{"text_format":"3","workbook":"xlsx","n_sheets":10,"sheets":["Supplementary Data 1","Supplementary Data 2","Supplementary Data 3","Supplementary Data 4","Supplementary Data 5","Supplementary Data 6","Supplementary Data 7","Supplementary Data 8","Supplementary Data 9","Supplementary Data 10"],"not_rendered":{"defined_names":1},"read":"whole","date_system":"1900"}

{"sheet":"Supplementary Data 1","index":0,"n_rows":43,"n_cols":15,"rows_kept":43,"merged":[[0,0,0,14]]}
["Supplementary Data 1: Public datasets used for assembly quality assessment"]
["Species Assembly","Genome size (Mb)","BUSCO completeness (%)","Contig N50 (Mb)","LTR Assembly Index (LAI)","QV","#NO. CRH (per Mb)","#NO. CSH (per Mb)","#NO. CRE (per Mb)","#NO. CSE (per Mb)","R-AQI","S-AQI","Assessmbly Level","Sequencing Technology","Data Source"]
["Oryza sativa ZS97",375,98.4,{"v":2.33907,"d":"2.34"},{"v":23.7,"d":"23.70"},{"v":36.9733,"d":"36.973"},{"v":0.078314,"d":"0.078"},{"v":2.581E-3,"d":"0.003"},{"v":0.153701212630468,"d":"0.15370"},{"v":0.020654,"d":"0.02065"},98.45,97.95574,"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/assembly/GCA_001623345.2"]
["Oryza sativa MH63",375,97.6,{"v":3.097358,"d":"3.10"},{"v":23.6,"d":"23.60"},35.818,{"v":0.1948,"d":"0.195"},{"v":0.0129,"d":"0.013"},0.38244,{"v":0.0516,"d":"0.05160"},{"v":96.2478,"d":"96.25"},{"v":94.9686851,"d":"94.96869"},"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/assembly/GCA_001623365.2"]
["Oryza sativa(R498)",373,98.5,{"v":2.5582588,"d":"2.56"},{"v":23.2,"d":"23.20"},{"v":43.8419,"d":"43.842"},{"v":0.68212,"d":"0.682"},{"v":7.685E-3,"d":"0.008"},0.30929,0.01793,96.96,98.22259,"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/bioproject/PRJNA318714"]
["Human HG002 (HIFI,Canu)",3365,94.7,65.28,"NA",{"v":46.57,"d":"46.570"},{"v":1.158824,"d":"1.159"},{"v":0.0181075,"d":"0.018"},{"v":0.10429103580975,"d":"0.10429"},{"v":0.0627314501111278,"d":"0.06273"},98.96,{"v":93.9195660715533,"d":"93.91957"},"contig","PacBio HiFi","https://zenodo.org/record/5895358"]
["Human HG002 (CLR,Canu)",2913,94.1,7.21,"NA",{"v":38.51,"d":"38.510"},{"v":1.021245,"d":"1.021"},{"v":0.0179025169,"d":"0.018"},{"v":0.425630121442287,"d":"0.42563"},{"v":0.0459530561855053,"d":"0.04595"},95.83,{"v":95.50867965557622,"d":"95.50868"},"contig","PacBio CLR","https://zenodo.org/record/5895359"]
["Human HG002 (ONT,Canu)",2901,43.4,{"v":33.1,"d":"33.10"},"NA",{"v":22.94,"d":"22.940"},{"v":2.963261,"d":"2.963"},{"v":0.02196237,"d":"0.022"},{"v":0.987932075002314,"d":"0.98793"},{"v":0.0740393760931037,"d":"0.07404"},90.59,{"v":92.86351270981402,"d":"92.86351"},"contig","Oxford Nanopore Ultra","https://zenodo.org/record/5895360"]
["Solanum pennellii (Canu_SMARTdenovo）",885,98.7,2.52,{"v":14.8,"d":"14.80"},{"v":26.1847,"d":"26.185"},{"v":2.78,"d":"2.780"},{"v":0.036606,"d":"0.037"},{"v":5.75070077617121,"d":"5.75070"},{"v":0.1190032,"d":"0.11900"},56.27,{"v":88.78049597815331,"d":"88.78050"},"contig","Oxford Nanopore","http://www.plabipd.de/portal/solanum-pennellii"]
["Solanum pennellii (SMARTdenovo）",923,98.5,1.06,{"v":12.7,"d":"12.70"},{"v":22.8264,"d":"22.826"},3.342,{"v":0.048854660884035,"d":"0.049"},10.98007,{"v":0.08905575681911,"d":"0.08906"},28.82,{"v":91.47945661173125,"d":"91.47946"},"contig","Oxford Nanopore","http://www.plabipd.de/portal/solanum-pennellii"]
["Solanum pennellii (Canu）",918,98.6,1.55,{"v":12.9,"d":"12.90"},{"v":24.2822,"d":"24.282"},{"v":3.1706,"d":"3.171"},{"v":0.07208873,"d":"0.072"},{"v":9.4076085,"d":"9.40761"},{"v":0.13434086904713,"d":"0.13434"},{"v":39.033073,"d":"39.03"},{"v":87.4166724012142,"d":"87.41667"},"contig","Oxford Nanopore","http://www.plabipd.de/portal/solanum-pennellii"]
["Broomcorn millet (Panicum miliaceum)",810,98.4,2.55,13.28,{"v":44.0495,"d":"44.050"},{"v":0.338350396590195,"d":"0.338"},{"v":0.0154969647293219,"d":"0.015"},{"v":1.0878074523844,"d":"1.08781"},{"v":0.0238414841989568,"d":"0.02384"},{"v":89.6927,"d":"89.69"},{"v":97.6440478735579,"d":"97.64405"},"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/bioproject/PRJNA429322"]
["Sorghum bicolor TX430",636,98.1,{"v":3.053182,"d":"3.05"},11.09,{"v":26.4132,"d":"26.413"},{"v":3.089041,"d":"3.089"},{"v":0.6450357,"d":"0.645"},{"v":9.56278455196978,"d":"9.56278"},{"v":1.04184822937462,"d":"1.04185"},38.43,{"v":35.28020199533205,"d":"35.28020"},"contig","Oxford Nanopore","https://www.ebi.ac.uk/ena/data/view/QWKM01000000"]
["Arabis alpina V5",327,99.3,{"v":0.795916,"d":"0.80"},9.82,{"v":39.9435,"d":"39.944"},{"v":6.78482,"d":"6.785"},{"v":0.1703498,"d":"0.170"},{"v":3.47043347262189,"d":"3.47043"},{"v":0.656106251727734,"d":"0.65611"},70.68,{"v":51.88677466354308,"d":"51.88677"},"chromosome","PacBio CLR","http://arabis-alpina.org/refseq.html"]
["Arabis alpina V4",295,98.5,{"v":0.09659,"d":"0.10"},2.36,{"v":45.0552,"d":"45.055"},9.356,{"v":0.1244,"d":"0.124"},{"v":48.0584858620587,"d":"48.05849"},{"v":2.11974200197922,"d":"2.11974"},0.82,{"v":12.006260042921864,"d":"12.00626"},"chromosome","454, Illumina and BAC ","http://arabis-alpina.org/refseq.html"]
["Aristolochia fimbriata",250,98.7,5.47,20.93,26.741,13.417,0.303,{"v":17.351,"d":"17.35100"},{"v":0.2846,"d":"0.28460"},{"v":17.637,"d":"17.64"},{"v":75.2315120190273,"d":"75.23151"},"chromosome","Oxford Nanopore","https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA656149"]
["Anopheles funestus (AfunF3)",425,98.3,{"v":0.632,"d":"0.63"},"NA",{"v":28.5784,"d":"28.578"},53.534,4.312,{"v":26.0837792639819,"d":"26.08378"},{"v":1.54639513828843,"d":"1.54640"},7.37,{"v":21.301447916375693,"d":"21.30145"},"contig","PacBio CLR","https://www.ncbi.nlm.nih.gov/bioproject/PRJNA494870"]
["Arabidopsis thaliana KM74 (ONT)",119,98.4,{"v":12.334794,"d":"12.33"},{"v":14.6,"d":"14.60"},{"v":31.4657,"d":"31.466"},{"v":1.876145,"d":"1.876"},{"v":0.06211146,"d":"0.062"},{"v":1.51386901921063,"d":"1.51387"},{"v":0.0689730043799237,"d":"0.06897"},85.95,{"v":93.33518761507547,"d":"93.33519"},"contig","Oxford Nanopore","https://www.ebi.ac.uk/ena/data/view/PRJEB21270"]
["Arabidopsis thaliana KM74 (PacBio)",115,{"v":99,"d":"99.0"},{"v":10.401798,"d":"10.40"},{"v":17.2,"d":"17.20"},{"v":48.5017,"d":"48.502"},{"v":1.1554549,"d":"1.155"},{"v":0.05884,"d":"0.059"},{"v":0.453409516495751,"d":"0.45341"},{"v":0.0377841263746459,"d":"0.03778"},95.57,{"v":96.29207876574354,"d":"96.29208"},"contig","PacBio CLR","https://www.ebi.ac.uk/ena/data/view/PRJEB23084"]
["Acer yangbiense",617,95.5,{"v":5.479097,"d":"5.48"},9.55,{"v":35.7969,"d":"35.797"},2.544,{"v":0.32,"d":"0.320"},{"v":4.84516531557064,"d":"4.84517"},{"v":1.29009581332647,"d":"1.29010"},{"v":61.6,"d":"61.60"},{"v":27.52444097438237,"d":"27.52444"},"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/nuccore/VAHF00000000"]
["Cinnamomum kanehirae",697,88.5,{"v":0.9,"d":"0.90"},17.76,{"v":30.4187,"d":"30.419"},{"v":4.678234,"d":"4.678"},{"v":1.1123,"d":"1.112"},{"v":9.2295199299075,"d":"9.22952"},{"v":0.82109059629096,"d":"0.82109"},39.73,{"v":43.99515832067459,"d":"43.99516"},"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/bioproject/PRJNA477266"]
["C. hircus ARS1",2962,95.8,{"v":3.8,"d":"3.80"},"NA",{"v":32.6794,"d":"32.679"},{"v":0.4326818,"d":"0.433"},{"v":0.02747445,"d":"0.027"},{"v":0.693077292722001,"d":"0.69308"},{"v":0.238680071108215,"d":"0.23868"},{"v":93.3,"d":"93.30"},{"v":78.76668394454049,"d":"78.76668"},"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/assembly/GCF_001704415.1/"]
["Zea mays B73 v1",2046,92.3,{"v":0.039949,"d":"0.04"},9.52,{"v":31.7227,"d":"31.723"},{"v":2.866101,"d":"2.866"},{"v":0.1259898,"d":"0.126"},{"v":33.4538335960129,"d":"33.45383"},{"v":0.91837264823457,"d":"0.91837"},3.52,{"v":39.91680997297062,"d":"39.91681"},"chromosome","BAC-by-BAC","https://chinese.maizegdb.org/assembly"]
["Zea mays B73 v2",2058,94.9,{"v":0.04125,"d":"0.04"},9.82,{"v":31.8516,"d":"31.852"},{"v":2.863401,"d":"2.863"},{"v":0.1209701,"d":"0.121"},{"v":32.9422335681391,"d":"32.94223"},{"v":0.881779291055509,"d":"0.88178"},3.71,{"v":41.404554834337794,"d":"41.40455"},"chromosome","BAC-by-BAC","https://chinese.maizegdb.org/assembly"]
["Zea mays B73 v3",2059,94.9,{"v":0.0413,"d":"0.04"},11.42,{"v":31.8873,"d":"31.887"},{"v":1.96766101,"d":"1.968"},{"v":0.1216862,"d":"0.122"},{"v":32.901368062514,"d":"32.90137"},{"v":0.88699678109661,"d":"0.88700"},3.72,{"v":41.1890895645694,"d":"41.18909"},"chromosome","BAC-by-BAC","https://chinese.maizegdb.org/assembly"]
["Zea mays B73 v4",2134,98.1,{"v":1.279966,"d":"1.28"},20.72,{"v":39.4939,"d":"39.494"},{"v":1.091525,"d":"1.092"},{"v":0.109145397,"d":"0.109"},{"v":1.39822126102715,"d":"1.39822"},{"v":0.73973233825484,"d":"0.73973"},86.95,{"v":47.724163775671855,"d":"47.72416"},"chromosome","PacBio CLR","https://chinese.maizegdb.org/assembly"]
["Euclidium syriacum",223,99.3,{"v":4.197252,"d":"4.20"},15.23,{"v":43.6142,"d":"43.614"},{"v":0.2726586,"d":"0.273"},{"v":0.0398555,"d":"0.040"},{"v":0.508526062522318,"d":"0.50853"},{"v":0.181616450900828,"d":"0.18162"},95.04,{"v":83.392112878227,"d":"83.39211"},"chromosome","PacBio CLR","https://www.ebi.ac.uk/ena/data/view/GCA_900116095"]
["Nymphaea colorata",391,95.8,{"v":2.1,"d":"2.10"},11.45,{"v":27.1315,"d":"27.132"},{"v":2.759599,"d":"2.760"},{"v":0.04641875,"d":"0.046"},{"v":1.8202269911007,"d":"1.82023"},{"v":0.198078657109776,"d":"0.19808"},83.36,{"v":82.03053277539591,"d":"82.03053"},"chromosome","PacBio CLR","https://www.ncbi.nlm.nih.gov/bioproject/492326"]
["Brassica oleracea HDEM",539,95.8,{"v":9.491203,"d":"9.49"},13.51,{"v":27.0364,"d":"27.036"},{"v":6.592852,"d":"6.593"},{"v":0.210483,"d":"0.210"},{"v":9.57127651218962,"d":"9.57128"},{"v":0.517304210413161,"d":"0.51730"},{"v":38.4,"d":"38.40"},{"v":59.61254124891868,"d":"59.61254"},"chromosome","Oxford Nanopore","https://www.ebi.ac.uk/ena/data/view/PRJEB26621"]
["Brassica rapa Z1",390,96.6,{"v":5.519976,"d":"5.52"},{"v":6,"d":"6.00"},{"v":26.5704,"d":"26.570"},{"v":5.374046,"d":"5.374"},{"v":0.02806359,"d":"0.028"},{"v":9.35097794940317,"d":"9.35098"},{"v":0.0978734611297298,"d":"0.09787"},39.25,{"v":90.67636373409098,"d":"90.67636"},"chromosome","Oxford Nanopore","https://www.ebi.ac.uk/ena/data/view/PRJEB26620"]
["Musa schizocarpa",510,98.3,{"v":6.493909,"d":"6.49"},17.48,{"v":25.9064,"d":"25.906"},{"v":5.90608,"d":"5.906"},{"v":0.1005518,"d":"0.101"},{"v":23.6243175588567,"d":"23.62432"},{"v":0.539885918774152,"d":"0.53989"},9.42,{"v":58.28147368012216,"d":"58.28147"},"chromosome","Oxford Nanopore","https://www.ebi.ac.uk/ena/data/view/PRJEB26661"]
["Maylandia zebra (UMD2a)",957,81.1,3.16,1.74,{"v":32.4678,"d":"32.468"},{"v":13.13211,"d":"13.132"},{"v":0.03629293,"d":"0.036"},{"v":9.24223634946659,"d":"9.24224"},{"v":0.0491024393239348,"d":"0.04910"},39.68,{"v":95.20835939031508,"d":"95.20836"},"chromosome","PacBio RS II","https://www.ncbi.nlm.nih.gov/genome/2640"]
["Oreochromis niloticus Nile tilapia",1005,{"v":79.66,"d":"79.7"},{"v":2.92364,"d":"2.92"},"NA",{"v":24.1886,"d":"24.189"},{"v":4.25134,"d":"4.251"},{"v":0.02304421,"d":"0.023"},{"v":5.3454928601754,"d":"5.34549"},{"v":0.109461476195085,"d":"0.10946"},58.59,{"v":89.6316693226445,"d":"89.63167"},"contig","PacBio CLR","https://www.ncbi.nlm.nih.gov/assembly/GCF_001858045.2/"]
["Mangifera indica ",392,95.9,{"v":3.5,"d":"3.50"},18.52,{"v":40.6462,"d":"40.646"},{"v":0.9946885,"d":"0.995"},{"v":0.3477829,"d":"0.348"},{"v":2.08412580966995,"d":"2.08413"},{"v":0.21071641375741,"d":"0.21072"},81.19,{"v":81.00037402308119,"d":"81.00037"},"chromosome","PacBio Sequel II","https://www.ncbi.nlm.nih.gov/assembly/GCA_011075055.1/"]
["Drosophila melanogaster (Pacbio, Canu)",286,99.1,{"v":12.7002648,"d":"12.70"},"NA",{"v":32.9384,"d":"32.938"},{"v":12.01234,"d":"12.012"},{"v":0.010041,"d":"0.010"},1.26023,{"v":0.047589082930688,"d":"0.04759"},88.16,{"v":95.35255265006487,"d":"95.35255"},"contig","PacBio CLR","https://obj.umiacs.umd.edu/marbl_publications/hicanu/dmel_clr_canu_primary.fasta.gz"]
["Drosophila melanogaster (HIFI, Canu)",294,99.5,{"v":13.727855,"d":"13.73"},"NA",{"v":51.9445,"d":"51.945"},{"v":9.9801,"d":"9.980"},{"v":0.12,"d":"0.120"},{"v":0.781123,"d":"0.78112"},{"v":0.0534602698820963,"d":"0.05346"},92.49,{"v":94.79436021667371,"d":"94.79436"},"contig","PacBio HiFi","https://obj.umiacs.umd.edu/marbl_publications/hicanu/dmel_hifi_canu_primary.fasta.gz"]
["Zea mays NC358 (11k_50×)",2147,93.8,0.56,{"v":19.1,"d":"19.10"},{"v":31.5993,"d":"31.599"},{"v":2.56733,"d":"2.567"},{"v":0.1276652,"d":"0.128"},{"v":3.29355340619093,"d":"3.29355"},{"v":0.13952911946668,"d":"0.13953"},71.94,{"v":86.97676956642049,"d":"86.97677"},"chromosome","PacBio CLR","https://de.cyverse.org/dl/d/42938190-C7AF-4BF5-B953-0BB28F61887D/NC358_genome_annotation_April2020_public_release.tar"]
["Zea mays NC358 (16k_50×)",2127,95.7,4.24,{"v":21,"d":"21.00"},{"v":32.0791,"d":"32.079"},{"v":1.001732,"d":"1.002"},{"v":0.0135545,"d":"0.014"},{"v":0.626938397947854,"d":"0.62694"},{"v":0.0940586415631977,"d":"0.09406"},93.92,{"v":91.02293834017618,"d":"91.02294"},"chromosome","PacBio CLR","https://de.cyverse.org/dl/d/42938190-C7AF-4BF5-B953-0BB28F61887D/NC358_genome_annotation_April2020_public_release.tar"]
["Zea mays NC358 (21k_20×)",2117,{"v":67,"d":"67.0"},0.18,{"v":12.2,"d":"12.20"},{"v":24.7824,"d":"24.782"},{"v":0.85976,"d":"0.860"},{"v":0.023211,"d":"0.023"},{"v":8.4847205974878,"d":"8.48472"},{"v":0.175095675747061,"d":"0.17510"},42.81,{"v":83.93767089336284,"d":"83.93767"},"chromosome","PacBio CLR","https://de.cyverse.org/dl/d/42938190-C7AF-4BF5-B953-0BB28F61887D/NC358_genome_annotation_April2020_public_release.tar"]
["Zea mays NC358 (21k_30×)",2126,94.9,1.82,{"v":19.8,"d":"19.80"},{"v":27.9932,"d":"27.993"},{"v":0.957278,"d":"0.957"},{"v":0.021314,"d":"0.021"},{"v":1.29031136693347,"d":"1.29031"},{"v":0.111914761417699,"d":"0.11191"},87.89,{"v":89.41204678133643,"d":"89.41205"},"chromosome","PacBio CLR","https://de.cyverse.org/dl/d/42938190-C7AF-4BF5-B953-0BB28F61887D/NC358_genome_annotation_April2020_public_release.tar"]
["Zea mays NC358 (21k_40×)",2127,95.5,7.48,{"v":20.4,"d":"20.40"},{"v":29.1992,"d":"29.199"},{"v":0.77734,"d":"0.777"},{"v":0.01896733,"d":"0.019"},{"v":0.502754027859804,"d":"0.50275"},{"v":0.0756388919160334,"d":"0.07564"},{"v":95.1,"d":"95.10"},{"v":92.7150947819172,"d":"92.71509"},"chromosome","PacBio CLR","https://de.cyverse.org/dl/d/42938190-C7AF-4BF5-B953-0BB28F61887D/NC358_genome_annotation_April2020_public_release.tar"]
["Zea mays NC358 (21k_50×)",2131,95.4,16.27,{"v":20.2,"d":"20.20"},{"v":29.4499,"d":"29.450"},{"v":0.7841994,"d":"0.784"},{"v":0.01650744,"d":"0.017"},{"v":0.411568120135965,"d":"0.41157"},{"v":0.0521449272115561,"d":"0.05214"},95.97,{"v":94.91912932266894,"d":"94.91913"},"chromosome","PacBio CLR","https://de.cyverse.org/dl/d/42938190-C7AF-4BF5-B953-0BB28F61887D/NC358_genome_annotation_April2020_public_release.tar"]
["#CRE/CSE” and “#CRH/CSH” refer to total counts of CRE/CSEs and CRH/CSHs caculated at specific windows 50kb. 'NA' represents values that could not be calculated because LAI is only possible to calculate when the intact and total LTR-RTs contribute at least 0.1% and 5%."]

{"sheet":"Supplementary Data 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439,0,1440,0],[1441,0,1442,0],[1443,0,1444,0],[1445,0,1446,0],[1447,0,1448,0],[1449,0,1450,0],[1451,0,1452,0],[1453,0,1454,0],[1455,0,1456,0],[1457,0,1458,0],[1460,0,1461,0],[1463,0,1464,0],[1465,0,1466,0],[1467,0,1468,0],[1469,0,1470,0],[1471,0,1472,0],[1473,0,1474,0],[1476,0,1477,0],[1478,0,1479,0],[1480,0,1481,0],[1482,0,1483,0],[1484,0,1485,0],[1487,0,1488,0],[1489,0,1490,0],[1491,0,1492,0],[1493,0,1494,0],[1495,0,1496,0],[1497,0,1498,0],[1499,0,1500,0],[1501,0,1502,0],[1503,0,1504,0],[1505,0,1506,0],[1507,0,1508,0],[1509,0,1510,0],[1512,0,1513,0],[1514,0,1515,0],[1516,0,1517,0],[1518,0,1519,0],[1520,0,1521,0],[1522,0,1523,0],[1524,0,1525,0],[1526,0,1527,0],[1528,0,1529,0],[1531,0,1532,0],[1533,0,1534,0],[1535,0,1536,0],[1537,0,1538,0],[1539,0,1540,0],[1541,0,1542,0],[1543,0,1544,0],[1545,0,1546,0],[1547,0,1548,0],[1549,0,1550,0],[1551,0,1552,0],[1553,0,1554,0],[1555,0,1556,0],[1557,0,1558,0],[1559,0,1560,0],[1561,0,1562,0],[1563,0,1564,0],[1565,0,1566,0],[1567,0,1568,0],[1569,0,1570,0],[1571,0,1572,0],[1573,0,1574,0],[1577,0,1578,0],[1579,0,1580,0],[1581,0,1582,0],[1584,0,1585,0],[1586,0,1587,0],[1588,0,1589,0],[1590,0,1591,0],[1592,0,1593,0],[1594,0,1595,0],[1596,0,1597,0],[1598,0,1599,0],[1600,0,1601,0],[1602,0,1603,0],[1604,0,1605,0],[1606,0,1607,0],[1608,0,1609,0],[1610,0,1611,0],[1612,0,1613,0],[1616,0,1617,0],[1618,0,1619,0],[1620,0,1621,0],[1622,0,1623,0],[1624,0,1625,0],[1626,0,1627,0],[1628,0,1629,0],[1630,0,1631,0],[1632,0,1633,0],[1634,0,1635,0],[1636,0,1637,0],[1638,0,1639,0],[1640,0,1641,0],[1642,0,1643,0],[1644,0,1645,0],[1646,0,1647,0],[1648,0,1649,0],[1650,0,1651,0],[1652,0,1653,0],[1654,0,1655,0],[1656,0,1657,0],[1658,0,1659,0],[1660,0,1661,0],[1662,0,1663,0],[1664,0,1665,0],[1667,0,1668,0],[1669,0,1670,0],[1671,0,1672,0],[1673,0,1674,0],[1675,0,1676,0],[1677,0,1678,0],[1679,0,1680,0],[1681,0,1682,0],[1683,0,1684,0],[1685,0,1686,0],[1687,0,1688,0],[1689,0,1690,0],[1691,0,1692,0],[1693,0,1694,0],[1695,0,1696,0],[1697,0,1698,0],[1699,0,1700,0],[1701,0,1702,0],[1704,0,1705,0],[1706,0,1707,0],[1708,0,1709,0],[1710,0,1711,0],[1712,0,1713,0],[1714,0,1715,0],[1716,0,1717,0],[1718,0,1719,0],[1720,0,1721,0],[1722,0,1723,0],[1724,0,1725,0],[1726,0,1727,0],[1728,0,1729,0],[1730,0,1731,0],[1733,0,1734,0],[1735,0,1736,0],[1737,0,1738,0],[1739,0,1740,0],[1741,0,1742,0],[1743,0,1744,0],[1745,0,1746,0],[1748,0,1749,0],[1750,0,1751,0],[1752,0,1753,0],[1754,0,1755,0],[1756,0,1757,0],[1758,0,1759,0],[1760,0,1761,0],[1762,0,1763,0],[1764,0,1765,0],[1766,0,1767,0],[1768,0,1769,0],[1771,0,1772,0],[1773,0,1774,0],[1775,0,1776,0],[1777,0,1778,0],[1779,0,1780,0],[1781,0,1782,0],[1783,0,1784,0],[1785,0,1786,0],[1787,0,1788,0],[1789,0,1790,0],[1791,0,1792,0],[1793,0,1794,0],[1796,0,1797,0],[1798,0,1799,0],[1800,0,1801,0],[1802,0,1803,0],[1804,0,1805,0],[1806,0,1807,0],[1809,0,1810,0],[1811,0,1812,0],[1813,0,1814,0],[1816,0,1817,0],[1820,0,1821,0],[1822,0,1823,0],[1824,0,1825,0],[1826,0,1827,0],[1828,0,1829,0],[1830,0,1831,0],[1832,0,1833,0],[1834,0,1835,0],[1836,0,1837,0],[1838,0,1839,0],[1840,0,1841,0],[1842,0,1843,0],[1844,0,1845,0],[1846,0,1847,0],[1848,0,1849,0],[1850,0,1851,0],[1852,0,1853,0],[1854,0,1855,0],[1856,0,1857,0],[1858,0,1859,0],[1860,0,1861,0],[1862,0,1863,0],[1864,0,1865,0],[1866,0,1867,0],[1868,0,1869,0],[1870,0,1871,0],[1872,0,1873,0],[1874,0,1875,0],[1876,0,1877,0],[1879,0,1880,0],[1881,0,1882,0],[1883,0,1884,0],[1885,0,1886,0],[1887,0,1888,0],[1889,0,1890,0],[1892,0,1893,0],[1894,0,1895,0],[1896,0,1897,0],[1899,0,1900,0],[1901,0,1902,0],[1903,0,1904,0],[1905,0,1906,0],[1907,0,1908,0],[1909,0,1910,0],[1911,0,1912,0],[1913,0,1914,0],[1915,0,1916,0],[1917,0,1918,0],[1919,0,1920,0],[1921,0,1922,0],[1923,0,1924,0],[1925,0,1926,0],[1927,0,1928,0],[1929,0,1930,0],[1931,0,1932,0],[1933,0,1934,0],[1935,0,1936,0],[1937,0,1938,0],[1939,0,1940,0],[1941,0,1942,0],[1943,0,1944,0],[1945,0,1946,0],[1947,0,1948,0],[1949,0,1950,0],[1951,0,1952,0],[1953,0,1954,0],[1956,0,1957,0],[1958,0,1959,0],[1960,0,1961,0],[1962,0,1963,0],[1964,0,1965,0],[1967,0,1968,0],[1969,0,1970,0],[1971,0,1972,0],[1973,0,1974,0],[1975,0,1976,0],[1977,0,1978,0],[1979,0,1980,0],[1981,0,1982,0],[1983,0,1984,0],[1985,0,1986,0],[1987,0,1988,0],[1989,0,1990,0],[1991,0,1992,0],[1994,0,1995,0],[1996,0,1997,0],[1998,0,1999,0],[2000,0,2001,0],[2002,0,2003,0],[2004,0,2005,0],[2006,0,2007,0],[2008,0,2009,0],[2010,0,2011,0],[2012,0,2013,0],[2014,0,2015,0],[2016,0,2017,0],[2018,0,2019,0],[2020,0,2021,0],[2023,0,2024,0],[2025,0,2026,0],[2027,0,2028,0],[2029,0,2030,0],[2031,0,2032,0],[2033,0,2034,0],[2035,0,2036,0],[2037,0,2038,0],[2039,0,2040,0],[2041,0,2042,0],[2043,0,2044,0],[2045,0,2046,0],[2047,0,2048,0],[2049,0,2050,0],[2051,0,2052,0],[2053,0,2054,0],[2055,0,2056,0],[2057,0,2058,0],[2059,0,2060,0],[2061,0,2062,0],[2063,0,2064,0],[2065,0,2066,0],[2067,0,2068,0],[2069,0,2070,0],[2071,0,2072,0],[2073,0,2074,0],[2123,0,2124,0],[2125,0,2126,0],[2127,0,2128,0],[2129,0,2130,0],[2135,0,2136,0],[2137,0,2138,0],[2139,0,2140,0],[2141,0,2142,0],[2143,0,21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["Supplementary Data 2:  Introduced heterozygous variants and errors in the simulated hg38 assemblies"]
["Simulated_id","Simulated Class*","Simulated Type","Contig","Position","Located in Repeat/non-Repeat"]
[1,"ERR","Small_INS","contig1",133430,"Repeat"]
[{"$nulls":3},"contig1",134540,"Repeat"]
[2,"Het","Small_INS","contig1",136834,"Repeat"]
[{"$nulls":3},"contig1",137067,"Repeat"]
[3,"ERR","Small_INS","contig1",232816,"Repeat"]
[{"$nulls":3},"contig1",233144,"Repeat"]
[4,"ERR","Small_INS","contig1",341880,"Non_repeat"]
[{"$nulls":3},"contig1",342306,"Non_repeat"]
[5,"ERR","Small_DUP.Gain","contig1",859211,"Repeat"]
[{"$nulls":3},"contig1",860401,"Repeat"]
[6,"Het","Large_INS","contig1",933717,"Repeat"]
[{"$nulls":3},"contig1",972917,"Repeat"]
[7,"Het","Small_INS","contig1",1410006,"Repeat"]
[{"$nulls":3},"contig1",1410056,"Repeat"]
[8,"Het","Small_INS","contig1",1422576,"Non_repeat"]
[{"$nulls":3},"contig1",1424096,"Non_repeat"]
[9,"ERR","Small_INS","contig1",1684452,"Repeat"]
[{"$nulls":3},"contig1",1684700,"Repeat"]
[10,"ERR","Small_INS","contig1",1735104,"Non_repeat"]
[{"$nulls":3},"contig1",1735870,"Non_repeat"]
[11,"Het","Small_INS","contig1",1871310,"Non_repeat"]
[{"$nulls":3},"contig1",1871706,"Non_repeat"]
[12,"ERR","Small_INS","contig1",2337865,"Non_repeat"]
[{"$nulls":3},"contig1",2338316,"Non_repeat"]
[13,"Het","Small_INS","contig1",2434415,"Non_repeat"]
[{"$nulls":3},"contig1",2434631,"Non_repeat"]
[14,"ERR","INV","contig1",2461238,"Non_repeat"]
[{"$nulls":3},"contig1",2490101,"Repeat"]
[15,"Het","Small_INS","contig1",2681978,"Non_repeat"]
[{"$nulls":3},"contig1",2682452,"Non_repeat"]
[16,"Het","Small_INS","contig1",2791061,"Repeat"]
[{"$nulls":3},"contig1",2791432,"Repeat"]
[17,"ERR","Small_INS","contig1",2865817,"Repeat"]
[{"$nulls":3},"contig1",2866270,"Non_repeat"]
[18,"ERR","Small_INS","contig1",2963936,"Non_repeat"]
[{"$nulls":3},"contig1",2964332,"Non_repeat"]
[19,"Het","Small_INS","contig1",3029030,"Repeat"]
[{"$nulls":3},"contig1",3029250,"Repeat"]
[20,"ERR","Small_INS","contig1",3029395,"Repeat"]
[{"$nulls":3},"contig1",3029744,"Repeat"]
[21,"ERR","Small_INS","contig1",3082953,"Repeat"]
[{"$nulls":3},"contig1",3083450,"Repeat"]
[22,"Het","Small_INS","contig1",3381356,"Non_repeat"]
[{"$nulls":3},"contig1",3381547,"Non_repeat"]
[23,"ERR","Small_INS","contig1",3666662,"Non_repeat"]
[{"$nulls":3},"contig1",3667126,"Non_repeat"]
[24,"Het","Small_INS","contig1",3681591,"Non_repeat"]
[{"$nulls":3},"contig1",3681645,"Non_repeat"]
[25,"Het","Small_INS","contig1",3682029,"Repeat"]
[{"$nulls":3},"contig1",3682088,"Repeat"]
[26,"Het","Small_INS","contig1",3708624,"Repeat"]
[{"$nulls":3},"contig1",3708888,"Repeat"]
[27,"ERR","Small_INS","contig1",3787084,"Non_repeat"]
[{"$nulls":3},"contig1",3787492,"Non_repeat"]
[28,"Het","Large_INS","contig1",4013126,"Non_repeat"]
[{"$nulls":3},"contig1",4051467,"Non_repeat"]
[29,"ERR","Small_INS","contig1",4564463,"Repeat"]
[{"$nulls":3},"contig1",4564869,"Repeat"]
[30,"Het","Small_INS","contig1",4568619,"Non_repeat"]
[{"$nulls":3},"contig1",4568981,"Non_repeat"]
[31,"ERR","INV","contig1",4649450,"Repeat"]
[{"$nulls":3},"contig1",4690444,"Repeat"]
[32,"ERR","Small_INS","contig1",4755797,"Non_repeat"]
[{"$nulls":3},"contig1",4755854,"Non_repeat"]
[33,"ERR","Small_DEL","contig1",4756109,"Non_repeat"]
[34,"ERR","Small_INS","contig1",4771708,"Non_repeat"]
[{"$nulls":3},"contig1",4772104,"Non_repeat"]
[35,"ERR","Small_DUP.Gain","contig1",5257678,"Repeat"]
[{"$nulls":3},"contig1",5258831,"Repeat"]
[36,"Het","Small_INS","contig1",5654067,"Non_repeat"]
[{"$nulls":3},"contig1",5654316,"Non_repeat"]
[37,"Het","Small_INS","contig1",5836190,"Repeat"]
[{"$nulls":3},"contig1",5836243,"Repeat"]
[38,"Het","Small_INS","contig1",5837295,"Repeat"]
[{"$nulls":3},"contig1",5837351,"Repeat"]
[39,"Het","Large_INS","contig1",5862755,"Non_repeat"]
[{"$nulls":3},"contig1",5874693,"Non_repeat"]
[40,"ERR","Small_INS","contig1",6025121,"Non_repeat"]
[{"$nulls":3},"contig1",6025521,"Repeat"]
[41,"ERR","Large_INS","contig1",6311199,"Repeat"]
[{"$nulls":3},"contig1",6324206,"Non_repeat"]
[42,"ERR","INV","contig1",6346196,"Non_repeat"]
[{"$nulls":3},"contig1",6391216,"Non_repeat"]
[43,"ERR","Small_INS","contig1",6515932,"Non_repeat"]
[{"$nulls":3},"contig1",6516396,"Repeat"]
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[{"$nulls":3},"contig99",10721909,"Non_repeat"]
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[{"$nulls":3},"contig99",11416725,"Repeat"]
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[{"$nulls":3},"contig99",12188211,"Non_repeat"]
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[{"$nulls":3},"contig99",12270401,"Non_repeat"]
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[{"$nulls":3},"contig99",12310459,"Non_repeat"]
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[{"$nulls":3},"contig99",12502680,"Repeat"]
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[{"$nulls":3},"contig99",12682581,"Repeat"]
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[{"$nulls":3},"contig99",12835851,"Repeat"]
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[{"$nulls":3},"contig99",12900666,"Repeat"]
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[{"$nulls":3},"contig99",13050087,"Repeat"]
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[{"$nulls":3},"contig99",13138774,"Non_repeat"]
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[{"$nulls":3},"contig99",13409175,"Non_repeat"]
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[{"$nulls":3},"contig99",14239094,"Repeat"]
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[{"$nulls":3},"contig99",14834217,"Non_repeat"]
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[{"$nulls":3},"contig99",15677281,"Non_repeat"]
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[{"$nulls":3},"contig99",15981376,"Non_repeat"]
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[{"$nulls":3},"contig99",16185839,"Non_repeat"]
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[{"$nulls":3},"contig99",16301116,"Non_repeat"]
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[{"$nulls":3},"contig99",16432697,"Non_repeat"]
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[{"$nulls":3},"contig99",16573781,"Non_repeat"]
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[{"$nulls":3},"contig99",16754165,"Non_repeat"]
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[{"$nulls":3},"contig99",17077439,"Non_repeat"]
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[{"$nulls":3},"contig99",17177104,"Non_repeat"]
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[{"$nulls":3},"contig99",17189984,"Non_repeat"]
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[{"$nulls":3},"contig99",17288987,"Non_repeat"]
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[{"$nulls":3},"contig99",17392953,"Repeat"]
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[{"$nulls":3},"contig99",17431617,"Repeat"]
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[{"$nulls":3},"contig99",17711834,"Repeat"]
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[{"$nulls":3},"contig99",17791533,"Repeat"]
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[{"$nulls":3},"contig99",18220694,"Non_repeat"]
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[{"$nulls":3},"contig99",18288347,"Non_repeat"]
[19130,"Het","Small_DEL","contig99",18369931,"Non_repeat"]
[19131,"Het","Small_DEL","contig99",18371236,"Non_repeat"]
[19132,"Het","Small_INS","contig99",18389296,"Repeat"]
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[{"$nulls":3},"contig99",18389646,"Repeat"]
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[{"$nulls":3},"contig99",18413631,"Non_repeat"]
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[{"$nulls":3},"contig99",18460264,"Non_repeat"]
[19136,"Het","Small_INS","contig99",18486860,"Repeat"]
[{"$nulls":3},"contig99",18487293,"Repeat"]
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[{"$nulls":3},"contig99",18522170,"Non_repeat"]
[19138,"Het","Small_INS","contig99",18686795,"Repeat"]
[{"$nulls":3},"contig99",18687217,"Repeat"]
[19139,"Het","Small_INS","contig99",19615909,"Repeat"]
[{"$nulls":3},"contig99",19616227,"Repeat"]
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[{"$nulls":3},"contig99",19714611,"Non_repeat"]
[19141,"ERR","Small_INS","contig99",19827570,"Repeat"]
[{"$nulls":3},"contig99",19828038,"Non_repeat"]
[19142,"Het","Small_INS","contig99",19849006,"Repeat"]
[{"$nulls":3},"contig99",19849394,"Repeat"]
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[{"$nulls":3},"contig99",20281071,"Non_repeat"]
[19144,"Het","Small_INS","contig99",20835554,"Repeat"]
[{"$nulls":3},"contig99",20835837,"Non_repeat"]
[19145,"ERR","Small_INS","contig99",20948388,"Non_repeat"]
[{"$nulls":3},"contig99",20948831,"Non_repeat"]
[19146,"Het","Small_INS","contig99",21170600,"Non_repeat"]
[{"$nulls":3},"contig99",21172320,"Non_repeat"]
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[{"$nulls":3},"contig99",21329339,"Non_repeat"]
[19148,"Het","Small_INS","contig99",21410250,"Repeat"]
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[{"$nulls":3},"contig99",21799641,"Repeat"]
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[19151,"ERR","Small_DUP.Gain","contig99",21875191,"Repeat"]
[{"$nulls":3},"contig99",21875241,"Repeat"]
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[{"$nulls":3},"contig99",22104381,"Non_repeat"]
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[{"$nulls":3},"contig99",22520890,"Repeat"]
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[{"$nulls":3},"contig99",23219050,"Non_repeat"]
[19159,"Het","Small_INS","contig99",23338015,"Repeat"]
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[{"$nulls":3},"contig99",23450451,"Repeat"]
[19161,"ERR","Small_INS","contig99",23464370,"Repeat"]
[{"$nulls":3},"contig99",23464562,"Repeat"]
[19162,"ERR","Small_INS","contig99",23633300,"Repeat"]
[{"$nulls":3},"contig99",23633625,"Repeat"]
[19163,"Het","Large_INS","contig99",23686203,"Repeat"]
[{"$nulls":3},"contig99",23698163,"Repeat"]
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[{"$nulls":3},"contig99",23719597,"Non_repeat"]
[19165,"Het","Small_INS","contig99",23813331,"Non_repeat"]
[{"$nulls":3},"contig99",23813383,"Non_repeat"]
[19166,"Het","Small_INS","contig99",23813620,"Non_repeat"]
[{"$nulls":3},"contig99",23814048,"Non_repeat"]
[19167,"Het","Small_INS","contig99",24291059,"Repeat"]
[{"$nulls":3},"contig99",24291415,"Repeat"]
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[{"$nulls":3},"contig99",24328517,"Repeat"]
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[{"$nulls":3},"contig99",24468396,"Repeat"]
[19170,"Het","Small_INS","contig99",24472787,"Repeat"]
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[19172,"ERR","Small_INS","contig99",24794344,"Repeat"]
[{"$nulls":3},"contig99",24794744,"Repeat"]
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[{"$nulls":3},"contig99",24904092,"Non_repeat"]
[19174,"Het","Large_Het.DEL","contig99",25196194,"Repeat"]
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[{"$nulls":3},"contig99",25215896,"Non_repeat"]
[19176,"Het","Small_INS","contig99",25284019,"Non_repeat"]
[{"$nulls":3},"contig99",25285172,"Non_repeat"]
[19177,"ERR","Small_INS","contig99",25688290,"Non_repeat"]
[{"$nulls":3},"contig99",25688515,"Repeat"]
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[{"$nulls":3},"contig99",25749899,"Non_repeat"]
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[{"$nulls":3},"contig99",26119122,"Non_repeat"]
[19181,"Het","Small_INS","contig99",26328794,"Repeat"]
[{"$nulls":3},"contig99",26328850,"Repeat"]
[19182,"Het","Small_INS","contig99",26329028,"Repeat"]
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[{"$nulls":3},"contig99",26556896,"Non_repeat"]
[19184,"ERR","Small_INS","contig99",26694730,"Repeat"]
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[19187,"ERR","Small_INS","contig99",26887798,"Repeat"]
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[{"$nulls":3},"contig99",27343707,"Non_repeat"]
[19191,"ERR","Small_INS","contig99",27611785,"Non_repeat"]
[{"$nulls":3},"contig99",27611939,"Non_repeat"]
[19192,"ERR","Small_INS","contig99",27721851,"Non_repeat"]
[{"$nulls":3},"contig99",27722239,"Non_repeat"]
[19193,"Het","Small_INS","contig99",27830686,"Repeat"]
[{"$nulls":3},"contig99",27831282,"Repeat"]
[19194,"Het","Small_INS","contig99",27954450,"Non_repeat"]
[{"$nulls":3},"contig99",27954891,"Non_repeat"]
[19195,"ERR","Small_INS","contig99",28035212,"Non_repeat"]
[{"$nulls":3},"contig99",28035631,"Non_repeat"]
[19196,"Het","Small_INS","contig99",28095588,"Non_repeat"]
[{"$nulls":3},"contig99",28096306,"Non_repeat"]
[19197,"Het","Small_INS","contig99",29000906,"Non_repeat"]
[{"$nulls":3},"contig99",29001298,"Non_repeat"]
[19198,"ERR","MJ","contig99",29133419,"Non_repeat"]
[19199,"ERR","Small_INS","contig99",29275476,"Repeat"]
[{"$nulls":3},"contig99",29275526,"Repeat"]
[19200,"ERR","Small_DUP.Gain","contig99",29277081,"Repeat"]
[{"$nulls":3},"contig99",29277131,"Repeat"]
[]
["* Het - Heterozygous simulation; ERR- Simulated Errors"]

{"sheet":"Supplementary Data 3","index":2,"n_rows":33109,"n_cols":7,"rows_kept":4500,"cut":true,"bounds":{"rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0}}
["Supplementary Data 3: Comparison of CRAQ output and simulated errors  in the simulated hg38_sim2"]
["The breakage location","Coverage of clipped-reads at breakage","Local coverage near breakage","Detected Category","Simulated  Type","Simulated class","Overlapped with simulations"]
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["contig100:10153027",58,65,"CSE","INV","ERR","yes"]
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["contig100:10540518",21,46,"CRH","Small_INS","Het","yes"]
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["contig100:11056853",59,79,"CRH","INV","ERR","yes"]
["contig100:1109665",25,28,"CRE","Small_INS","ERR","yes"]
["contig100:1110014",38,38,"CRE","Small_INS","ERR","yes"]
["contig100:11241326",28,50,"CRH","Small_INS","Het","yes"]
["contig100:11241631",31,63,"CRH","Small_INS","Het","yes"]
["contig100:11300060",30,31,"CRE","Small_INS","ERR","yes"]
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["contig100:11865362",24,50,"CRH","Small_INS","Het","yes"]
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["contig100:12007174",20,22,"CRE","Small_INS","ERR","yes"]
["contig100:12146422",22,46,"CRH","Small_INS","Het","yes"]
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["contig100:12384028",25,47,"CSH","Large_INS","Het","yes"]
["contig100:1245314",19,44,"CRH","Small_INS","Het","yes"]
["contig100:1245462",21,45,"CRH","Small_INS","Het","yes"]
["contig100:12534191",51,52,"CRE","Small_INS","ERR","yes"]
["contig100:12534591",59,61,"CRE","Small_INS","ERR","yes"]
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["contig100:12592167",45,47,"CRE","Small_INS","ERR","yes"]
["contig100:1279637",31,56,"CRH","Small_INS","Het","yes"]
["contig100:1279637",31,56,"CRH","Small_INS","Het","yes"]
["contig100:1279980",26,48,"CRH","Small_DEL","Het","yes"]
["contig100:12959249",18,37,"CRH","Small_INS","Het","yes"]
["contig100:12959613",25,45,"CRH","Small_INS","Het","yes"]
["contig100:13161793",18,40,"CSH","Large_INS","Het","yes"]
["contig100:13163774",23,51,"CSH","Large_INS","Het","yes"]
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["contig100:13381506",26,52,"CRH","Small_INS","Het","yes"]
["contig100:13381566",37,79,"CRH","Small_INS","Het","yes"]
["contig100:13693520",18,36,"CRH","Small_INS","Het","yes"]
["contig100:13693784",23,49,"CRH","Small_INS","Het","yes"]
["contig100:1445878",50,61,"CSE","INV","ERR","yes"]
["contig100:1447153",9,11,"CSE","DUP.Gain","ERR","yes"]
["contig100:1448232",31,40,"CRE","Small_DUP.Gain","ERR","yes"]
["contig100:14518495",26,56,"CRH","Small_INS","Het","yes"]
["contig100:14518796",29,49,"CRH","Small_INS","Het","yes"]
["contig100:14563786",31,34,"CRE","Small_INS","ERR","yes"]
["contig100:14564003",42,42,"CRE","Small_INS","ERR","yes"]
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["contig100:14607034",42,45,"CRE","Small_INS","ERR","yes"]
["contig100:14617704",21,46,"CRH","Small_INS","Het","yes"]
["contig100:14617943",22,50,"CRH","Small_INS","Het","yes"]
["contig100:1463993",47,47,"CRE","Small_INS","ERR","yes"]
["contig100:1464348",49,53,"CRE","Small_INS","ERR","yes"]
["contig100:1480841",25,28,"CSE","INV","ERR","yes"]
["contig100:1480847",69,82,"CSE","INV","ERR","yes"]
["contig100:14947748",52,52,"CRE","Small_INS","ERR","yes"]
["contig100:14948319",42,43,"CRE","Small_INS","ERR","yes"]
["contig100:15152905",31,59,"CRH","Small_INS","Het","yes"]
["contig100:15154416",16,36,"CRH","Small_INS","Het","yes"]
["contig100:15700028",27,46,"CRH","Small_INS","Het","yes"]
["contig100:15700180",26,54,"CRH","Small_INS","Het","yes"]
["contig100:15703993",26,54,"CSH","Large_INS","Het","yes"]
["contig100:15705759",31,57,"CSH","Large_INS","Het","yes"]
["contig100:15751553",33,59,"CRH","Small_INS","Het","yes"]
["contig100:15751834",26,52,"CRH","Small_INS","Het","yes"]
["contig100:15913729",19,44,"CRH","Small_INS","Het","yes"]
["contig100:15914446",23,47,"CRH","Small_INS","Het","yes"]
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["contig99:27329633",41,42,"CRE","Small_INS","ERR","yes"]
["contig99:27343067",38,69,"CRH","Small_INS","Het","yes"]
["contig99:27343713",25,42,"CRH","Small_INS","Het","yes"]
["contig99:27611789",30,31,"CRE","Small_INS","ERR","yes"]
["contig99:27611945",44,45,"CRE","Small_INS","ERR","yes"]
["contig99:27721857",43,43,"CRE","Small_INS","ERR","yes"]
["contig99:27722245",40,44,"CRE","Small_INS","ERR","yes"]
["contig99:2772434",28,29,"CRE","Small_INS","ERR","yes"]
["contig99:2772716",36,36,"CRE","Small_INS","ERR","yes"]
["contig99:27831286",20,46,"CRH","Small_INS","Het","yes"]
["contig99:27954454",20,46,"CRH","Small_INS","Het","yes"]
["contig99:27954897",24,55,"CRH","Small_INS","Het","yes"]
["contig99:28035216",49,52,"CRE","Small_INS","ERR","yes"]
["contig99:28035637",42,44,"CRE","Small_INS","ERR","yes"]
["contig99:28095592",28,49,"CRH","Small_INS","Het","yes"]
["contig99:28096312",23,48,"CRH","Small_INS","Het","yes"]
["contig9:9285071",18,37,"CRH","Small_INS","Het","yes"]
["contig9:9285446",17,38,"CRH","Small_INS","Het","yes"]
["contig99:29000910",20,42,"CRH","Small_INS","Het","yes"]
["contig99:29001302",22,51,"CRH","Small_INS","Het","yes"]
["contig99:29133423",7,8,"CSE","MJ","ERR","yes"]
["contig99:303594",44,48,"CRE","Small_INS","ERR","yes"]
["contig99:303839",40,41,"CRE","Small_INS","ERR","yes"]
["contig99:3083414",19,35,"CRH","Small_INS","Het","yes"]
["contig99:3084926",20,44,"CRH","Small_INS","Het","yes"]
["contig99:3225588",36,36,"CRE","Small_INS","ERR","yes"]
["contig99:3226374",31,31,"CRE","Small_INS","ERR","yes"]
["contig99:3509160",40,40,"CRE","Small_INS","ERR","yes"]
["contig99:3509557",45,45,"CRE","Small_INS","ERR","yes"]
["contig99:3589376",59,67,"CSE","INV","ERR","yes"]
["contig99:3793395",34,37,"CRE","Small_DUP.Gain","ERR","yes"]
["contig99:3794691",34,35,"CRE","Small_DUP.Gain","ERR","yes"]
["contig99:3820931",46,48,"CRE","Small_INS","ERR","yes"]
["contig99:3821234",38,40,"CRE","Small_INS","ERR","yes"]
["contig99:3902944",24,24,"CRE","Small_INS","ERR","yes"]
["contig99:3903361",31,34,"CRE","Small_INS","ERR","yes"]
["contig99:4044377",20,42,"CRH","Small_INS","Het","yes"]
["contig99:4044732",18,38,"CRH","Small_INS","Het","yes"]
["contig99:4129580",23,49,"CRH","Small_INS","Het","yes"]
["contig99:4130378",33,64,"CRH","Small_INS","Het","yes"]
["contig99:4521668",46,46,"CRE","Small_INS","ERR","yes"]
["contig99:4522447",44,44,"CRE","Small_INS","ERR","yes"]
["contig99:4588701",24,43,"CSH","Large_INS","Het","yes"]
["contig99:4625697",15,32,"CSH","Large_INS","Het","yes"]
["contig99:462865",36,39,"CRE","Small_INS","ERR","yes"]
["contig99:463125",31,31,"CRE","Small_INS","ERR","yes"]
["contig99:5312067",37,74,"CSH","Large_Het.DEL","Het","yes"]
["contig99:5373523",22,46,"CRH","Small_INS","Het","yes"]
["contig99:5373714",22,46,"CRH","Small_INS","Het","yes"]
["contig99:5504442",15,33,"CRH","Small_INS","Het","yes"]
["contig99:5504502",24,52,"CRH","Small_INS","Het","yes"]
["contig99:5551955",31,53,"CSH","Large_Het.DEL","Het","yes"]
["contig99:5625408",19,42,"CSH","Large_INS","Het","yes"]
["contig99:5642124",10,11,"CRE","Small_INS","ERR","yes"]
["contig99:5642371",10,10,"CRE","Small_INS","ERR","yes"]
["contig99:5656094",18,44,"CSH","Large_INS","Het","yes"]
["contig99:5787641",38,40,"CRE","Small_DUP.Gain","ERR","yes"]
["contig99:5788814",30,32,"CRE","Small_DUP.Gain","ERR","yes"]
["contig99:5791733",27,27,"CRE","Small_INS","ERR","yes"]
["contig99:5792449",38,39,"CRE","Small_INS","ERR","yes"]
["contig99:5892311",29,56,"CRH","Small_INS","Het","yes"]
["contig99:5892502",29,64,"CRH","Small_INS","Het","yes"]
["contig99:590317",46,47,"CRE","Small_INS","ERR","yes"]
["contig99:591212",52,52,"CRE","Small_INS","ERR","yes"]
["contig99:5960726",76,98,"CSE","INV","ERR","yes"]
["contig99:6170753",20,41,"CSH","Large_INS","Het","yes"]
["contig99:6172627",20,42,"CSH","Large_INS","Het","yes"]
["contig99:6199181",36,36,"CRE","Small_INS","ERR","yes"]
["contig99:6199516",32,33,"CRE","Small_INS","ERR","yes"]
["contig99:6293175",37,37,"CRE","Small_INS","ERR","yes"]
["contig99:6293342",44,44,"CRE","Small_INS","ERR","yes"]
["contig99:6364630",23,44,"CRH","Small_INS","Het","yes"]
["contig99:6364867",21,48,"CRH","Small_INS","Het","yes"]
["contig99:6376648",30,31,"CRE","Small_INS","ERR","yes"]
["contig99:6376883",35,37,"CRE","Small_INS","ERR","yes"]
["contig99:6453903",30,55,"CRH","Small_INS","Het","yes"]
["contig99:6454253",19,42,"CRH","Small_INS","Het","yes"]
["contig99:6523602",20,45,"CRH","Small_INS","Het","yes"]
["contig99:6525300",22,45,"CRH","Small_INS","Het","yes"]
["contig99:6534912",49,50,"CRE","Small_INS","ERR","yes"]
["contig99:6535276",53,53,"CRE","Small_INS","ERR","yes"]
["contig9:9657974",29,50,"CRH","Small_INS","Het","yes"]
["contig9:9658265",22,54,"CRH","Small_INS","Het","yes"]
["contig99:665222",87,99,"CSE","MJ","ERR","yes"]
["contig99:665226",66,74,"CSE","MJ","ERR","yes"]
["contig99:6701976",47,47,"CRE","Small_INS","ERR","yes"]
["contig99:6702470",51,53,"CRE","Small_INS","ERR","yes"]
["contig99:6777138",20,47,"CRH","Small_INS","Het","yes"]
["contig99:6778730",25,44,"CRH","Small_INS","Het","yes"]
["contig99:700072",2,1,"CSE","INV","ERR","yes"]
["contig99:7017788",42,43,"CRE","Small_INS","ERR","yes"]
["contig99:7018213",34,39,"CRE","Small_INS","ERR","yes"]
["contig99:7027947",25,51,"CRH","Small_INS","Het","yes"]
["contig99:7028484",28,54,"CRH","Small_INS","Het","yes"]
["contig99:7095079",22,41,"CRH","Small_INS","Het","yes"]
["contig99:7470353",18,36,"CRH","Small_INS","Het","yes"]
["contig99:7470626",17,34,"CRH","Small_INS","Het","yes"]
["contig99:7747004",33,34,"CRE","Small_INS","ERR","yes"]
["contig99:7747341",41,41,"CRE","Small_INS","ERR","yes"]
["contig9:9788156",20,39,"CRH","Small_INS","Het","yes"]
["contig9:9788470",28,49,"CRH","Small_INS","Het","yes"]
["contig99:8162285",21,22,"CRE","Small_INS","ERR","yes"]
["contig99:8162500",12,13,"CRE","Small_INS","ERR","yes"]
["contig99:8402322",20,45,"CRH","Small_INS","Het","yes"]
["contig99:8402618",27,46,"CRH","Small_INS","Het","yes"]
["contig99:8480551",39,41,"CRE","Small_DUP.Gain","ERR","yes"]
["contig99:8481801",33,37,"CRE","Small_DUP.Gain","ERR","yes"]
["contig99:8728675",26,48,"CRH","Small_INS","Het","yes"]
["contig99:8729116",28,53,"CRH","Small_INS","Het","yes"]
["contig99:8764488",34,34,"CRE","Small_INS","ERR","yes"]
["contig99:8765185",36,39,"CRE","Small_INS","ERR","yes"]
["contig99:8971812",25,46,"CSH","Large_INS","Het","yes"]
["contig99:8973599",23,48,"CSH","Large_INS","Het","yes"]
["contig99:9222082",17,42,"CSH","Large_INS","Het","yes"]
["contig99:9224082",20,36,"CSH","Large_INS","Het","yes"]
["contig99:9529901",32,33,"CRE","Small_INS","ERR","yes"]
["contig99:9530312",30,30,"CRE","Small_INS","ERR","yes"]
["contig99:9730204",22,49,"CRH","Small_INS","Het","yes"]
["contig99:9730493",25,58,"CRH","Small_INS","Het","yes"]
["contig99:9776054",43,43,"CRE","Small_INS","ERR","yes"]
["contig99:9776209",38,40,"CRE","Small_INS","ERR","yes"]
["contig99:9930612",26,27,"CRE","Small_INS","ERR","yes"]
["contig99:9931008",28,29,"CRE","Small_INS","ERR","yes"]

{"sheet":"Supplementary Data 4","index":3,"n_rows":518,"n_cols":5,"rows_kept":518}
["Supplementary Data 4: Simulated errors missed by  CRAQ (false negatives)"]
["Simulated contig","Simulated position","Located in Repeat/Non_repeat","Simulated type","Simulated_id"]
["contig1",860401,"Repeat","Small_DUP.Gain",5]
["contig10",147122,"Repeat","Small_DUP.Gain",97]
["contig10",148343,"Repeat","Small_DUP.Gain",97]
["contig10",3572987,"Repeat","Small_DUP.Gain",124]
["contig10",9833606,"Repeat","Small_DUP.Gain",184]
["contig101",470735,"Repeat","Small_DUP.Gain",397]
["contig101",2217877,"Non_repeat","Small_INS",402]
["contig102",638542,"Repeat","Small_DUP.Gain",446]
["contig102",5546372,"Repeat","Small_DUP.Gain",474]
["contig102",16756020,"Repeat","Small_DUP.Gain",533]
["contig103",17986568,"Non_repeat","Small_INS",666]
["contig104",2112445,"Repeat","Small_DUP.Loss",764]
["contig105",119509,"Repeat","Small_INS",776]
["contig105",808194,"Repeat","Small_INS",783]
["contig105",1784416,"Repeat","Small_DUP.Gain",789]
["contig105",2675143,"Repeat","Large_DUP.Loss",800]
["contig105",4301623,"Non_repeat","Small_INS",808]
["contig105",4470335,"Repeat","Small_INS",809]
["contig107",418767,"Repeat","Small_DUP.Gain",1010]
["contig108",21426609,"Non_repeat","Small_INS",1169]
["contig11",796931,"Repeat","Small_DUP.Gain",1257]
["contig11",4309846,"Repeat","Small_DUP.Gain",1274]
["contig110",7203409,"Non_repeat","Small_INS",1379]
["contig110",7203870,"Non_repeat","Small_INS",1379]
["contig111",144758,"Repeat","Small_DUP.Gain",1382]
["contig111",19943087,"Repeat","Small_DUP.Gain",1509]
["contig112",7308273,"Non_repeat","Small_INS",1580]
["contig113",131488,"Repeat","Small_INS",1778]
["contig113",4070078,"Non_repeat","Small_INS",1804]
["contig113",4070468,"Non_repeat","Small_INS",1805]
["contig114",153794,"Repeat","Small_DUP.Gain",1822]
["contig114",155059,"Repeat","Small_DUP.Gain",1822]
["contig114",7737976,"Non_repeat","Small_INS",1875]
["contig116",17733302,"Repeat","Small_INS",2091]
["contig117",1398279,"Repeat","Small_DEL",2111]
["contig119",521996,"Repeat","Small_DEL",2158]
["contig119",12651155,"Repeat","Small_DUP.Gain",2236]
["contig12",144759,"Repeat","Small_DUP.Gain",2252]
["contig12",13566604,"Repeat","Small_INS",2339]
["contig121",1226319,"Repeat","MJ",2389]
["contig121",1226336,"Repeat","Small_DUP.Gain",2390]
["contig121",1227450,"Repeat","Small_DUP.Gain",2390]
["contig121",6107365,"Repeat","Small_DUP.Gain",2413]
["contig121",22726260,"Repeat","Small_DUP.Gain",2535]
["contig123",118442,"Repeat","Small_INS",2636]
["contig126",872984,"Repeat","Small_DUP.Gain",2877]
["contig127",9155790,"Repeat","Small_DUP.Gain",3045]
["contig127",12559647,"Repeat","Small_DUP.Gain",3067]
["contig127",25114259,"Repeat","Small_DUP.Gain",3147]
["contig128",130233,"Repeat","Small_DUP.Gain",3201]
["contig128",131609,"Repeat","Small_DUP.Gain",3201]
["contig128",5982088,"Repeat","Small_INS",3251]
["contig13",26711488,"Repeat","Small_DUP.Gain",3568]
["contig13",31469219,"Repeat","Small_INS",3603]
["contig13",41754995,"Repeat","Small_DUP.Gain",3663]
["contig130",997748,"Repeat","Large_DUP.Gain",3673]
["contig130",8960835,"Repeat","Small_DEL",3731]
["contig131",128586,"Repeat","Small_DUP.Gain",3732]
["contig132",11614437,"Non_repeat","Small_DEL",3872]
["contig133",5772367,"Repeat","Small_DUP.Gain",3976]
["contig134",1477292,"Repeat","Small_DUP.Gain",4013]
["contig135",3282238,"Non_repeat","Small_INS",4096]
["contig135",9125752,"Repeat","Small_DUP.Gain",4125]
["contig135",9126948,"Repeat","Small_DUP.Gain",4125]
["contig135",11056814,"Non_repeat","Small_INS",4134]
["contig135",28786766,"Repeat","Small_DUP.Gain",4240]
["contig136",251747,"Repeat","Small_DUP.Gain",4243]
["contig136",8619340,"Repeat","Small_DUP.Gain",4297]
["contig136",12604982,"Non_repeat","Small_INS",4323]
["contig136",12605417,"Non_repeat","Small_INS",4323]
["contig136",29130340,"Repeat","Small_DUP.Gain",4432]
["contig136",29130398,"Repeat","Small_DUP.Gain",4432]
["contig136",30059006,"Repeat","Small_DUP.Gain",4443]
["contig136",30060431,"Repeat","Small_DUP.Gain",4443]
["contig137",1271693,"Repeat","Small_DUP.Gain",4539]
["contig137",8457044,"Repeat","Small_INS",4572]
["contig137",9980304,"Repeat","Small_DUP.Gain",4581]
["contig137",10404961,"Repeat","Small_DUP.Gain",4587]
["contig137",15523956,"Repeat","Small_DUP.Gain",4618]
["contig139",5439034,"Repeat","Small_DUP.Gain",4749]
["contig139",7770053,"Repeat","Small_DUP.Gain",4765]
["contig14",768463,"Repeat","Small_DUP.Loss",4794]
["contig141",230835,"Repeat","Small_DUP.Gain",4970]
["contig142",237885,"Repeat","Small_DUP.Gain",5001]
["contig142",611026,"Repeat","Small_DUP.Gain",5005]
["contig142",34659266,"Repeat","Small_DUP.Gain",5238]
["contig142",48126050,"Repeat","Small_INS",5323]
["contig143",15823245,"Repeat","Small_DUP.Gain",5439]
["contig144",857500,"Repeat","Small_DUP.Gain",5472]
["contig145",131092,"Repeat","Small_DUP.Gain",5546]
["contig145",807295,"Repeat","Small_DUP.Gain",5555]
["contig145",808670,"Repeat","Small_DUP.Gain",5555]
["contig145",2187931,"Repeat","Small_DUP.Gain",5563]
["contig146",4163797,"Repeat","Small_INS",5691]
["contig147",16252503,"Repeat","Small_INS",5848]
["contig148",335362,"Repeat","Small_DUP.Gain",5854]
["contig148",336728,"Repeat","Small_DUP.Gain",5854]
["contig149",21453820,"Repeat","Small_DUP.Loss",6055]
["contig150",439571,"Repeat","Small_DUP.Gain",6096]
["contig150",6705389,"Repeat","Small_DUP.Gain",6125]
["contig151",4270635,"Repeat","Small_DUP.Gain",6207]
["contig151",19285323,"Repeat","Small_DUP.Gain",6308]
["contig151",34767531,"Repeat","Small_INS",6400]
["contig152",222885,"Repeat","Small_DUP.Gain",6451]
["contig152",551455,"Repeat","Small_DUP.Gain",6456]
["contig152",552637,"Repeat","Small_DUP.Gain",6456]
["contig152",34739602,"Repeat","Small_INS",6713]
["contig153",442248,"Repeat","Small_INS",6755]
["contig153",442604,"Repeat","Small_INS",6755]
["contig153",663434,"Repeat","Small_DUP.Gain",6761]
["contig153",680929,"Repeat","Small_DUP.Gain",6762]
["contig153",683056,"Repeat","Small_DUP.Gain",6763]
["contig153",696117,"Repeat","Small_DUP.Gain",6764]
["contig153",772502,"Repeat","Small_DUP.Gain",6767]
["contig153",780350,"Repeat","Small_DUP.Gain",6768]
["contig153",796229,"Non_repeat","Small_DEL",6771]
["contig153",832170,"Repeat","Small_DUP.Gain",6772]
["contig153",981751,"Repeat","Small_DUP.Gain",6774]
["contig153",3506491,"Repeat","Small_INS",6792]
["contig156",3496953,"Non_repeat","Small_INS",6978]
["contig158",1103828,"Repeat","Small_DUP.Gain",7193]
["contig158",2356821,"Repeat","Small_DUP.Gain",7205]
["contig158",12554300,"Repeat","Small_INS",7284]
["contig159",1135890,"Repeat","Small_DUP.Gain",7351]
["contig16",4687417,"Repeat","Small_INS",7445]
["contig16",6621572,"Repeat","Small_INS",7451]
["contig16",28925701,"Non_repeat","Small_INS",7616]
["contig16",28926004,"Non_repeat","Small_INS",7616]
["contig160",371009,"Repeat","Small_DUP.Gain",7757]
["contig160",3992703,"Repeat","Small_DUP.Gain",7776]
["contig161",4292888,"Repeat","Small_DUP.Gain",7822]
["contig161",15442029,"Non_repeat","INV",7881]
["contig162",926851,"Repeat","Small_DUP.Gain",8012]
["contig162",16087345,"Repeat","Small_DEL",8117]
["contig163",4250550,"Non_repeat","Small_INS",8153]
["contig164",9041368,"Non_repeat","Small_INS",8232]
["contig17",164890,"Repeat","Small_DUP.Gain",8310]
["contig17",1600938,"Repeat","Small_DUP.Gain",8317]
["contig17",10300942,"Repeat","Small_DUP.Gain",8394]
["contig18",8272655,"Repeat","Small_DUP.Gain",8562]
["contig18",15243107,"Repeat","Small_INS",8614]
["contig19",168028,"Non_repeat","Small_INS",8615]
["contig19",647832,"Repeat","Small_INS",8616]
["contig2",3580648,"Repeat","Small_INS",8739]
["contig20",2385271,"Repeat","Small_DUP.Gain",8784]
["contig20",16012260,"Repeat","Small_INS",8883]
["contig20",16066498,"Non_repeat","Small_INS",8885]
["contig20",20512760,"Repeat","Large_DUP.Gain",8920]
["contig20",20512817,"Repeat","Small_DUP.Gain",8921]
["contig20",25766348,"Repeat","Small_INS",8964]
["contig21",5343249,"Repeat","Small_DEL",9002]
["contig22",6232776,"Repeat","Small_DUP.Gain",9034]
["contig22",11386341,"Repeat","Small_INS",9081]
["contig22",16128650,"Non_repeat","Small_INS",9115]
["contig22",16536551,"Repeat","Small_INS",9118]
["contig23",182095,"Repeat","Small_DUP.Gain",9124]
["contig23",4697057,"Non_repeat","Small_INS",9157]
["contig23",8622450,"Repeat","Small_DUP.Gain",9181]
["contig23",15332138,"Repeat","Small_DUP.Gain",9222]
["contig24",31667077,"Repeat","Small_DUP.Gain",9452]
["contig26",135919,"Non_repeat","Small_INS",9657]
["contig27",270927,"Repeat","Small_DUP.Gain",9732]
["contig28",340254,"Repeat","Small_INS",9835]
["contig29",328689,"Repeat","Small_DUP.Gain",9870]
["contig30",6088057,"Repeat","Small_DUP.Gain",10058]
["contig31",16156749,"Repeat","Small_DUP.Gain",10240]
["contig31",24873132,"Repeat","Small_DUP.Gain",10293]
["contig31",28510229,"Non_repeat","Small_INS",10325]
["contig31",28666089,"Repeat","Small_INS",10326]
["contig33",239709,"Repeat","Small_DUP.Gain",10409]
["contig33",2647129,"Non_repeat","Small_DEL",10420]
["contig33",11143488,"Repeat","Small_DUP.Gain",10484]
["contig33",26467438,"Repeat","Small_DUP.Gain",10596]
["contig33",30597947,"Repeat","Small_DUP.Gain",10630]
["contig33",31973604,"Repeat","Small_DUP.Gain",10636]
["contig33",31974919,"Repeat","Small_DUP.Gain",10637]
["contig34",7750159,"Non_repeat","Small_INS",10692]
["contig35",1986343,"Repeat","Small_DUP.Gain",10707]
["contig35",6713495,"Repeat","Small_DUP.Gain",10738]
["contig35",19717820,"Repeat","Small_INS",10818]
["contig35",20354250,"Non_repeat","Small_INS",10819]
["contig36",158382,"Repeat","Small_DUP.Gain",10835]
["contig36",8732116,"Repeat","Small_INS",10902]
["contig37",282091,"Repeat","Small_DUP.Gain",10916]
["contig38",124138,"Non_repeat","Small_INS",11010]
["contig38",124847,"Repeat","Small_INS",11010]
["contig38",3215392,"Repeat","Small_DUP.Gain",11031]
["contig38",5880677,"Repeat","Small_DUP.Gain",11046]
["contig38",7036791,"Non_repeat","Small_INS",11060]
["contig39",4590937,"Repeat","Small_DUP.Gain",11203]
["contig39",4592337,"Repeat","Small_DUP.Gain",11203]
["contig4",350741,"Repeat","Small_INS",11246]
["contig4",350741,"Repeat","Small_INS",11246]
["contig4",2259396,"Non_repeat","Small_INS",11250]
["contig40",1279776,"Repeat","Small_INS",11275]
["contig40",5037433,"Repeat","Small_DUP.Gain",11302]
["contig41",4307574,"Repeat","Small_DUP.Gain",11342]
["contig42",3217766,"Repeat","Small_DUP.Gain",11478]
["contig42",3219162,"Repeat","Small_DUP.Gain",11478]
["contig43",16096629,"Repeat","Small_DUP.Gain",11623]
["contig43",28557484,"Non_repeat","Small_INS",11692]
["contig43",41204892,"Repeat","Small_INS",11780]
["contig43",43216595,"Repeat","Small_DUP.Gain",11795]
["contig43",43218438,"Repeat","Small_DUP.Gain",11796]
["contig43",43227285,"Repeat","Small_DUP.Gain",11797]
["contig43",43264632,"Repeat","Small_DUP.Gain",11799]
["contig45",635987,"Non_repeat","Small_INS",11851]
["contig46",202757,"Repeat","Small_DUP.Gain",11853]
["contig48",162180,"Repeat","Small_DEL",12008]
["contig48",343735,"Repeat","Small_DUP.Gain",12010]
["contig48",2750554,"Repeat","Small_DUP.Gain",12021]
["contig5",750830,"Repeat","Small_INS",12110]
["contig5",1643262,"Non_repeat","Small_INS",12113]
["contig5",1643611,"Non_repeat","Small_INS",12114]
["contig50",148277,"Repeat","Small_DUP.Gain",12159]
["contig50",149608,"Repeat","Small_DUP.Gain",12159]
["contig50",1210078,"Repeat","Small_DUP.Gain",12168]
["contig50",1211082,"Repeat","Small_DUP.Gain",12168]
["contig53",973746,"Repeat","Large_DUP.Gain",12480]
["contig54",4288151,"Repeat","Small_DUP.Gain",12522]
["contig54",8142247,"Non_repeat","Small_DEL",12543]
["contig55",119238,"Non_repeat","Small_INS",12686]
["contig55",5704375,"Repeat","Small_DUP.Gain",12731]
["contig56",2728430,"Repeat","Small_DUP.Gain",12804]
["contig57",5005352,"Repeat","Small_INS",13006]
["contig57",5005583,"Non_repeat","Small_INS",13006]
["contig57",11126330,"Repeat","Small_DUP.Gain",13041]
["contig58",259035,"Repeat","Small_DUP.Gain",13148]
["contig58",14909764,"Repeat","Small_DUP.Gain",13240]
["contig58",17593395,"Repeat","Small_INS",13249]
["contig59",297057,"Repeat","Small_INS",13389]
["contig6",15283316,"Non_repeat","Small_INS",13525]
["contig60",131266,"Repeat","Small_DUP.Gain",13535]
["contig61",143296,"Repeat","Small_DEL",13606]
["contig61",560250,"Repeat","Small_DUP.Loss",13608]
["contig61",604419,"Repeat","Small_DUP.Gain",13610]
["contig63",1705162,"Repeat","Small_INS",13794]
["contig64",106112,"Repeat","Small_INS",13996]
["contig64",377857,"Repeat","Small_INS",13997]
["contig67",148890,"Repeat","Small_DUP.Gain",14132]
["contig67",1192214,"Repeat","Large_DUP.Gain",14143]
["contig68",830925,"Repeat","Small_INS",14282]
["contig68",14149920,"Repeat","Small_DUP.Gain",14355]
["contig68",14812584,"Repeat","Small_INS",14358]
["contig69",248714,"Repeat","Small_DUP.Gain",14361]
["contig7",12233003,"Repeat","Small_DUP.Gain",14468]
["contig7",19529009,"Repeat","Small_DEL",14535]
["contig7",23659351,"Repeat","Small_INS",14557]
["contig71",5157265,"Non_repeat","Small_INS",14742]
["contig71",5158021,"Non_repeat","Small_INS",14742]
["contig71",11733384,"Repeat","Small_DUP.Gain",14784]
["contig72",1629381,"Repeat","Small_DUP.Gain",14790]
["contig72",1630791,"Repeat","Small_DUP.Gain",14790]
["contig72",6987169,"Repeat","Small_INS",14835]
["contig72",22699740,"Non_repeat","Small_INS",14951]
["contig72",26257367,"Non_repeat","Small_INS",14968]
["contig73",144451,"Repeat","Small_DUP.Gain",15001]
["contig73",1115398,"Repeat","Small_DUP.Gain",15012]
["contig74",9759295,"Non_repeat","Small_DEL",15240]
["contig74",13080918,"Repeat","Small_DUP.Gain",15269]
["contig74",14309077,"Non_repeat","Small_INS",15279]
["contig76",384051,"Repeat","Small_DUP.Gain",15420]
["contig76",5411900,"Non_repeat","Small_INS",15453]
["contig76",6865679,"Repeat","Small_INS",15465]
["contig77",525641,"Repeat","Small_DUP.Gain",15633]
["contig78",13007848,"Repeat","Small_DUP.Gain",15803]
["contig8",12147154,"Repeat","Small_INS",16145]
["contig8",12517818,"Repeat","Small_DUP.Gain",16150]
["contig8",12518859,"Repeat","Small_DUP.Gain",16150]
["contig8",13142590,"Non_repeat","Small_INS",16155]
["contig8",13143018,"Non_repeat","Small_INS",16155]
["contig8",15095845,"Non_repeat","Small_INS",16170]
["contig8",15096647,"Non_repeat","Small_INS",16170]
["contig8",21755094,"Repeat","Small_INS",16220]
["contig80",5590169,"Repeat","Small_DUP.Gain",16314]
["contig82",2979757,"Repeat","Small_DUP.Gain",16434]
["contig82",2980769,"Repeat","Small_DUP.Gain",16434]
["contig82",15175794,"Repeat","Small_DUP.Loss",16500]
["contig83",187721,"Repeat","Small_DUP.Gain",16671]
["contig83",188882,"Repeat","Small_DUP.Gain",16671]
["contig83",3242026,"Repeat","Large_DUP.Gain",16688]
["contig83",20529572,"Repeat","Small_DUP.Gain",16829]
["contig84",6504793,"Repeat","Small_INS",16882]
["contig84",12808769,"Repeat","Small_DUP.Gain",16938]
["contig84",14222501,"Repeat","Small_DEL",16951]
["contig84",16529928,"Repeat","Small_DUP.Gain",16980]
["contig84",22934674,"Repeat","Small_INS",17019]
["contig85",4801604,"Repeat","Small_DUP.Gain",17045]
["contig86",4326105,"Non_repeat","Small_INS",17170]
["contig86",5463652,"Non_repeat","Small_INS",17184]
["contig86",8240965,"Repeat","Small_DUP.Gain",17211]
["contig86",13784233,"Non_repeat","Small_DEL",17249]
["contig87",3003194,"Repeat","Small_DUP.Loss",17266]
["contig89",220122,"Repeat","Small_DUP.Gain",17487]
["contig89",2901013,"Repeat","Small_DUP.Gain",17508]
["contig89",9543374,"Repeat","Small_DUP.Gain",17553]
["contig9",294965,"Repeat","Small_DUP.Gain",17650]
["contig9",2013649,"Repeat","Small_INS",17663]
["contig9",5322404,"Repeat","Small_INS",17684]
["contig9",22173082,"Non_repeat","Small_INS",17788]
["contig90",150599,"Repeat","Small_DUP.Gain",17792]
["contig90",151975,"Repeat","Small_DUP.Gain",17792]
["contig90",1259465,"Repeat","Small_DUP.Gain",17799]
["contig90",6355445,"Non_repeat","Small_INS",17844]
["contig90",13714119,"Repeat","Small_DUP.Gain",17904]
["contig90",37396124,"Repeat","Small_INS",18060]
["contig91",207183,"Repeat","Small_DUP.Gain",18093]
["contig91",208324,"Repeat","Small_DUP.Gain",18093]
["contig92",5336780,"Repeat","Small_DUP.Gain",18157]
["contig92",12892886,"Non_repeat","Small_INS",18214]
["contig92",21259325,"Repeat","Small_DUP.Gain",18262]
["contig93",1310296,"Repeat","Small_DUP.Gain",18278]
["contig93",10294041,"Repeat","Small_DUP.Gain",18343]
["contig93",10295339,"Repeat","Small_DUP.Gain",18344]
["contig95",263312,"Non_repeat","Small_INS",18508]
["contig96",3078627,"Repeat","Small_DUP.Gain",18563]
["contig96",3413157,"Repeat","Small_DEL",18569]
["contig97",143030,"Repeat","Small_DUP.Gain",18732]
["contig97",1055030,"Repeat","Small_DUP.Gain",18744]
["contig97",3341647,"Repeat","Small_DUP.Gain",18751]
["contig97",3342959,"Repeat","Small_DUP.Gain",18751]
["contig97",9583184,"Repeat","Small_DUP.Gain",18793]
["contig98",5054023,"Repeat","Small_DUP.Gain",18871]
["contig99",196742,"Repeat","Small_DUP.Gain",19012]
["contig99",1008667,"Repeat","Small_INS",19019]
["contig99",29275476,"Repeat","Small_INS",19199]
["contig99",29277081,"Repeat","Small_DUP.Gain",19200]
["contig149",21455158,"Repeat","Small_DUP.Loss",6056]
["contig50",9859257,"Repeat","Small_DUP.Gain",12230]
["contig102",16765713,"Repeat","Small_DUP.Gain",537]
["contig90",23522518,"Repeat","Large_DUP.Loss",17963]
["contig113",337493,"Repeat","Small_DUP.Gain",1780]
["contig163",299222,"Repeat","Small_DUP.Gain",8123]
["contig135",164018,"Repeat","Small_DUP.Gain",4075]
["contig41",4307624,"Repeat","Small_DUP.Gain",11342]
["contig153",893899,"Repeat","Small_DUP.Gain",6773]
["contig7",12231866,"Repeat","Small_DUP.Gain",14468]
["contig50",1210139,"Repeat","Small_DUP.Gain",12169]
["contig144",3549963,"Repeat","Small_DUP.Gain",5491]
["contig126",11772205,"Repeat","Small_DUP.Gain",2953]
["contig97",12123386,"Repeat","Small_DUP.Gain",18812]
["contig35",21932670,"Repeat","Small_DUP.Gain",10829]
["contig13",12265359,"Repeat","Small_DUP.Gain",3471]
["contig7",11739389,"Repeat","Small_DUP.Gain",14460]
["contig94",21784750,"Repeat","Small_DUP.Gain",18505]
["contig155",8702334,"Repeat","Small_DUP.Gain",6920]
["contig150",6705440,"Repeat","Small_DUP.Gain",6125]
["contig71",10754464,"Repeat","Small_DUP.Gain",14775]
["contig83",18982401,"Repeat","Small_DUP.Gain",16813]
["contig46",8109293,"Repeat","Small_DUP.Gain",11906]
["contig108",22842419,"Repeat","Small_DUP.Gain",1178]
["contig130",7328910,"Repeat","Small_DUP.Gain",3714]
["contig68",14149971,"Repeat","Small_DUP.Gain",14355]
["contig133",5771118,"Repeat","Small_DUP.Gain",3975]
["contig153",747392,"Repeat","Small_DUP.Gain",6766]
["contig102",506140,"Repeat","Small_DUP.Gain",444]
["contig67",148947,"Repeat","Small_DUP.Gain",14132]
["contig31",26560068,"Repeat","Small_DUP.Gain",10313]
["contig5",6743346,"Repeat","Small_DUP.Gain",12138]
["contig30",14602648,"Repeat","Small_DUP.Gain",10111]
["contig48",2750605,"Repeat","Small_DUP.Gain",12021]
["contig10",3571888,"Repeat","Small_DUP.Gain",124]
["contig148",11544297,"Repeat","Small_DUP.Gain",5915]
["contig71",169032,"Repeat","Large_DUP.Gain",14714]
["contig33",11142066,"Repeat","Small_DUP.Gain",10484]
["contig102",16756070,"Repeat","Small_DUP.Gain",533]
["contig24",31667135,"Repeat","Small_DUP.Gain",9452]
["contig121",6107425,"Repeat","Small_DUP.Gain",2413]
["contig159",145383,"Repeat","Small_DUP.Gain",7342]
["contig73",17791042,"Repeat","Small_DUP.Gain",15124]
["contig94",592352,"Repeat","Small_DUP.Gain",18376]
["contig142",612330,"Repeat","Small_DUP.Gain",5005]
["contig101",4125316,"Repeat","Small_DUP.Gain",413]
["contig153",793238,"Repeat","Small_DUP.Gain",6770]
["contig24",32201068,"Repeat","Small_DUP.Gain",9453]
["contig137",15524008,"Repeat","Small_DUP.Gain",4618]
["contig58",260297,"Repeat","Small_DUP.Gain",13148]
["contig134",8081832,"Repeat","Small_DUP.Gain",4059]
["contig77",15994129,"Repeat","Small_DUP.Gain",15726]
["contig43",43264692,"Repeat","Small_DUP.Gain",11799]
["contig151",17649147,"Repeat","Small_DUP.Gain",6293]
["contig31",5910396,"Repeat","Small_DUP.Gain",10164]
["contig33",31973661,"Repeat","Small_DUP.Gain",10636]
["contig67",12939117,"Repeat","Large_DUP.Loss",14232]
["contig43",16096679,"Repeat","Small_DUP.Gain",11623]
["contig66",4631566,"Repeat","Small_DUP.Gain",14110]
["contig135",164070,"Repeat","Small_DUP.Gain",4075]
["contig153",696177,"Repeat","Small_DUP.Gain",6764]
["contig103",11996295,"Repeat","Large_DUP.Gain",618]
["contig103",21354555,"Repeat","Large_DUP.Loss",685]
["contig153",641897,"Repeat","Small_DUP.Gain",6760]
["contig83",20569505,"Repeat","Small_DUP.Gain",16830]
["contig76",3176873,"Repeat","Small_DUP.Gain",15434]
["contig151",17647679,"Repeat","Small_DUP.Gain",6292]
["contig126",11773265,"Repeat","Small_DUP.Gain",2954]
["contig61",1691405,"Repeat","Small_DUP.Gain",13616]
["contig12",11356834,"Repeat","Small_DUP.Gain",2321]
["contig78",268470,"Repeat","Small_DUP.Gain",15731]
["contig84",16529979,"Repeat","Small_DUP.Gain",16980]
["contig9",295017,"Repeat","Small_DUP.Gain",17650]
["contig151",19285381,"Repeat","Small_DUP.Gain",6309]
["contig89",2899865,"Repeat","Small_DUP.Gain",17507]
["contig96",19501117,"Repeat","Small_DUP.Gain",18690]
["contig73",144453,"Repeat","Small_DUP.Gain",15002]
["contig24",9615728,"Repeat","Small_DUP.Gain",9300]
["contig134",1926421,"Repeat","Small_DUP.Gain",4018]
["contig54",9145534,"Repeat","Small_DUP.Gain",12551]
["contig72",1630793,"Repeat","Small_DUP.Gain",14792]
["contig32",3745178,"Repeat","Small_DUP.Gain",10354]
["contig101",4125372,"Repeat","Small_DUP.Gain",414]
["contig126",135354,"Repeat","Small_DUP.Gain",2869]
["contig12",11357960,"Repeat","Small_DUP.Gain",2322]
["contig103",6827646,"Repeat","Small_DUP.Gain",582]
["contig153",664772,"Repeat","Small_DUP.Gain",6761]
["contig86",5488220,"Repeat","Small_DUP.Gain",17185]
["contig113",4651119,"Repeat","Small_DUP.Gain",1811]
["contig124",2758790,"Repeat","Small_DUP.Gain",2669]
["contig93",10295341,"Repeat","Small_DUP.Gain",18343]
["contig162",135982,"Repeat","Small_DUP.Gain",8004]
["contig15",325471,"Repeat","Small_DUP.Gain",6060]
["contig147",15496347,"Repeat","Small_DUP.Gain",5844]
["contig74",13079896,"Repeat","Small_DUP.Gain",15269]
["contig37",12392390,"Repeat","Small_DUP.Gain",10993]
["contig77",12918840,"Repeat","Small_DUP.Gain",15708]
["contig33",7133077,"Repeat","Small_DUP.Gain",10448]
["contig131",128641,"Repeat","Small_DUP.Gain",3732]
["contig99",196792,"Repeat","Small_DUP.Gain",19012]
["contig93",1310353,"Repeat","Small_DUP.Gain",18279]
["contig71",203830,"Repeat","Large_DUP.Gain",14714]
["contig37",8655341,"Repeat","Small_DUP.Gain",10970]
["contig96",10759617,"Repeat","Small_DUP.Loss",18632]
["contig27",270979,"Repeat","Small_DUP.Gain",9732]
["contig96",3077346,"Repeat","Small_DUP.Gain",18563]
["contig71",7942821,"Repeat","Large_DUP.Gain",14760]
["contig100",22364777,"Repeat","Small_DUP.Gain",348]
["contig39",11282854,"Repeat","Small_DUP.Gain",11237]
["contig111",19944557,"Repeat","Small_DUP.Gain",1510]
["contig127",2922743,"Repeat","Large_DUP.Gain",3005]
["contig105",19575573,"Repeat","Small_DUP.Gain",924]
["contig70",127313,"Repeat","Small_DUP.Gain",14639]
["contig77",15995561,"Repeat","Small_DUP.Gain",15727]
["contig24",32201008,"Repeat","Small_DUP.Gain",9453]
["contig134",1477298,"Repeat","Small_DUP.Gain",4013]
["contig71",10755600,"Repeat","Small_DUP.Gain",14776]
["contig35",1986397,"Repeat","Small_DUP.Gain",10707]
["contig146",5133282,"Repeat","Small_DUP.Gain",5698]
["contig90",5317655,"Repeat","Small_DUP.Gain",17838]
["contig153",1043043,"Repeat","Small_DUP.Gain",6776]
["contig142",239204,"Repeat","Small_DUP.Gain",5002]
["contig50",1211084,"Repeat","Small_DUP.Gain",12170]
["contig153",772557,"Repeat","Small_DUP.Gain",6767]
["contig153",832220,"Repeat","Small_DUP.Gain",6772]
["contig13",39153077,"Repeat","Small_DUP.Gain",3644]
["contig57",154342,"Repeat","Small_DUP.Loss",12977]
["contig10",9629279,"Repeat","Small_DUP.Gain",175]
["contig127",8638727,"Repeat","Large_DUP.Gain",3040]
["contig76",382750,"Repeat","Small_DUP.Gain",15420]
["contig86",8241017,"Repeat","Small_DUP.Gain",17211]
["contig84",19241134,"Repeat","Small_DUP.Gain",17001]
["contig26",276070,"Repeat","Small_DUP.Gain",9660]
["contig127",8598156,"Repeat","Large_DUP.Gain",3040]
["contig113",4649924,"Repeat","Small_DUP.Gain",1810]
["contig46",8109242,"Repeat","Small_DUP.Gain",11906]
["contig153",506124,"Repeat","Small_DUP.Gain",6756]
["contig84",208616,"Repeat","Large_DUP.Gain",16845]
["contig77",620705,"Repeat","Small_DUP.Gain",15635]
["contig157",11051976,"Repeat","Small_DUP.Gain",7131]
["contig58",38012251,"Repeat","Small_DUP.Gain",13374]
["contig152",36519694,"Repeat","Small_DUP.Gain",6728]
["contig127",28780448,"Repeat","Small_DUP.Gain",3167]
["contig17",164947,"Repeat","Small_DUP.Gain",8310]
["contig11",796986,"Repeat","Small_DUP.Gain",1257]
["contig17",26499015,"Repeat","Small_DUP.Gain",8505]
["contig43",31263283,"Repeat","Small_DUP.Gain",11710]
["contig163",5426103,"Repeat","Small_DUP.Gain",8162]
["contig99",21875191,"Repeat","Small_DUP.Gain",19151]
["contig137",150781,"Repeat","Small_DUP.Gain",4524]
["contig18",5776070,"Repeat","Small_DUP.Gain",8541]
["contig46",19127765,"Repeat","Small_DUP.Gain",11976]
["contig74",11610201,"Repeat","Small_DUP.Gain",15259]
["contig67",18054273,"Repeat","Small_DUP.Gain",14256]
["contig159",1136996,"Repeat","Small_DUP.Gain",7351]
["contig20",23211907,"Repeat","Small_DUP.Gain",8943]
["contig39",11281728,"Repeat","Small_DUP.Gain",11236]
["contig66",662467,"Repeat","Small_DUP.Gain",14091]
["contig114",10091257,"Repeat","Small_DUP.Gain",1896]
["contig164",9041939,"Non_repeat","Small_INS",8233]
["contig43",257771,"Non_repeat","Small_INS",11515]
["contig12",13566143,"Non_repeat","Small_INS",2339]
["contig33",16500029,"Non_repeat","Small_INS",10520]
["contig35",20362694,"Non_repeat","Small_INS",10820]
["contig31",5497430,"Non_repeat","Small_INS",10158]
["contig93",15161887,"Non_repeat","Small_INS",18371]
["contig86",5253767,"Non_repeat","Small_INS",17180]
["contig10",10871682,"Non_repeat","Small_INS",191]
["contig3",118416,"Non_repeat","Small_INS",9903]
["contig136",277021,"Non_repeat","Small_INS",4244]
["contig16",40983554,"Non_repeat","Small_INS",7694]
["contig35",20362271,"Non_repeat","Small_INS",10820]
["contig112",5697144,"Non_repeat","Small_INS",1567]
["contig136",276620,"Non_repeat","Small_INS",4244]
["contig56",378235,"Non_repeat","Small_INS",12786]
["contig43",43355870,"Non_repeat","Small_INS",11801]
["contig24",40945462,"Non_repeat","Small_INS",9508]
["contig59",611597,"Non_repeat","Small_INS",13392]
["contig138",3687962,"Non_repeat","Small_INS",4694]
["contig137",8457521,"Non_repeat","Small_INS",4572]
["contig126",116506,"Non_repeat","Small_INS",2868]
["contig116",17732956,"Non_repeat","Small_INS",2091]
["contig130",8960647,"Non_repeat","Small_INS",3730]
["contig54",9163025,"Non_repeat","Small_INS",12552]
["contig5",750382,"Non_repeat","Small_INS",12110]
["contig95",115808,"Non_repeat","Small_INS",18507]
["contig68",14598172,"Non_repeat","Small_INS",14357]
["contig43",43355614,"Non_repeat","Small_INS",11801]
["contig123",118821,"Non_repeat","Small_INS",2636]

{"sheet":"Supplementary Data 5","index":4,"n_rows":3062,"n_cols":5,"rows_kept":3062,"merged":[[1,0,1,1]]}
["Supplementary Data 5: Potential error locus in the HiCanu assembly of D. melanogaster hybrid F1"]
["The breakage location",null,"Coverage of clipped-reads at breakage","Local coverage near breakage","Category"]
["tig00000001",10457253,23,25,"CSE"]
["tig00000031",20131412,19,20,"CSE"]
["tig00000519",1353423,51,51,"CSE"]
["tig00000519",8680429,14,15,"CSE"]
["tig00000623",387838,17,27,"CSE"]
["tig00000623",2130769,34,34,"CSE"]
["tig00000678",335480,31,31,"CSE"]
["tig00000678",1247033,20,20,"CSE"]
["tig00000678",1273488,28,34,"CSE"]
["tig00000794",530309,4,4,"CSE"]
["tig00000794",1205054,20,31,"CSE"]
["tig00000810",117839,3,4,"CSE"]
["tig00000810",180796,8,8,"CSE"]
["tig00000810",533993,3,4,"CSE"]
["tig00000810",600706,6,7,"CSE"]
["tig00000814",278470,21,21,"CSE"]
["tig00000873",169928,8,13,"CSE"]
["tig00000876",248604,23,30,"CSE"]
["tig00001006",171767,2,3,"CSE"]
["tig00001050",51306,24,24,"CSE"]
["tig00001073",60837,2,2,"CSE"]
["tig00003567",8559651,22,24,"CSE"]
["tig00003567",15858560,37,37,"CSE"]
["tig00003571",277610,2,3,"CSE"]
["tig00003571",301023,4,5,"CSE"]
["tig00000001",11432739,26,45,"CSH"]
["tig00000001",6972964,10,23,"CSH"]
["tig00000031",56327,17,34,"CSH"]
["tig00000031",20126268,33,61,"CSH"]
["tig00000519",8200437,10,22,"CSH"]
["tig00000519",8685925,14,24,"CSH"]
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{"sheet":"Supplementary Data 6","index":5,"n_rows":8031,"n_cols":5,"rows_kept":8031,"merged":[[1,0,1,1]]}
["Supplementary Data 6: CREs and CSEs identified in the Canu assembly of S. pennellii"]
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["Canu_ctg122",364830,2,2,"CRE"]
["Canu_ctg122",399744,3,3,"CRE"]
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["Canu_ctg122",441981,9,11,"CRE"]
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["Canu_ctg123",307575,6,7,"CRE"]
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["Canu_ctg126",1656736,12,13,"CRE"]
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["Canu_ctg127",148590,9,10,"CRE"]
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["Canu_ctg132",1000856,14,15,"CRE"]
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["Canu_ctg132",1382474,6,6,"CRE"]
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["Canu_ctg133",190898,4,4,"CRE"]
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["Canu_ctg133",467508,16,17,"CRE"]
["Canu_ctg133",525724,18,21,"CRE"]
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["Canu_ctg133",781603,5,6,"CRE"]
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["Canu_ctg133",1066506,5,5,"CRE"]
["Canu_ctg133",1089480,15,18,"CRE"]
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["Canu_ctg133",1159880,5,6,"CRE"]
["Canu_ctg133",1223476,9,11,"CRE"]
["Canu_ctg133",1253329,12,14,"CRE"]
["Canu_ctg133",1360716,13,17,"CRE"]
["Canu_ctg133",1377101,5,6,"CRE"]
["Canu_ctg133",1386659,17,19,"CRE"]
["Canu_ctg133",1655521,19,21,"CRE"]
["Canu_ctg133",1816584,19,20,"CRE"]
["Canu_ctg133",1831699,5,6,"CRE"]
["Canu_ctg134",132744,15,16,"CRE"]
["Canu_ctg134",187928,4,5,"CRE"]
["Canu_ctg134",403004,15,15,"CRE"]
["Canu_ctg134",669590,5,6,"CRE"]
["Canu_ctg134",700182,14,15,"CRE"]
["Canu_ctg134",708825,6,6,"CRE"]
["Canu_ctg134",896602,5,6,"CRE"]
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["Canu_ctg504",417982,2,2,"CRE"]
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["Canu_ctg505",365898,20,22,"CRE"]
["Canu_ctg505",427727,16,17,"CRE"]
["Canu_ctg505",462178,9,9,"CRE"]
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["Canu_ctg1",4887204,40,51,"CSE"]
["Canu_ctg10",4812722,2,1,"CSE"]
["Canu_ctg102",1054745,4,2,"CSE"]
["Canu_ctg103",249607,35,16,"CSE"]
["Canu_ctg108",372438,3,3,"CSE"]
["Canu_ctg11",5849389,3,1,"CSE"]
["Canu_ctg11",5853032,3,2,"CSE"]
["Canu_ctg110",2015449,5,2,"CSE"]
["Canu_ctg110",2023970,23,1,"CSE"]
["Canu_ctg111",1754401,2,1,"CSE"]
["Canu_ctg115",220280,2,1,"CSE"]
["Canu_ctg119",257804,19,14,"CSE"]
["Canu_ctg12",3492130,2,1,"CSE"]
["Canu_ctg12",4496493,2,1,"CSE"]
["Canu_ctg121",992196,22,28,"CSE"]
["Canu_ctg127",299043,2,1,"CSE"]
["Canu_ctg128",296971,5,5,"CSE"]
["Canu_ctg128",311887,3,2,"CSE"]
["Canu_ctg14",1379806,33,35,"CSE"]
["Canu_ctg144",1567051,5,5,"CSE"]
["Canu_ctg150",1644210,2,1,"CSE"]
["Canu_ctg152",1113344,2,2,"CSE"]
["Canu_ctg163",678342,30,40,"CSE"]
["Canu_ctg167",852595,3,3,"CSE"]
["Canu_ctg167",901303,6,2,"CSE"]
["Canu_ctg178",205994,35,43,"CSE"]
["Canu_ctg178",395352,8,11,"CSE"]
["Canu_ctg183",616871,40,51,"CSE"]
["Canu_ctg198",1013309,2,1,"CSE"]
["Canu_ctg20",1695010,13,5,"CSE"]
["Canu_ctg20",2349873,5,5,"CSE"]
["Canu_ctg212",1284378,2,1,"CSE"]
["Canu_ctg213",369685,17,20,"CSE"]
["Canu_ctg213",869848,2,2,"CSE"]
["Canu_ctg223",252717,16,20,"CSE"]
["Canu_ctg225",585146,31,37,"CSE"]
["Canu_ctg23",2667908,12,15,"CSE"]
["Canu_ctg230",1228289,3,3,"CSE"]
["Canu_ctg233",1064178,24,29,"CSE"]
["Canu_ctg24",3209925,3,4,"CSE"]
["Canu_ctg241",573480,18,23,"CSE"]
["Canu_ctg245",706377,4,5,"CSE"]
["Canu_ctg245",711382,23,4,"CSE"]
["Canu_ctg254",1037663,2,2,"CSE"]
["Canu_ctg255",793249,2,1,"CSE"]
["Canu_ctg26",1373090,10,1,"CSE"]
["Canu_ctg26",2895513,5,4,"CSE"]
["Canu_ctg261",28414,8,10,"CSE"]
["Canu_ctg268",571059,24,32,"CSE"]
["Canu_ctg269",608768,3,4,"CSE"]
["Canu_ctg272",565531,34,35,"CSE"]
["Canu_ctg278",144601,27,28,"CSE"]
["Canu_ctg279",899200,30,35,"CSE"]
["Canu_ctg28",1476044,2,1,"CSE"]
["Canu_ctg280",504940,3,2,"CSE"]
["Canu_ctg288",511412,15,19,"CSE"]
["Canu_ctg29",1981079,13,17,"CSE"]
["Canu_ctg295",722678,3,1,"CSE"]
["Canu_ctg30",2316551,3,4,"CSE"]
["Canu_ctg302",954436,36,43,"CSE"]
["Canu_ctg310",329586,3,4,"CSE"]
["Canu_ctg338",584170,2,1,"CSE"]
["Canu_ctg341",723840,7,2,"CSE"]
["Canu_ctg350",27988,8,11,"CSE"]
["Canu_ctg354",708267,30,33,"CSE"]
["Canu_ctg36",2551087,31,37,"CSE"]
["Canu_ctg36",2633428,35,50,"CSE"]
["Canu_ctg362",777482,6,3,"CSE"]
["Canu_ctg37",99582,3,4,"CSE"]
["Canu_ctg37",746548,3,3,"CSE"]
["Canu_ctg379",86805,2,2,"CSE"]
["Canu_ctg380",406532,2,2,"CSE"]
["Canu_ctg385",636479,3,3,"CSE"]
["Canu_ctg391",641129,4,4,"CSE"]
["Canu_ctg395",186902,2,1,"CSE"]
["Canu_ctg4",2132434,27,31,"CSE"]
["Canu_ctg405",554392,4,4,"CSE"]
["Canu_ctg41",1002430,24,26,"CSE"]
["Canu_ctg41",2058651,12,2,"CSE"]
["Canu_ctg41",2478479,2,1,"CSE"]
["Canu_ctg412",241802,19,23,"CSE"]
["Canu_ctg424",635881,29,1,"CSE"]
["Canu_ctg426",519794,3,4,"CSE"]
["Canu_ctg428",575980,2,2,"CSE"]
["Canu_ctg437",364587,3,1,"CSE"]
["Canu_ctg440",183590,24,26,"CSE"]
["Canu_ctg45",1309906,2,1,"CSE"]
["Canu_ctg460",247992,5,6,"CSE"]
["Canu_ctg465",417140,26,29,"CSE"]
["Canu_ctg465",460020,3,1,"CSE"]
["Canu_ctg467",438181,15,9,"CSE"]
["Canu_ctg47",104459,26,30,"CSE"]
["Canu_ctg473",541048,2,1,"CSE"]
["Canu_ctg490",111510,3,3,"CSE"]
["Canu_ctg490",305332,20,13,"CSE"]
["Canu_ctg493",426419,2,1,"CSE"]
["Canu_ctg50",2135484,2,2,"CSE"]
["Canu_ctg504",44289,24,27,"CSE"]
["Canu_ctg504",428714,6,3,"CSE"]
["Canu_ctg504",435549,2,2,"CSE"]
["Canu_ctg56",1755738,6,2,"CSE"]
["Canu_ctg57",553242,4,2,"CSE"]
["Canu_ctg6",1885938,2,1,"CSE"]
["Canu_ctg76",1023327,29,35,"CSE"]
["Canu_ctg77",1439957,4,5,"CSE"]
["Canu_ctg8",730424,2,1,"CSE"]
["Canu_ctg8",2862905,4,3,"CSE"]
["Canu_ctg8",2910401,24,30,"CSE"]
["Canu_ctg8",6871007,10,5,"CSE"]
["Canu_ctg82",144347,2,2,"CSE"]
["Canu_ctg87",737080,15,16,"CSE"]
["Canu_ctg92",227993,5,2,"CSE"]
["Canu_ctg92",440684,12,5,"CSE"]
["Canu_ctg92",715910,15,19,"CSE"]
["Canu_ctg92",1416650,10,12,"CSE"]
["Canu_ctg93",876795,3,4,"CSE"]
["Canu_ctg98",233382,27,3,"CSE"]
["Canu_ctg98",306811,2,2,"CSE"]

{"sheet":"Supplementary Data 7","index":6,"n_rows":20879,"n_cols":5,"rows_kept":4500,"cut":true,"bounds":{"rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0}}
["Supplementary Data 7:  Reported SVs  for the Canu assembly of S. pennellii using SyRI"]
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["contig108",822894,822948,54,"DEL"]
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["contig108",1583939,1584010,71,"DEL"]
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["contig11",5849389,5849389,"TRANS","MJ"]
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["contig110",176210,181173,4963,"HDR"]
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["contig110",2015449,2015449,"TRANS","MJ"]
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["contig110",2023970,2023970,"TRANS","MJ"]
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["contig111",1664278,1664405,127,"HDR"]
["contig111",1710276,1710419,143,"DEL"]
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["contig112",19714,19755,41,"DEL"]
["contig112",242203,243905,1702,"HDR"]
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["contig112",1016886,1016886,68,"INS"]
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["contig12",1945034,1948734,3700,"DEL"]
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["contig126",875724,875821,97,"DEL"]
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["contig126",1388587,1388785,198,"DEL"]
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{"sheet":"Supplementary Data 8","index":7,"n_rows":120,"n_cols":6,"rows_kept":120,"merged":[[1,0,1,1],[1,4,1,5]]}
["Supplementary Data 8: Statistics for CSE breakages and overlaps with BioNano conflicts in A. oxysepala"]
["CSE breakpoint detected by CRAQ",null,"Number of clipped-reads","Local coverage"," Conflict regions in optical mapping "]
["contig102",797205,1,1,"contig102","759975-8041143"]
["contig103",5273,5,5,"*","*"]
["contig107",14313,27,31,"contig107","98-14643"]
["contig108",304362,1,1,"contig108","297955-304562"]
["contig11",1051386,17,19,"contig11","1044571-1072310"]
["contig111",671944,1,1,"contig111","665562-681908"]
["contig116",123462,1,1,"contig116","119760-131263"]
["contig116",786166,10,15,"contig116","776696-803142"]
["contig11",6975,2,2,"*","*"]
["contig120",561680,3,3,"*","*"]
["contig121",547886,1,1,"contig121","537257-554715"]
["contig122",524913,1,1,"*","*"]
["contig123",19134,1,1,"contig123","19130-38459"]
["contig126",6792,1,1,"*","*"]
["contig128",18740,3,2,"contig128","934-17987"]
["contig13",3721900,8,10,"contig13","3721016-3728998"]
["contig135",528562,1,1,"contig135","516579-546253"]
["contig13",6892877,10,10,"contig13","6887810-6896532"]
["contig137",13963,1,1,"contig137","380-70945"]
["contig138",8643,3,2,"*","*"]
["contig143",40422,4,5,"contig143","40402-60623"]
["contig151",10360,7,7,"contig151","3032-34558"]
["contig152",353963,1,1,"contig152","351255-361435"]
["contig101",12323,2,2,"contig101","*"]
["contig164",162322,4,5,"contig164","157630-184997"]
["contig165",140893,23,23,"contig165","119333-146975"]
["contig16",63236,20,23,"contig16","60984-64661"]
["contig17",14620,1,1,"*","*"]
["contig171",57072,1,1,"*","*"]
["contig17",2797597,1,1,"contig17","2776149-2797697"]
["contig17",3075177,41,60,"contig17","3075100-3086593"]
["contig173",5663,1,1,"*","*"]
["contig17",5060582,20,20,"contig17","5056070-5070644"]
["contig176",40909,36,44,"contig176","13677-44863"]
["contig178",95239,1,1,"*","*"]
["contig187",45216,1,1,"*","*"]
["contig19",6976124,12,13,"contig19","6975835-6982206"]
["contig206",22202,9,12,"contig206","18179-38807"]
["contig206",34006,8,9,"contig206","18179-38807"]
["contig207",8596,1,1,"*","*"]
["contig208",7029,9,9,"*","*"]
["contig2",11366,4,4,"*","*"]
["contig21",1459786,1,1,"contig21","1443208-1459698"]
["contig218",49342,2,2,"contig218","48941-56690"]
["contig23",2496190,12,12,"contig23","2487248-2498124"]
["contig23",692027,15,14,"contig23","687270-692424"]
["contig25",33861,1,1,"contig25","*"]
["contig102",803779,14,21,"contig102","759975-8041143"]
["contig26",13261,1,1,"*","*"]
["contig27",18510,1,1,"*","*"]
["contig289",58091,1,1,"contig289","51895-64213"]
["contig31",11395,1,1,"contig31","566-46535"]
["contig31",23570,17,17,"contig31","566-46535"]
["contig317",14951,1,1,"*","*"]
["contig32",20086,19,22,"contig32","16738-22483"]
["contig34",2258965,2,2,"contig34","2257596-2272181"]
["contig372",29381,1,1,"*","*"]
["contig37",660415,1,1,"*","*"]
["contig38",1103819,2,1,"*","*"]
["contig38",2595117,2,2,"contig38","2590286-2624276"]
["contig38",612942,25,26,"contig38","611078-619746"]
["contig40",1956729,12,15,"contig40","1955927-1968987"]
["contig41",467019,12,12,"contig41","459879-469267"]
["contig41",5759,2,2,"*","*"]
["contig42",1746041,14,20,"contig42","1746521-1763451"]
["contig42",1759641,11,13,"contig42","1746521-1763451"]
["contig46",15463,2,2,"*","*"]
["contig48",1419878,1,1,"contig48","1419008-1474070"]
["contig48",1426289,17,16,"contig48","1419008-1474070"]
["contig48",1473977,1,1,"contig48","1419008-1474070"]
["contig48",47536,1,1,"*","*"]
["contig48",494544,16,20,"contig48","468107-514931"]
["contig50",3326858,4,4,"contig50","3322261-3328315"]
["contig50",927505,2,2,"contig50","925999-932836"]
["contig5",135215,1,1,"*","*"]
["contig51",6979,27,31,"*","*"]
["contig52",1779094,17,25,"contig52","1771233-1787251"]
["contig5",3349682,1,1,"contig5","3331283-3355728"]
["contig54",1140524,1,1,"contig54","1114398-1141844"]
["contig54",16893,1,1,"contig54","580-27136"]
["contig54",27133,20,18,"contig54","580-27136"]
["contig5",4616406,1,1,"*","*"]
["contig54",8168,1,1,"contig54","580-27136"]
["contig57",107227,1,1,"*","*"]
["contig5",925787,1,1,"*","*"]
["contig60",1099089,124,144,"*","*"]
["contig64",15879,12,14,"*","*"]
["contig6",4490757,8,8,"contig6","4473754-4592779"]
["contig6",4515456,4,5,"contig6","4473754-4592779"]
["contig6",4554297,13,13,"contig6","4473754-4592779"]
["contig6",4918355,1,1,"contig6","4847802-4918356"]
["contig65",45906,20,27,"contig65","40818-48207"]
["contig66",741768,1,1,"*","*"]
["contig66",864266,1,1,"*","*"]
["contig69",1245519,19,20,"*","*"]
["contig69",851104,2,2,"contig69","842240-854292"]
["contig7",218263,5,5,"contig7","213260-229199"]
["contig73",15244,1,1,"*","*"]
["contig74",11877,1,1,"*","*"]
["contig7",471204,3,4,"contig7","469505-478355"]
["contig75",58705,21,21,"contig75","53572-69793"]
["contig8",1874290,4,4,"contig8","1866302-1875790"]
["contig8",25629,1,1,"*","*"]
["contig85",1010001,13,15,"contig85","1009924-1014884"]
["contig86",228709,6,6,"contig86","232195-250983"]
["contig86",6472,4,4,"*","*"]
["contig88",12033,2,2,"*","*"]
["contig89",28343,1,1,"*","*"]
["contig89",298906,181,194,"contig89","229643-318686"]
["contig89",305903,158,168,"contig89","229643-318686"]
["contig89",314155,1,1,"contig89","229643-318686"]
["contig90",395925,34,50,"contig90","387694-416933"]
["contig90",414997,162,167,"contig90","387694-416933"]
["contig95",502250,18,23,"contig95","496764-503254"]
["contig95",739037,1,1,"*","*"]
["contig97",116233,1,1,"*","*"]
["contig99",875433,1,1,"*","*"]
["*represent specific errors detected by CRAQ"]

{"sheet":"Supplementary Data 9","index":8,"n_rows":79,"n_cols":5,"rows_kept":79,"merged":[[1,0,1,1]]}
["Supplementary Data 9: Bionano conflicts in A. oxysepala and overlaps with CSEs"]
["Conflict location of  optical mapping ",null,"CSE location","Coverage of clipped-reads","Local coverage near CSE"]
["contig10","3660322--3694381",3663029,27,1]
["contig102","759975-8041143",803779,14,21]
["contig108","297955-304562",304362,1,1]
["contig11","1044571-1072310",1051386,17,19]
["contig11","4916916-4931209","*","*","*"]
["contig111","665562-681908",671944,1,1]
["contig115","578104-618065","*","*","*"]
["contig116","119760-131263",123462,1,1]
["contig116","776696-803142",786166,10,15]
["contig121","537257-554715",547886,1,1]
["contig123","19130-38459",19134,1,1]
["contig128","934-17987",18740,3,2]
["contig13","3311260-3323023","*","*","*"]
["contig13","3721016-3728998",3721900,8,10]
["contig13","6887810-6896532",6892877,10,10]
["contig135","516579-546253",528562,1,1]
["contig137","13800-70945",13963,1,1]
["contig140","294510-313314","*","*","*"]
["contig140","633876-648629","*","*","*"]
["contig143","40402-60623",40422,4,5]
["contig151","10303-34558",10360,7,7]
["contig152","351255-361435",353963,1,1]
["contig16","60984-64661",63236,20,23]
["contig164","157630-184997",162322,4,5]
["contig165","119333-146975",140893,23,23]
["contig107","1980-14643","*","*","*"]
["contig17","2776149-2797697",2797597,1,0]
["contig17","3075100-3086593",3075177,41,60]
["contig17","5056070-5070644",5060582,20,20]
["contig176","13677-44863",40909,36,44]
["contig18","3025373-3042326","*","*","*"]
["contig19","6975835-6982206",6976124,12,13]
["contig206","18179-38807",22202,9,12]
["contig21","1443208-1459698",1459786,1,1]
["contig218","48941-56690",49342,2,2]
["contig22","2738196-2743923","*","*","*"]
["contig23","687270-692424",692027,15,14]
["contig23","2487248-2498124",2496190,12,12]
["contig289","51895-64213",58091,1,0]
["contig3","4134700-4153134","*","*","*"]
["contig31","566-46535",23570,17,17]
["contig32","16738-22483",20086,19,22]
["contig33","2415361-2439309","*","*","*"]
["contig34","1042720-1045894","*","*","*"]
["contig34","2257596-2272181",2258965,2,2]
["contig38","323882-323911","*","*","*"]
["contig38","611078-619746",612942,25,26]
["contig38","2590286-2624276",2595117,2,2]
["contig40","1955927-1968987",1956729,12,15]
["contig41","459879-469267",467019,12,12]
["contig42","1746521-1763451",1746041,14,20]
["contig43","1220255-1232582","*","*","*"]
["contig48","59295-105164",47536,1,1]
["contig48","468107-514931",494544,16,20]
["contig48","1419008-1474070",1419878,1,1]
["contig48","1723426-1730883","*","*","*"]
["contig5","3331283-3355728",3349682,1,1]
["contig50","925999-932836",927505,2,2]
["contig50","3322261-3328315",3326858,4,4]
["contig52","1771233-1787251",1779094,17,25]
["contig54","580-27136",27133,20,18]
["contig54","1114398-1141844",1140524,1,1]
["contig6","4473754-4592779",4554297,13,13]
["contig45","646718-651138","*","*","*"]
["contig65","40818-48207",45906,20,27]
["contig69","842240-854292",851104,2,2]
["contig7","213260-229199",218263,5,5]
["contig7","469505-478355",471204,3,4]
["contig75","53572-69793",58705,21,21]
["contig8","1866302-1875790",1874290,4,4]
["contig85","1009924-1014884",1010001,13,15]
["contig86","232195-250983",228709,6,6]
["contig89","229643-318686",314155,1,1]
["contig90","387694-416933",395925,34,50]
["contig110","683486-693538","*","*","*"]
["contig95","496764-503254",502250,18,23]
["lines with '*' represent specific conflict regions in optical maps"]

{"sheet":"Supplementary Data 10","index":9,"n_rows":16,"n_cols":3,"rows_kept":16}
["Supplementary Data 10: Comparison of quality evaluation for A. oxysepala before and after CRAQ correction"]
[null,"Before CRAQ correcting","After CRAQ correcting"]
["Number of used contigs (>30Kb)",332,390]
["Length (bp) of used contigs (>30Kb)",{"v":286674497,"d":"286,674,497"},{"v":285863544,"d":"285,863,544"}]
["Contig N50 (bp)",{"v":2417444,"d":"2,417,444"},{"v":1956729,"d":"1,956,729"}]
["Number of generated scaffolds*",14,11]
["Length of generated scaffolds*",{"v":283963349,"d":"283,963,349"},{"v":280114952,"d":"280,114,952"}]
["Scaffold N50 (bp)",{"v":20174754,"d":"20,174,754"},{"v":27881766,"d":"27,881,766"}]
["Busco completeness (%)",93.7,93.6]
["QV score",16.5677,16.5677]
["LTR Assembly Index (LAI)",10.86,10.86]
["length of mismatch regions found by 3D-DNA ",{"v":12525000,"d":"12,525,000"},{"v":11600000,"d":"11,600,000"}]
["Average count of CRE (per Mbp)",2.34014737280847,2.39106013619903]
["Average count of CSE (per Mbp)",0.941241605068159,0.543647887]
["Final R/S-AQI score","79.06/39.01","78.733/58.06"]
["*scaffolding was performed by 3D-DNA without error-correction option (r=0)"]