965.1","Human herpesvirus 5 strain PAV11, complete genome",236310]
["KJ361966.1","Human herpesvirus 5 strain PAV12, complete genome",235616]
["KJ361967.1","Human herpesvirus 5 strain PAV23, complete genome",235700]
["KJ361968.1","Human herpesvirus 5 strain PAV24, complete genome",235361]
["KJ361969.1","Human herpesvirus 5 strain PAV25, complete genome",235902]
["KJ361970.1","Human herpesvirus 5 strain PAV26, complete genome",236180]
["KJ361971.1","Human herpesvirus 5 strain UKNEQAS1, complete genome",235190]
["KJ426589.1","Human herpesvirus 5 isolate HAN, complete genome",236144]
["KJ872539.1","Human herpesvirus 5 strain PAV16, complete genome",236240]
["KJ872540.1","Human herpesvirus 5 strain PAV18, complete genome",234739]
["KJ872541.1","Human herpesvirus 5 strain PAV20, complete genome",236293]
["KJ872542.1","Human herpesvirus 5 strain PAV21, complete genome",235901]
["KP745633.1","Human herpesvirus 5 strain BE/45/2011, complete genome",235352]
["KP745634.1","Human herpesvirus 5 strain BE/32/2010, complete genome",235205]
["KP745635.1","Human herpesvirus 5 strain BE/5/2012, complete genome",235184]
["KP745636.1","Human herpesvirus 5 strain BE/7/2011, complete genome",237117]
["KP745637.1","Human herpesvirus 5 strain BE/9/2011, complete genome",235865]
["KP745638.1","Human herpesvirus 5 strain BE/15/2010, complete genome",235514]
["KP745639.1","Human herpesvirus 5 strain BE/10/2011, complete genome",235054]
["KP745640.1","Human herpesvirus 5 strain BE/22/2010, complete genome",235632]
["KP745641.1","Human herpesvirus 5 strain BE/31/2011, complete genome",235844]
["KP745642.1","Human herpesvirus 5 strain CZ/1/2012, complete genome",235030]
["KP745643.1","Human herpesvirus 5 strain CZ/2/2012, complete genome",235226]
["KP745644.1","Human herpesvirus 5 strain BE/31/2010, complete genome",236028]
["KP745645.1","Human herpesvirus 5 strain BE/13/2010, complete genome",236032]
["KP745646.1","Human herpesvirus 5 strain BE/8/2012, complete genome",235889]
["KP745647.1","Human herpesvirus 5 strain BE/18/2010, complete genome",235871]
["KP745648.1","Human herpesvirus 5 strain BE/8/2011, complete genome",235111]
["KP745649.1","Human herpesvirus 5 strain BE/10/2012, complete genome",234754]
["KP745650.1","Human herpesvirus 5 strain BE/1/2011, complete genome",235833]
["KP745651.1","Human herpesvirus 5 strain BE/9/2012, complete genome",235836]
["KP745652.1","Human herpesvirus 5 strain BE/2/2011, complete genome",235810]
["KP745653.1","Human herpesvirus 5 strain BE/22/2011, complete genome",235612]
["KP745654.1","Human herpesvirus 5 strain BE/19/2011, complete genome",235446]
["KP745655.1","Human herpesvirus 5 strain BE/3/2010, complete genome",236597]
["KP745656.1","Human herpesvirus 5 strain BE/2/2013, complete genome",235156]
["KP745657.1","Human herpesvirus 5 strain BE/13/2011, complete genome",235713]
["KP745658.1","Human herpesvirus 5 strain BE/14/2012, complete genome",234931]
["KP745659.1","Human herpesvirus 5 strain BE/3/2011, complete genome",235726]
["KP745660.1","Human herpesvirus 5 strain BE/6/2011, complete genome",235101]
["KP745661.1","Human herpesvirus 5 strain BE/33/2010, complete genome",235605]
["KP745662.1","Human herpesvirus 5 strain BE/20/2010, complete genome",235516]
["KP745663.1","Human herpesvirus 5 strain BE/5/2010, complete genome",236345]
["KP745664.1","Human herpesvirus 5 strain CZ/2/2013, complete genome",235191]
["KP745665.1","Human herpesvirus 5 strain BE/16/2012, complete genome",235910]
["KP745666.1","Human herpesvirus 5 strain BE/7/2012, complete genome",236053]
["KP745667.1","Human herpesvirus 5 strain BE/5/2011, complete genome",235621]
["KP745668.1","Human herpesvirus 5 strain BE/18/2011, complete genome",235416]
["KP745669.1","Human herpesvirus 5 strain BE/28/2011, complete genome",235732]
["KP745670.1","Human herpesvirus 5 strain BE/30/2011, complete genome",235350]
["KP745671.1","Human herpesvirus 5 strain BE/14/2011, complete genome",235498]
["KP745672.1","Human herpesvirus 5 strain BE/29/2011, complete genome",236364]
["KP745673.1","Human herpesvirus 5 strain BE/42/2011, complete genome",235462]
["KP745674.1","Human herpesvirus 5 strain BE/33/2011, complete genome",235276]
["KP745675.1","Human herpesvirus 5 strain BE/23/2011, complete genome",235425]
["KP745676.1","Human herpesvirus 5 strain BE/28/2010, complete genome",235974]
["KP745677.1","Human herpesvirus 5 strain BE/1/2010, complete genome",235705]
["KP745678.1","Human herpesvirus 5 strain BE/25/2010, complete genome",235904]
["KP745679.1","Human herpesvirus 5 strain BE/24/2010, complete genome",235744]
["KP745680.1","Human herpesvirus 5 strain BE/11/2012, complete genome",235893]
["KP745681.1","Human herpesvirus 5 strain BE/43/2011, complete genome",235100]
["KP745682.1","Human herpesvirus 5 strain BE/46/2011, complete genome",236239]
["KP745683.1","Human herpesvirus 5 strain BE/12/2011, complete genome",235258]
["KP745684.1","Human herpesvirus 5 strain BE/11/2011, complete genome",234806]
["KP745685.1","Human herpesvirus 5 strain CZ/3/2012, complete genome",234598]
["KP745686.1","Human herpesvirus 5 strain BE/39/2011, complete genome",235982]
["KP745687.1","Human herpesvirus 5 strain BE/36/2011, complete genome",234373]
["KP745688.1","Human herpesvirus 5 strain BE/12/2012, complete genome",235362]
["KP745689.1","Human herpesvirus 5 strain BE/17/2011, complete genome",235827]
["KP745690.1","Human herpesvirus 5 strain BE/34/2011, complete genome",235290]
["KP745691.1","Human herpesvirus 5 strain CZ/1/2013, complete genome",235139]
["KP745692.1","Human herpesvirus 5 strain BE/3/2012, complete genome",236051]
["KP745693.1","Human herpesvirus 5 strain BE/15/2012, complete genome",235508]
["KP745694.1","Human herpesvirus 5 strain BE/12/2010, complete genome",235195]
["KP745695.1","Human herpesvirus 5 strain BE/6/2012, complete genome",235164]
["KP745696.1","Human herpesvirus 5 strain BE/27/2011, complete genome",235392]
["KP745697.1","Human herpesvirus 5 strain BE/23/2010, complete genome",236066]
["KP745698.1","Human herpesvirus 5 strain BE/20/2011, complete genome",235272]
["KP745699.1","Human herpesvirus 5 strain BE/1/2012, complete genome",235150]
["KP745700.1","Human herpesvirus 5 strain BE/4/2011, complete genome",235808]
["KP745701.1","Human herpesvirus 5 strain BE/6/2010, complete genome",235329]
["KP745702.1","Human herpesvirus 5 strain BE/21/2011, complete genome",235849]
["KP745703.1","Human herpesvirus 5 strain BE/26/2011, complete genome",234902]
["KP745704.1","Human herpesvirus 5 strain BE/32/2011, complete genome",235633]
["KP745705.1","Human herpesvirus 5 strain BE/38/2011, complete genome",235775]
["KP745706.1","Human herpesvirus 5 strain BE/41/2011, complete genome",235332]
["KP745707.1","Human herpesvirus 5 strain BE/13/2012, complete genome",235015]
["KP745708.1","Human herpesvirus 5 strain BE/8/2010, complete genome",235964]
["KP745709.1","Human herpesvirus 5 strain BE/48/2011, complete genome",235747]
["KP745710.1","Human herpesvirus 5 strain BE/2/2012, complete genome",236100]
["KP745711.1","Human herpesvirus 5 strain BE/24/2011, complete genome",235745]
["KP745712.1","Human herpesvirus 5 strain BE/19/2010, complete genome",235365]
["KP745713.1","Human herpesvirus 5 strain BE/35/2011, complete genome",235941]
["KP745714.1","Human herpesvirus 5 strain BE/29/2010, complete genome",234922]
["KP745715.1","Human herpesvirus 5 strain BE/44/2011, complete genome",235301]
["KP745716.1","Human herpesvirus 5 strain BE/16/2010, complete genome",235366]
["KP745717.1","Human herpesvirus 5 strain BE/2/2010, complete genome",235138]
["KP745718.1","Human herpesvirus 5 strain CZ/1/2011, complete genome",234758]
["KP745719.1","Human herpesvirus 5 strain BE/26/2010, complete genome",235908]
["KP745720.1","Human herpesvirus 5 strain BE/15/2011, complete genome",235905]
["KP745721.1","Human herpesvirus 5 strain BE/14/2010, complete genome",234537]
["KP745722.1","Human herpesvirus 5 strain BE/40/2011, complete genome",235716]
["KP745723.1","Human herpesvirus 5 strain BE/37/2011, complete genome",234858]
["KP745724.1","Human herpesvirus 5 strain BE/4/2012, complete genome",234950]
["KP745725.1","Human herpesvirus 5 strain BE/49/2011, complete genome",235317]
["KP745726.1","Human herpesvirus 5 strain BE/30/2010, complete genome",235642]
["KP745727.1","Human herpesvirus 5 strain BE/17/2010, complete genome",235836]
["KP745728.1","Human herpesvirus 5 strain BE/4/2010, complete genome",236428]
["KR534196.1","Human herpesvirus 5 strain JER847, complete genome",235713]
["KR534197.1","Human herpesvirus 5 strain JER851, complete genome",235435]
["KR534198.1","Human herpesvirus 5 strain JER893, complete genome",235790]
["KR534199.1","Human herpesvirus 5 strain JER1070, complete genome",235492]
["KR534200.1","Human herpesvirus 5 strain JER1289, complete genome",235841]
["KR534201.1","Human herpesvirus 5 strain JER2002, complete genome",235339]
["KR534202.1","Human herpesvirus 5 strain JER2282, complete genome",234549]
["KR534203.1","Human herpesvirus 5 strain JER3230, complete genome",235857]
["KR534204.1","Human herpesvirus 5 strain JER3855, complete genome",234804]
["KR534205.1","Human herpesvirus 5 strain JER4035, complete genome",235314]
["KR534206.1","Human herpesvirus 5 strain JER4041, complete genome",234917]
["KR534207.1","Human herpesvirus 5 strain JER4053, complete genome",235126]
["KR534208.1","Human herpesvirus 5 strain JER4559, complete genome",235673]
["KR534209.1","Human herpesvirus 5 strain JER4755, complete genome",235266]
["KR534210.1","Human herpesvirus 5 strain JER5268, complete genome",235445]
["KR534211.1","Human herpesvirus 5 strain JER5409, complete genome",235943]
["KR534212.1","Human herpesvirus 5 strain JER5550, complete genome",235160]
["KR534213.1","Human herpesvirus 5 strain JER5695, complete genome",235797]
["KT634296.1","Human herpesvirus 5 strain UKNEQAS2, complete genome",234873]
["KT959235.1","Human herpesvirus 5 strain DB, complete genome",235512]
["KU550087.1","Human herpesvirus 5 strain NAN1LA, complete genome",235062]
["KU550088.1","Human herpesvirus 5 strain NAN2LA, complete genome",234396]
["KU550089.1","Human herpesvirus 5 strain NAN4LA, complete genome",237120]
["KU550090.1","Human herpesvirus 5 strain NANU, complete genome",235634]
["GU937742.2","Human herpesvirus 5 strain Toledo, complete genome",235404]
["KY123649.1","Human herpesvirus 5 strain HANChild4, complete genome",235275]
["KY123650.1","Human herpesvirus 5 strain HANRTR2, complete genome",235472]
["KY123651.1","Human herpesvirus 5 strain HANRTR4, complete genome",235329]
["KY123652.1","Human herpesvirus 5 strain HANRTR5, complete genome",235233]
["KY123653.1","Human herpesvirus 5 strain HANSCTR4, complete genome",235510]
["KT726940.2","Human betaherpesvirus 5 strain NL/Rot1/Urine/2012, partial genome",235186]
["KT726941.2","Human betaherpesvirus 5 strain NL/Rot2/Urine/2012, partial genome",236214]
["KT726942.2","Human betaherpesvirus 5 strain NL/Rot3/Nasal/2012, partial genome",235930]
["KT726943.2","Human betaherpesvirus 5 strain NL/Rot4/Nasal/2012, partial genome",235714]
["KT726944.2","Human betaherpesvirus 5 strain NL/Rot5/Urine/2012, partial genome",235159]
["KT726945.2","Human betaherpesvirus 5 strain NL/Rot6/Nasal/2012, complete genome",234696]
["KT726946.2","Human betaherpesvirus 5 strain NL/Rot7/Urine/2012, partial genome",235843]
["KT726947.2","Human betaherpesvirus 5 strain UK/Lon1/Blood/2013, complete genome",235143]
["KT726948.2","Human betaherpesvirus 5 strain UK/Lon2/Blood/2013, partial genome",235442]
["KT726949.2","Human betaherpesvirus 5 strain UK/Lon6/Urine/2011, complete genome",235199]
["KT726950.2","Human betaherpesvirus 5 strain UK/Lon7/Urine/2011, complete genome",235743]
["KT726951.2","Human betaherpesvirus 5 strain UK/Lon8/Urine/2012, complete genome",235801]
["KT726952.2","Human betaherpesvirus 5 strain UK/Lon3/Plasma/2012, partial genome",234560]
["KT726953.2","Human betaherpesvirus 5 strain UK/Lon9/Urine/2012, partial genome",234925]
["KT726954.2","Human betaherpesvirus 5 strain UK/Lon4/Bile/2011, partial genome",235925]
["KT726955.2","Human betaherpesvirus 5 strain UK/Lon5/Blood/2010, partial genome",235381]
["KY490061.1","Human betaherpesvirus 5 strain PAV31, complete genome",235221]
["KY490062.1","Human betaherpesvirus 5 strain PAV32, complete genome",234316]
["KY490063.1","Human betaherpesvirus 5 strain PRA1, complete genome",235826]
["KY490064.1","Human betaherpesvirus 5 strain PRA2, complete genome",234791]
["KY490065.1","Human betaherpesvirus 5 strain PRA3, complete genome",235442]
["KY490066.1","Human betaherpesvirus 5 strain PRA4, complete genome",235513]
["KY490067.1","Human betaherpesvirus 5 strain PRA5, complete genome",234989]
["KY490068.1","Human betaherpesvirus 5 strain PRA6, complete genome",235717]
["KY490069.1","Human betaherpesvirus 5 strain PRA7, complete genome",236373]
["KY490070.1","Human betaherpesvirus 5 strain PRA8, complete genome",234832]
["KY490071.1","Human betaherpesvirus 5 strain HANChild1, complete genome",235397]
["KY490072.1","Human betaherpesvirus 5 strain HANChild2&3, complete genome",235913]
["KY490073.1","Human betaherpesvirus 5 strain HANRTR1A, complete genome",235221]
["KY490074.1","Human betaherpesvirus 5 strain HANRTR1B, complete genome",235385]
["KY490075.1","Human betaherpesvirus 5 strain HANRTR6, complete genome",235930]
["KY490076.1","Human betaherpesvirus 5 strain HANRTR8, complete genome",235791]
["KY490077.1","Human betaherpesvirus 5 strain HANRTR9, complete genome",235175]
["KY490078.1","Human betaherpesvirus 5 strain HANRTR10, complete genome",234360]
["KY490079.1","Human betaherpesvirus 5 strain HANSCTR1A, complete genome",235579]
["KY490080.1","Human betaherpesvirus 5 strain HANSCTR1B, complete genome",235688]
["KY490081.1","Human betaherpesvirus 5 strain HANSCTR2, complete genome",235843]
["KY490082.1","Human betaherpesvirus 5 strain HANSCTR8, complete genome",235058]
["KY490083.1","Human betaherpesvirus 5 strain HANSCTR9, complete genome",235153]
["KY490084.1","Human betaherpesvirus 5 strain HANSCTR10, complete genome",235018]
["KY490085.1","Human betaherpesvirus 5 strain HANSCTR11A, complete genome",235632]
["KY490086.1","Human betaherpesvirus 5 strain HANSCTR11B, complete genome",234962]
["KY490087.1","Human betaherpesvirus 5 strain HANSCTR12, complete genome",235848]
["KY490088.1","Human betaherpesvirus 5 strain HANSCTR13, complete genome",235403]

{"sheet":"sup8","index":7,"n_rows":19,"n_cols":12,"rows_kept":19,"merged":[[0,0,0,11],[18,0,18,11]]}
["Supplementary Table 8. Counts and % of errors of substitutions, deletions, and insertions in mapped reads as detected for PacBio and Illumina sequencing. Two different stringency parameters were used for quality trimming of reads prior to mapping."]
["Sequencing platform","Quality trimming","Input DNA","Base counts in mapping","Substitutions (base counts)","Substitutions in %","Deletions (base counts)","Deletions in %","Insertions (base counts)","Insertions in %","Total error counts","Total error in %"]
["PacBio","pError 0.01","amplicons Mer",107435393,96278,{"v":0.09,"d":"0.090"},62688,0.058,302792,0.282,461758,{"v":0.43,"d":"0.430"}]
[null,null,"amplicons TB",141025402,107857,0.076,87211,0.062,415467,0.295,610535,0.433]
[null,null,"non-enriched Mer",10375405,1738,0.017,6091,0.059,22724,0.219,30553,0.294]
[null,null,"non-enriched TB",17264753,2208,0.013,7414,0.043,32577,0.189,42199,0.244]
["PacBio","pError 0.001","amplicons Mer",38138220,33357,0.087,5788,0.015,26446,0.069,65591,0.172]
[null,null,"amplicons TB",48527647,36219,0.075,10163,0.021,41064,0.085,87446,{"v":0.18,"d":"0.180"}]
[null,null,"non-enriched Mer",5696379,580,{"v":0.01,"d":"0.010"},811,0.014,1751,0.031,3142,0.055]
[null,null,"non-enriched TB",10802372,706,0.007,1134,{"v":0.01,"d":"0.010"},2769,0.026,4609,0.043]
["Illumina","pError 0.01","amplicons Mer",192753216,321931,0.167,6834,0.004,1988,1E-3,330753,0.172]
[null,null,"amplicons TB",213713102,338166,0.158,11300,0.005,3577,2E-3,353043,0.165]
[null,null,"non-enriched Mer",8486973,7395,0.087,294,0.003,70,1E-3,7759,0.091]
[null,null,"non-enriched TB",34660213,27408,0.079,1471,0.004,359,1E-3,29238,0.084]
["Illumina","pError 0.001","amplicons Mer",120779340,152741,0.126,4030,0.003,1011,1E-3,157782,0.131]
[null,null,"amplicons TB",123217370,140298,0.114,6335,0.005,1625,1E-3,148258,{"v":0.12,"d":"0.120"}]
[null,null,"non-enriched Mer",6510091,1938,{"v":0.03,"d":"0.030"},203,0.003,48,1E-3,2189,0.034]
[null,null,"non-enriched TB",26953220,6446,0.024,1080,0.004,220,1E-3,7746,0.029]
["Mer, Merlin; TB, TB-BAC4-luc."]

{"sheet":"sup9a","index":8,"n_rows":35,"n_cols":8,"rows_kept":35,"merged":[[0,0,0,7],[34,0,34,7]]}
["Supplementary Table 9a. Errors of substitutions, deletions, and insertions in mapped reads per base upon PacBio sequencing. Two different stringency parameters were used for quality trimming of reads prior to mapping."]
["Sequencing platform","Quality trimming","Input DNA","Reference base","Base counts in mapping","Substitutions in %","Deletions in %","Insertions in %"]
["PacBio","pError 0.01","amplicons Mer","Reference: A",23300000,0.13,0.06,0.31]
[{"$nulls":3},"Reference: C",25400000,0.06,0.04,0.25]
[{"$nulls":3},"Reference: G",32300000,0.06,0.06,0.25]
[{"$nulls":3},"Reference: T",26500000,0.12,0.07,0.32]
["PacBio","pError 0.01","amplicons TB","Reference: A",30400000,{"v":0.1,"d":"0.10"},0.06,0.33]
[{"$nulls":3},"Reference: C",36700000,0.05,0.06,0.27]
[{"$nulls":3},"Reference: G",41000000,0.06,0.06,0.26]
[{"$nulls":3},"Reference: T",33000000,{"v":0.1,"d":"0.10"},0.08,0.33]
["PacBio","pError 0.01","non-enriched Mer","Reference: A",2200000,0.02,0.06,0.27]
[{"$nulls":3},"Reference: C",2980000,0.02,0.06,0.18]
[{"$nulls":3},"Reference: G",3050000,0.02,0.06,0.19]
[{"$nulls":3},"Reference: T",2150000,0.01,0.06,0.26]
["PacBio","pError 0.01","non-enriched TB","Reference: A",3680000,0.01,0.05,0.23]
[{"$nulls":3},"Reference: C",4960000,0.01,0.04,0.16]
[{"$nulls":3},"Reference: G",5040000,0.01,0.04,0.16]
[{"$nulls":3},"Reference: T",3590000,0.01,0.05,0.23]
["PacBio","pError 0.001","amplicons Mer","Reference: A",8300000,0.13,0.02,0.08]
[{"$nulls":3},"Reference: C",8930000,0.06,0.01,0.07]
[{"$nulls":3},"Reference: G",11500000,0.06,0.01,0.06]
[{"$nulls":3},"Reference: T",9430000,0.12,0.02,0.07]
["PacBio","pError 0.001","amplicons TB","Reference: A",10400000,0.09,0.02,{"v":0.1,"d":"0.10"}]
[{"$nulls":3},"Reference: C",12500000,0.05,0.02,0.08]
[{"$nulls":3},"Reference: G",14200000,0.07,0.02,0.07]
[{"$nulls":3},"Reference: T",11400000,0.09,0.03,0.09]
["PacBio","pError 0.001","non-enriched Mer","Reference: A",1210000,0.01,0.02,0.05]
[{"$nulls":3},"Reference: C",1630000,0.01,0.01,0.02]
[{"$nulls":3},"Reference: G",1680000,0.01,0.01,0.02]
[{"$nulls":3},"Reference: T",1180000,0.01,0.02,0.05]
["PacBio","pError 0.001","non-enriched TB","Reference: A",2300000,0.01,0.01,0.04]
[{"$nulls":3},"Reference: C",3110000,0.01,0.01,0.02]
[{"$nulls":3},"Reference: G",3160000,0.01,0.01,0.02]
[{"$nulls":3},"Reference: T",2240000,0.01,0.01,0.04]
["Mer, Merlin; TB, TB-BAC4-luc."]

{"sheet":"sup9b","index":9,"n_rows":35,"n_cols":8,"rows_kept":35,"merged":[[0,0,0,7],[34,0,34,7]]}
["Supplementary Table 9b. Errors of substitutions, deletions, and insertions in mapped reads per base upon Illumina sequencing. Two different stringency parameters were used for quality trimming of reads prior to mapping."]
["Sequencing platform","Quality trimming","Input DNA","Reference base","Base counts in mapping","Substitutions in %","Deletions in %","Insertions in %"]
["Illumina","pError 0.01","amplicons Mer","Reference: A",43300000,{"v":0.24,"d":"0.2400"},{"v":0.003,"d":"0.0030"},0.0011]
[{"$nulls":3},"Reference: C",43600000,{"v":0.1,"d":"0.1000"},{"v":2E-3,"d":"0.0020"},0.0007]
[{"$nulls":3},"Reference: G",56200000,{"v":0.09,"d":"0.0900"},{"v":2E-3,"d":"0.0020"},0.0007]
[{"$nulls":3},"Reference: T",49700000,{"v":0.25,"d":"0.2500"},{"v":0.007,"d":"0.0070"},0.0016]
["Illumina","pError 0.01","amplicons TB","Reference: A",47900000,{"v":0.24,"d":"0.2400"},{"v":0.003,"d":"0.0030"},0.0005]
[{"$nulls":3},"Reference: C",53800000,{"v":0.09,"d":"0.0900"},{"v":2E-3,"d":"0.0020"},0.0005]
[{"$nulls":3},"Reference: G",60900000,{"v":0.09,"d":"0.0900"},{"v":2E-3,"d":"0.0020"},0.0005]
[{"$nulls":3},"Reference: T",51200000,{"v":0.23,"d":"0.2300"},{"v":0.015,"d":"0.0150"},0.0054]
["Illumina","pError 0.01","non-enriched Mer","Reference: A",1850000,{"v":0.1,"d":"0.1000"},{"v":0.004,"d":"0.0040"},0.0008]
[{"$nulls":3},"Reference: C",2390000,{"v":0.08,"d":"0.0800"},{"v":2E-3,"d":"0.0020"},0.0006]
[{"$nulls":3},"Reference: G",2440000,{"v":0.08,"d":"0.0800"},{"v":0.004,"d":"0.0040"},0.0008]
[{"$nulls":3},"Reference: T",1810000,{"v":0.09,"d":"0.0900"},{"v":0.004,"d":"0.0040"},0.0012]
["Illumina","pError 0.01","non-enriched TB","Reference: A",7720000,{"v":0.09,"d":"0.0900"},{"v":0.005,"d":"0.0050"},0.0011]
[{"$nulls":3},"Reference: C",9640000,{"v":0.08,"d":"0.0800"},{"v":0.004,"d":"0.0040"},0.0008]
[{"$nulls":3},"Reference: G",9840000,{"v":0.07,"d":"0.0700"},{"v":0.004,"d":"0.0040"},0.0009]
[{"$nulls":3},"Reference: T",7460000,{"v":0.09,"d":"0.0900"},{"v":0.005,"d":"0.0050"},{"v":1.4E-3,"d":"0.0014"}]
["Illumina","pError 0.001","amplicons Mer","Reference: A",27300000,{"v":0.19,"d":"0.1900"},{"v":1E-3,"d":"0.0010"},0.0008]
[{"$nulls":3},"Reference: C",27100000,{"v":0.07,"d":"0.0700"},{"v":1E-3,"d":"0.0010"},0.0007]
[{"$nulls":3},"Reference: G",34900000,{"v":0.07,"d":"0.0700"},{"v":1E-3,"d":"0.0010"},0.0006]
[{"$nulls":3},"Reference: T",31400000,{"v":0.18,"d":"0.1800"},{"v":1E-3,"d":"0.0010"},0.0013]
["Illumina","pError 0.001","amplicons TB","Reference: A",27900000,{"v":0.17,"d":"0.1700"},{"v":0.003,"d":"0.0030"},0.0004]
[{"$nulls":3},"Reference: C",30700000,{"v":0.07,"d":"0.0700"},{"v":2E-3,"d":"0.0020"},0.0004]
[{"$nulls":3},"Reference: G",34900000,{"v":0.07,"d":"0.0700"},{"v":1E-3,"d":"0.0010"},0.0005]
[{"$nulls":3},"Reference: T",29800000,{"v":0.16,"d":"0.1600"},{"v":0.015,"d":"0.0150"},0.0041]
["Illumina","pError 0.001","non-enriched Mer","Reference: A",1420000,{"v":0.03,"d":"0.0300"},{"v":0.003,"d":"0.0030"},0.0009]
[{"$nulls":3},"Reference: C",1830000,{"v":0.03,"d":"0.0300"},{"v":2E-3,"d":"0.0020"},0.0004]
[{"$nulls":3},"Reference: G",1870000,{"v":0.03,"d":"0.0300"},{"v":0.003,"d":"0.0030"},0.0006]
[{"$nulls":3},"Reference: T",1390000,{"v":0.03,"d":"0.0300"},{"v":0.004,"d":"0.0040"},0.0011]
["Illumina","pError 0.001","non-enriched TB","Reference: A",6010000,{"v":0.03,"d":"0.0300"},{"v":0.005,"d":"0.0050"},0.0008]
[{"$nulls":3},"Reference: C",7490000,{"v":0.02,"d":"0.0200"},{"v":0.003,"d":"0.0030"},0.0007]
[{"$nulls":3},"Reference: G",7650000,{"v":0.02,"d":"0.0200"},{"v":0.003,"d":"0.0030"},0.0007]
[{"$nulls":3},"Reference: T",5800000,{"v":0.03,"d":"0.0300"},{"v":0.005,"d":"0.0050"},0.0012]
["Mer, Merlin; TB, TB-BAC4-luc."]

{"sheet":"sup10","index":10,"n_rows":14,"n_cols":13,"rows_kept":14,"merged":[[0,0,0,12],[1,1,1,6],[1,7,1,12],[13,0,13,12]]}
["Supplementary Table 10. Ratio estimation of artificial mixtures as estimated by read mappings to genotype-specific sequences."]
["Artificial mixture (TB:Mer ratio)","Ratio of reads mapped to genotype-specific reference sequences",{"$nulls":5},"Average coverage of genotype-specific mapping"]
[null,"TB40_gH1","Mer_gH2","TB_gO1c","Mer_gO5","TB_gN4c","Merlin_gN4d","TB40_gH1","Mer_gH2","TB_gO1c","Mer_gO5","TB_gN4c","Merlin_gN4d"]
["1:99",{"v":2,"d":"2.0"},{"v":98,"d":"98.0"},0.5,99.5,{"v":2,"d":"2.0"},{"v":98,"d":"98.0"},{"v":61.1,"d":"61"},{"v":3683.1,"d":"3683"},{"v":29.1,"d":"29"},{"v":6441.2,"d":"6441"},118,5012]
["1:99",2.9,97.1,{"v":1,"d":"1.0"},{"v":99,"d":"99.0"},2.3,97.7,{"v":165.5,"d":"166"},{"v":6155.9,"d":"6156"},{"v":105.3,"d":"105"},{"v":10876.4,"d":"10876"},{"v":192.2,"d":"192"},{"v":7871.9,"d":"7872"}]
["99:1",99.2,0.8,99.7,0.3,{"v":99,"d":"99.0"},{"v":1,"d":"1.0"},{"v":1423.1,"d":"1423"},{"v":10.4,"d":"10"},{"v":1665.3,"d":"1665"},{"v":4.4,"d":"4"},{"v":1652.4,"d":"1652"},{"v":14.7,"d":"15"}]
["99:1",99.4,0.6,99.6,0.4,98.9,1.1,{"v":5867.5,"d":"5868"},{"v":32.8,"d":"33"},{"v":7061.6,"d":"7062"},24,{"v":6689.1,"d":"6689"},{"v":71.6,"d":"72"}]
["95:5",96.3,3.7,97.8,2.2,95.3,4.7,{"v":3037.4,"d":"3037"},{"v":104.9,"d":"105"},3419,{"v":69.8,"d":"70"},{"v":3531.6,"d":"3532"},{"v":159.7,"d":"160"}]
["95:5",97.2,2.8,98.4,1.6,96.5,3.5,{"v":1812.1,"d":"1812"},{"v":46.6,"d":"47"},{"v":2011.1,"d":"2011"},{"v":30.5,"d":"31"},1943,{"v":66.6,"d":"67"}]
["5:95",7.4,92.6,{"v":2,"d":"2.0"},{"v":98,"d":"98.0"},6.8,93.2,{"v":120.7,"d":"121"},{"v":1707.3,"d":"1707"},{"v":54.8,"d":"55"},{"v":2908.7,"d":"2909"},{"v":158.3,"d":"158"},{"v":2145.3,"d":"2145"}]
["5:95",9.4,90.6,3.9,96.1,7.8,92.2,{"v":141.9,"d":"142"},{"v":1557.3,"d":"1557"},{"v":170.5,"d":"171"},{"v":4415.2,"d":"4415"},{"v":233.5,"d":"234"},{"v":2685.2,"d":"2685"}]
["50:50",58.8,41.2,53.6,46.4,55.7,44.3,{"v":2855.7,"d":"2856"},{"v":2040.6,"d":"2041"},3073,{"v":2638.2,"d":"2638"},{"v":3557.3,"d":"3557"},{"v":2686.6,"d":"2687"}]
["50:50",58.7,41.3,55.9,44.1,54.1,45.9,{"v":1311.1,"d":"1311"},{"v":947.6,"d":"948"},{"v":1456.8,"d":"1457"},{"v":1113.1,"d":"1113"},{"v":1477.3,"d":"1477"},{"v":1197.8,"d":"1198"}]
["Mer, Merlin; TB, TB-BAC4-luc."]

{"sheet":"sup11","index":11,"n_rows":7,"n_cols":19,"rows_kept":7,"merged":[[0,0,0,18],[6,0,6,18]]}
["Supplementary Table 11. Number of reads assigned to a specific genotype1 as identified by short Illumina amplicon sequencing of BAL samples."]
["Sample","VIral load in copies/ml","HCMV DNA copies/reaction","gN1","gN2","gN3a","gN3b","gO1a","gO1b","gO2a","gO2b","UL146-1","Ul146-2","UL146-6","UL146-7","UL146-11","UL146-12","UL146-13","UL146-14"]
["BAL2",{"v":420000,"d":"4.20E+05"},{"v":2100,"d":"2.10E+03"},1919,null,null,6282,197,null,2909,{"$nulls":6},24276,246594]
["BAL4",{"v":320000,"d":"3.20E+05"},{"v":1300,"d":"1.30E+03"},38784,null,null,3725,491,null,62,{"$nulls":7},1130,43703]
["BAL5",{"v":1000000,"d":"1.00E+06"},{"v":5000,"d":"5.00E+03"},null,422,1168,4534,null,11,1799,319,null,null,30443,8935,4016]
["BAL6",{"v":35000,"d":"3.50E+04"},{"v":175,"d":"1.75E+02"},3524,null,null,1051,309,null,293,null,84057,70493]
["1) genotype-specific reference sequences are listed in supplementary table 6, assignment according to Suarez et al., 2019,  doi: 10.1093/infdis/jiz208; BAL, bronchoalveolar lavage."]

{"sheet":"sup12a","index":12,"n_rows":12,"n_cols":14,"rows_kept":12,"merged":[[0,0,0,13],[1,2,1,7],[1,8,1,10],[1,11,1,13],[11,0,11,13]]}
["Supplementary Table 12a. Trimming, filtering, and mapping of PacBio-derived reads for haplotype determination of reads mapping to F3 target site (7,7kb)."]
["BAL sample","Input DNA","Number and average read length of sequencing reads",{"$nulls":5},"Number of reads assigned to haplotype sequences",null,null,"Relative frequency of haplotypes in %"]
[{"$nulls":3},"raw reads","after ltrim <7500 bases","after qtrim","after hu removal and ltrim <4500","re-map to consensus sequence","hap1","hap2","hap3","hap1","hap2","hap3"]
[2,"F3+F4 amplicons","number",297908,47945,20510,20474,19113,11215,6704,1194,58.7,35.1,6.2]
[null,null,"length",{"v":6802.6,"d":"6803"},7781,7383,7383,7441]
[4,"F3+F4 amplicons","number",147590,7163,2274,1566,1302,1302,null,null,{"v":100,"d":"100.0"}]
[null,null,"length",{"v":7993.6,"d":"7994"},7745,7294,7294,7485]
[5,"F3+F4 amplicons","number",171476,13113,4926,4418,4018,3139,566,313,78.1,14.1,7.8]
[null,null,"length",{"v":7189.7,"d":"7190"},7766,7330,7354,7420]
[6,"F3+F4 amplicons","number",156628,26542,11552,11502,10753,10753,null,null,{"v":100,"d":"100.0"}]
[null,null,"length",{"v":6853.1,"d":"6853"},7789,7395,7400,7460]
["qtrim, quality trim; hu, human DNA-specific reads; ltrim, length trim."]

{"sheet":"sup12b","index":13,"n_rows":12,"n_cols":14,"rows_kept":12,"merged":[[0,0,0,13],[1,2,1,7],[1,8,1,10],[1,11,1,13],[11,0,11,13]]}
["Supplementary Table 12b. Trimming, filtering, and mapping of PacBio-derived reads for haplotype determination of reads mapping to F4 target site (6,7 kb)."]
["BAL sample","Input DNA","Number and average read length of sequencing reads",{"$nulls":5},"Number of reads assigned to haplotype sequences",null,null,"Relative frequency of haplotypes in %"]
[{"$nulls":3},"raw reads","after ltrim <6500 bases","after qtrim","after hu removal and ltrim <3500","re-map to consensus sequence","hap1","hap2","hap3","hap1","hap2","hap3"]
[2,"F3+F4 amplicons","number",297908,102151,49850,49776,46903,27785,15142,3976,59.2,32.3,8.5]
[null,null,"length",{"v":6802.6,"d":"6803"},6739,6434,6434,6477]
[4,"F3+F4 amplicons","number",147590,29146,13281,10429,9839,9839,null,null,{"v":100,"d":"100.0"}]
[null,null,"length",{"v":7993.6,"d":"7994"},6715,6395,6378,6410]
[5,"F3+F4 amplicons","number",171476,41242,23069,21800,21400,16070,3590,1740,75.1,16.8,8.1]
[null,null,"length",{"v":7189.7,"d":"7190"},6660,6428,6427,6439]
[6,"F3+F4 amplicons","number",156628,55365,27046,26626,25442,21782,3660,null,85.6,14.4]
[null,null,"length",{"v":6853.1,"d":"6853"},6746,6438,6439,6472]
["qtrim, quality trim; hu, human DNA-specific reads; ltrim, length trim."]