{"text_format":"3","workbook":"xlsx","n_sheets":23,"sheets":["Supplementary Table 1","Supplementary Table 2","Supplementary Table 3","Supplementary Table 4","Supplementary Table 5","Supplementary Table 6","Supplementary Table 7","Supplementary Table 8","Supplementary Table 9","Supplementary Table 10","Supplementary Table 11","Supplementary Table 12","Supplementary Table 13","Supplementary Table 14","Supplementary Table 15","Supplementary Table 16","Supplementary Table 17","Supplementary Table 18","Supplementary Table 19","Supplementary Table 20","Supplementary Table 21","Supplementary Table 22","Supplementary Table 23"],"read":"whole","date_system":"1900"}

{"sheet":"Supplementary Table 1","index":0,"n_rows":11,"n_cols":4,"rows_kept":11}
["Table S1 - Sample identification and pla quantification"]
["Note that all negative controls were free of amplification products"]
[]
["Individual ID","Sample ID","Archaeological ID","pla (copies/µL)"]
["AGU003","A","Gr 2.51.1",{"v":0.534,"d":"0.53"}]
["AGU007","A","Gr 3.104.1",{"v":0.1082,"d":"0.11"}]
["AGU009","A","Gr 2.41.2",{"v":0.575,"d":"0.58"}]
["AGU010","A","Gr 3.94.2",{"v":0.8272,"d":"0.83"}]
["AGU013","A","Gr 2.29",{"v":0.3136,"d":"0.31"}]
["AGU020","A","Gr 1.30",{"v":0.3063,"d":"0.31"}]
["AGU025","A","Gr 1.8",{"v":0.323,"d":"0.32"}]

{"sheet":"Supplementary Table 2","index":1,"n_rows":57,"n_cols":26,"rows_kept":57,"merged":[[3,0,35,0],[36,0,56,0]]}
["Table S2 - Shotgun Mapping of Libraries from the first tooth to hg19 in EAGER"]
[]
["Sample Type","Sample ID","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","# of reads on mitochondrion","Average coverage on mitochondron","MT/NUC Ratio","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU001.A0101.SG1.1",10409076,3422749,3422597,65.762,6208,5190,525,4665,0.181,0.152,1.113,{"v":1E-4,"d":"0.0001"},0.0107,0.01,400,{"v":1.56539320417647,"d":"1.565"},{"v":17497.35,"d":"17497"},0.1901,0.0972,0.1581,0.0929,64.93,{"v":66,"d":"66.0"},43.43]
[null,"AGU002.A0101.SG1.1",11770306,4242932,4242853,72.094,5034,3892,355,3537,0.119,0.092,{"v":1.1,"d":"1.100"},{"v":1E-4,"d":"0.0001"},0.0088,0.01,233,{"v":0.891423743134769,"d":"0.891"},{"v":13632.04,"d":"13632"},0.1521,0.1015,0.1498,0.0923,{"v":61.4,"d":"61.40"},{"v":61,"d":"61.0"},43.78]
[null,"AGU003.A0101.SG1.1",11532790,3052577,3052396,52.934,466096,392718,35861,356857,15.269,12.865,{"v":1.1,"d":"1.100"},0.0071,0.0889,{"v":0.7,"d":"0.70"},217,{"v":0.828233448005311,"d":"0.828"},{"v":116.76,"d":"117"},0.1879,0.0982,0.1822,0.0895,61.57,{"v":61,"d":"61.0"},44.41]
[null,"AGU003.A0102.SG1.1",15140198,3168566,3168421,41.854,384334,321187,26619,294568,{"v":12.13,"d":"12.130"},10.137,{"v":1.09,"d":"1.090"},0.0057,0.0786,0.56,294,{"v":1.07218299233508,"d":"1.072"},{"v":188.86,"d":"189"},0.0139,0.0096,0.0135,0.0094,59.72,{"v":59,"d":"59.0"},45.88]
[null,"AGU004.A0101.SG1.1",8478490,3045140,3045068,71.83,1783,1377,102,1275,0.059,0.045,{"v":1.08,"d":"1.080"},{"v":0,"d":"0.0000"},0.0052,{"v":0,"d":"0.00"},21,{"v":0.0771319934818033,"d":"0.077"},{"v":3110.21,"d":"3110"},0.1054,0.0789,0.1222,0.0828,{"v":61.2,"d":"61.20"},{"v":61,"d":"61.0"},44.91]
[null,"AGU005.A0101.SG1.1",11327172,3398582,3398473,60.006,272179,235443,19006,216437,8.009,6.928,1.088,0.0045,0.0706,0.45,784,{"v":3.20478001086366,"d":"3.205"},{"v":708.8,"d":"709"},0.1637,0.0919,0.1532,0.0857,64.92,{"v":66,"d":"66.0"},43.55]
[null,"AGU006.A0101.SG1.1",9715716,3145591,3145433,64.749,3041,2544,189,2355,0.097,0.081,{"v":1.08,"d":"1.080"},{"v":0,"d":"0.0000"},0.0072,{"v":0,"d":"0.00"},166,{"v":0.641740599915504,"d":"0.642"},{"v":14538.43,"d":"14538"},0.2338,0.1407,0.1743,0.1556,62.54,{"v":63,"d":"63.0"},{"v":42.3,"d":"42.30"}]
[null,"AGU007.A0101.SG1.1",15338608,5405761,5405626,70.484,417738,358944,29876,329068,7.728,{"v":6.64,"d":"6.640"},1.091,0.0067,0.0876,0.66,1301,{"v":4.98774820447824,"d":"4.988"},{"v":746.09,"d":"746"},{"v":0.187,"d":"0.1870"},0.1141,0.1729,0.1028,63.14,{"v":63,"d":"63.0"},42.88]
[null,"AGU007.A0102.SG1.1",8703769,8512836,"N/A","N/A",1107758,970152,117858,852294,13.013,11.396,1.138,0.0174,{"v":0.146,"d":"0.1460"},{"v":1.7,"d":"1.70"},2798,{"v":10.4986420423682,"d":"10.499"},{"v":603.93,"d":"604"},0.0233,0.0113,0.0135,0.0079,63.34,{"v":70,"d":"70.0"},42.76]
[null,"AGU008.A0101.SG1.1",12028758,3571855,3571759,59.387,701,576,51,525,{"v":0.02,"d":"0.020"},0.016,1.097,{"v":0,"d":"0.0000"},0.0036,{"v":0,"d":"0.00"},123,{"v":0.503953165550123,"d":"0.504"},{"v":62244.05,"d":"62244"},0.2148,0.0976,0.1654,0.1154,63.64,{"v":65,"d":"65.0"},44.04]
[null,"AGU009.A0101.SG1.1",9220186,3118792,3118703,67.649,1516,945,63,882,0.049,{"v":0.03,"d":"0.030"},1.071,{"v":0,"d":"0.0000"},0.0046,{"v":0,"d":"0.00"},207,{"v":0.838433218661355,"d":"0.838"},{"v":64526.97,"d":"64527"},0.2468,0.0933,0.2152,0.1273,61.34,{"v":61,"d":"61.0"},45.26]
[null,"AGU009.A0102.SG1.1",13749514,4251728,4251547,61.843,2930,1963,169,1794,0.069,0.046,1.094,{"v":0,"d":"0.0000"},0.0074,{"v":0,"d":"0.00"},472,{"v":1.70915565212143,"d":"1.709"},{"v":69479.76,"d":"69480"},{"v":0.008,"d":"0.0080"},0.0133,0.0185,0.0058,58.22,{"v":57,"d":"57.0"},45.41]
[null,"AGU010.A0101.SG1.1",12078670,4153366,4152992,68.766,49649,41903,3889,38014,1.195,1.009,1.102,0.0008,0.0279,0.08,48,{"v":0.18673426277989,"d":"0.187"},{"v":247.03,"d":"247"},0.2066,0.1168,0.1878,{"v":0.105,"d":"0.1050"},61.64,{"v":61,"d":"61.0"},42.08]
[null,"AGU010.A0102.SG1.1",11309862,3605200,3605136,63.752,58510,49631,3843,45788,1.623,1.377,1.084,0.0009,0.0298,0.09,99,{"v":0.346912909650552,"d":"0.347"},{"v":399.94,"d":"400"},0.0176,0.0107,0.0173,{"v":0.013,"d":"0.0130"},58.77,{"v":57,"d":"57.0"},41.71]
[null,"AGU011.A0101.SG1.1",10736338,4029125,4028993,75.053,888,536,163,373,0.022,0.013,1.437,{"v":0,"d":"0.0000"},0.0034,{"v":0,"d":"0.00"},51,{"v":0.189329470698291,"d":"0.189"},{"v":37362.54,"d":"37363"},0.1826,0.1238,0.1531,{"v":0.022,"d":"0.0220"},50.34,{"v":49,"d":"49.0"},52.62]
[null,"AGU012.A0101.SG1.1",9999868,3356477,3356346,67.128,58851,48410,3757,44653,1.753,1.442,1.084,0.0009,{"v":0.03,"d":"0.0300"},0.08,608,{"v":2.25427002233085,"d":"2.254"},{"v":2685.83,"d":"2686"},0.2775,0.1538,0.2522,0.1343,59.02,{"v":58,"d":"58.0"},43.83]
[null,"AGU013.A0101.SG1.1",11320298,3460522,3460451,61.137,2765,2292,181,2111,{"v":0.08,"d":"0.080"},0.066,1.086,{"v":0,"d":"0.0000"},0.0065,{"v":0,"d":"0.00"},111,{"v":0.430019916711931,"d":"0.430"},{"v":11008.74,"d":"11009"},0.3086,{"v":0.197,"d":"0.1970"},0.2505,0.1673,60.65,{"v":60,"d":"60.0"},43.12]
[null,"AGU013.A0102.SG1.1",19962938,6104039,6103876,61.152,3957,3304,280,3024,0.065,0.054,1.093,{"v":1E-4,"d":"0.0001"},0.0077,0.01,184,{"v":0.662200494900114,"d":"0.662"},{"v":12768.66,"d":"12769"},0.0172,0.0123,0.0164,{"v":0.007,"d":"0.0070"},56.72,{"v":55,"d":"55.0"},44.15]
[null,"AGU014.A0101.SG1.1",12847184,4049172,4049057,63.034,3657,2993,258,2735,{"v":0.09,"d":"0.090"},0.074,1.094,{"v":1E-4,"d":"0.0001"},0.0078,0.01,81,{"v":0.332005552537871,"d":"0.332"},{"v":5796.52,"d":"5797"},0.1927,0.1009,0.1547,0.1082,66.83,{"v":69,"d":"69.0"},42.63]
[null,"AGU015.A0101.SG1.1",9233100,3455702,3455638,74.853,3088,2557,213,2344,0.089,0.074,1.091,{"v":0,"d":"0.0000"},0.0075,{"v":0,"d":"0.00"},246,{"v":1.00935481924075,"d":"1.009"},{"v":23665.52,"d":"23666"},0.2118,0.1195,0.2069,0.1157,63.45,{"v":64,"d":"64.0"},44.44]
[null,"AGU016.A0101.SG1.1",8803024,3539607,3539563,80.417,1421391,1154336,102028,1052308,40.157,32.612,1.097,0.0201,0.1568,1.96,313,{"v":1.13223489649345,"d":"1.132"},{"v":56.21,"d":"56"},0.2107,0.1147,{"v":0.198,"d":"0.1980"},0.1014,59.27,{"v":58,"d":"58.0"},{"v":45.3,"d":"45.30"}]
[null,"AGU017.A0101.SG1.1",10628088,3034036,3033897,57.092,3733,2931,261,2670,0.123,0.097,1.098,{"v":1E-4,"d":"0.0001"},0.0083,{"v":0,"d":"0.00"},405,{"v":1.65212143158911,"d":"1.652"},{"v":38579.04,"d":"38579"},{"v":0.264,"d":"0.2640"},0.1541,0.1897,0.1067,{"v":59.9,"d":"59.90"},58.5,43.27]
[null,"AGU018.A0101.SG1.1",8902716,2194559,2194497,49.299,815,442,48,394,0.037,{"v":0.02,"d":"0.020"},1.122,{"v":0,"d":"0.0000"},0.0032,{"v":0,"d":"0.00"},41,{"v":0.175629187036031,"d":"0.176"},{"v":23013.51,"d":"23014"},0.1963,0.0779,{"v":0.16,"d":"0.1600"},0.1053,67.32,{"v":69,"d":"69.0"},44.34]
[null,"AGU019.A0101.SG1.1",11534596,4045826,4045658,70.148,351117,296905,29218,267687,8.678,7.339,1.109,{"v":0.005,"d":"0.0050"},0.0744,0.49,1271,{"v":4.98804997284084,"d":"4.988"},{"v":1000.43,"d":"1000"},0.1025,0.0503,0.0987,0.0462,57.97,{"v":57,"d":"57.0"},42.98]
[null,"AGU020.A0101.SG1.1",11277678,3218890,3218776,57.082,11089,9063,764,8299,0.344,0.282,1.092,0.0002,0.0135,0.01,406,{"v":1.60015691954855,"d":"1.600"},{"v":10948.26,"d":"10948"},0.2067,0.1194,0.1979,0.1156,57.71,{"v":56,"d":"56.0"},43.67]
[null,"AGU020.A0102.SG1.1",12627960,2870365,2870222,45.458,10194,8268,576,7692,0.355,0.288,1.075,{"v":1E-4,"d":"0.0001"},0.0126,0.01,451,{"v":1.61228800772527,"d":"1.612"},{"v":12503.16,"d":"12503"},0.0175,0.0132,0.0141,0.0114,55.37,{"v":53,"d":"53.0"},44.45]
[null,"AGU021.A0101.SG1.1",10880300,3810449,3810361,70.041,1373961,1200797,110042,1090755,36.058,31.513,1.101,0.0227,0.1634,2.22,540,{"v":2.002896976281,"d":"2.003"},{"v":88.25,"d":"88"},0.2457,0.1485,0.2291,0.1316,64.44,{"v":64,"d":"64.0"},42.46]
[null,"AGU022.A0101.SG1.1",8594676,3406047,3405485,79.246,122044,101556,8390,93166,3.583,2.982,{"v":1.09,"d":"1.090"},{"v":1.8E-3,"d":"0.0018"},0.0428,0.17,36,{"v":0.136580360914961,"d":"0.137"},{"v":77.88,"d":"78"},0.2301,{"v":0.126,"d":"0.1260"},0.2128,0.1134,{"v":58.3,"d":"58.30"},{"v":57,"d":"57.0"},42.82]
[null,"AGU023.A0101.SG1.1",9783000,4042304,4042225,82.638,19322,16570,1441,15129,0.478,{"v":0.41,"d":"0.410"},1.095,0.0003,0.0176,0.03,115,{"v":0.445047981169654,"d":"0.445"},{"v":1467.1,"d":"1467"},0.1961,0.1197,0.1798,0.1044,62.56,{"v":62,"d":"62.0"},44.17]
[null,"AGU024.A0101.SG1.1",10580150,3245282,3245209,61.345,23560,20443,1761,18682,0.726,{"v":0.63,"d":"0.630"},1.094,0.0004,0.0231,0.04,1107,{"v":4.5536845917074,"d":"4.554"},{"v":12165.39,"d":"12165"},0.2087,0.1216,0.2001,0.1125,66.06,{"v":67,"d":"67.0"},42.27]
[null,"AGU025.A0101.SG1.1",11195430,3411987,3411914,60.952,83215,71898,6139,65759,2.439,2.107,1.093,{"v":1.4E-3,"d":"0.0014"},0.0391,0.14,894,{"v":3.62423803488442,"d":"3.624"},{"v":2656.82,"d":"2657"},0.2275,0.1347,0.2141,0.1211,65.13,{"v":66,"d":"66.0"},41.57]
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["Blank","EXB035.A0101.SG1.1",2827756,833228,149470,17.939,303171,4848,3101,1747,36.385,0.582,2.775,{"v":0,"d":"0.0000"},0.0171,{"v":0,"d":"0.00"},1,{"v":0.00603536725209729,"d":"0.006"},{"v":164.26,"d":"164"},0.0178,0.0183,0.0031,{"v":6.3E-3,"d":"0.0063"},65.13,{"v":69,"d":"69.0"},52.75]
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[null,"EXB035.A0301.SG1.1",2481204,794238,194965,24.547,264174,3588,2209,1379,33.261,0.452,2.602,{"v":0,"d":"0.0000"},0.0165,{"v":0,"d":"0.00"},2,{"v":0.0091134045506669,"d":"0.009"},{"v":311.55,"d":"312"},0.0217,0.0286,0.0122,0.0163,65.73,{"v":69,"d":"69.0"},54.39]
[null,"EXB035.A0401.SG1.1",2386704,735260,175783,23.908,250311,6169,3582,2587,34.044,0.839,2.385,{"v":1E-4,"d":"0.0001"},0.0179,0.01,1,{"v":3.50051300621642E-3,"d":"0.004"},{"v":62.63,"d":"63"},0.0206,0.0158,{"v":0.007,"d":"0.0070"},0.0041,66.88,{"v":68,"d":"68.0"},49.19]
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[null,"EXB035.A0601.SG1.1",2523692,780534,309474,39.649,203262,9448,5272,4176,26.041,{"v":1.21,"d":"1.210"},2.262,{"v":1E-4,"d":"0.0001"},0.0181,0.01,3,{"v":0.00929446556822982,"d":"0.009"},{"v":97.66,"d":"98"},0.0112,0.0166,0.0077,0.0046,70.58,{"v":72,"d":"72.0"},48.7]
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[null,"LIB035.A0109.SG1.1",2077232,629214,97864,15.553,235111,1926,1269,657,37.366,0.306,2.932,{"v":0,"d":"0.0000"},0.0159,{"v":0,"d":"0.00"},0,{"v":0,"d":"0.000"},0,0.0094,0.0099,{"v":0.013,"d":"0.0130"},0.0213,68.74,{"v":75,"d":"75.0"},62.64]
[null,"LIB035.A0110.SG1.1",3050928,893276,198521,22.224,305445,3214,2135,1079,34.194,{"v":0.36,"d":"0.360"},2.979,{"v":0,"d":"0.0000"},0.0168,{"v":0,"d":"0.00"},0,{"v":0,"d":"0.000"},0,0.0288,0.0259,{"v":0.022,"d":"0.0220"},0.0181,72.14,{"v":75,"d":"75.0"},54.79]
[null,"LIB035.A0111.SG1.1",2477328,668331,115057,17.216,247224,2917,1914,1003,36.991,0.436,2.908,{"v":0,"d":"0.0000"},0.0158,{"v":0,"d":"0.00"},1,{"v":0.00494900114671977,"d":"0.005"},{"v":222.82,"d":"223"},0.0204,{"v":0.023,"d":"0.0230"},{"v":0,"d":"0.0000"},{"v":6.6E-3,"d":"0.0066"},68.58,{"v":74,"d":"74.0"},54.76]
[null,"LIB035.A0112.SG1.1",2176626,584509,127865,21.876,200143,2607,1609,998,34.241,0.446,2.612,{"v":0,"d":"0.0000"},{"v":0.016,"d":"0.0160"},{"v":0,"d":"0.00"},0,{"v":0,"d":"0.000"},0,0.0339,0.0276,0.0226,0.0121,67.95,{"v":74,"d":"74.0"},56.51]
[null,"LIB035.A0115.SG1.1",1801938,424950,86739,20.412,150866,3935,1676,2259,35.502,0.926,1.742,{"v":0,"d":"0.0000"},0.0144,{"v":0,"d":"0.00"},1,{"v":0.00301768362604864,"d":"0.003"},{"v":64.83,"d":"65"},0.0048,0.0052,0.0021,0.0024,63.79,{"v":62,"d":"62.0"},46.67]
[null,"LIB035.A0116.SG1.1",42114,11389,2935,25.77,3866,96,6,90,33.945,0.843,1.067,{"v":0,"d":"0.0000"},{"v":1.5E-3,"d":"0.0015"},{"v":0,"d":"0.00"},0,{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},0.0357,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},60.97,{"v":55,"d":"55.0"},52.01]
[null,"LIB035.A0130.SG1.1",2017266,902083,201810,22.372,331652,6143,3688,2455,36.765,0.681,2.502,{"v":0,"d":"0.0000"},0.0138,{"v":0,"d":"0.00"},1,{"v":0.00458687911159394,"d":"0.005"},{"v":93.01,"d":"93"},0.0108,0.0078,{"v":1.9E-3,"d":"0.0019"},0.0021,62.19,{"v":59,"d":"59.0"},46.69]
[null,"LIB035.A0131.SG1.1",2625802,1144135,413828,36.17,348772,19510,12034,7476,30.483,1.705,{"v":2.61,"d":"2.610"},0.0002,0.0179,0.02,11,{"v":0.040014484881405,"d":"0.040"},{"v":246.89,"d":"247"},0.0096,0.0105,0.0092,0.0078,67.19,{"v":66,"d":"66.0"},45.09]

{"sheet":"Supplementary Table 3","index":2,"n_rows":57,"n_cols":24,"rows_kept":57,"merged":[[3,0,35,0],[36,0,56,0]]}
["Table S3 - Shotgun Mapping of Libraries from the first tooth to Y. pestis CO92 in EAGER"]
[]
["Sample Type","Sample ID","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU001.A0101.SG1.1","non-UDG",10409076,3422749,3422597,65.762,645,35,4,31,0.019,{"v":1E-3,"d":"0.001"},1.129,0.0003,0.0192,0.03,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.1667,{"v":0,"d":"0.0000"},49.32,{"v":47,"d":"47.0"},50.52]
[null,"AGU002.A0101.SG1.1","non-UDG",11770306,4242932,4242853,72.094,742,32,6,26,0.017,{"v":1E-3,"d":"0.001"},1.231,0.0002,0.0189,0.02,{"v":0.1,"d":"0.1000"},0.0909,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},44.35,{"v":43,"d":"43.0"},58.98]
[null,"AGU003.A0101.SG1.1","non-UDG",11532790,3052577,3052396,52.934,318,5,0,5,{"v":0.01,"d":"0.010"},{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":0,"d":"0.0000"},0.0074,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":39,"d":"39.00"},{"v":36,"d":"36.0"},64.1]
[null,"AGU003.A0102.SG1.1","UDG",15140198,3168566,3168421,41.854,363,12,1,11,0.011,{"v":0,"d":"0.000"},1.091,{"v":1E-4,"d":"0.0001"},{"v":0.011,"d":"0.0110"},0.01,{"v":0,"d":"0.0000"},0.3333,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},39.27,{"v":37,"d":"37.0"},61.57]
[null,"AGU004.A0101.SG1.1","non-UDG",8478490,3045140,3045068,71.83,251,7,0,7,0.008,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":1E-4,"d":"0.0001"},{"v":0.014,"d":"0.0140"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":53,"d":"53.00"},{"v":52,"d":"52.0"},64.15]
[null,"AGU005.A0101.SG1.1","non-UDG",11327172,3398582,3398473,60.006,351,14,2,12,{"v":0.01,"d":"0.010"},{"v":0,"d":"0.000"},1.167,{"v":1E-4,"d":"0.0001"},{"v":0.016,"d":"0.0160"},0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},48.75,{"v":45,"d":"45.0"},62.56]
[null,"AGU006.A0101.SG1.1","non-UDG",9715716,3145591,3145433,64.749,294,3,0,3,0.009,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":0,"d":"0.0000"},0.0051,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},40.33,{"v":36,"d":"36.0"},51.67]
[null,"AGU007.A0101.SG1.1","non-UDG",15338608,5405761,5405626,70.484,611,96,9,87,0.011,{"v":2E-3,"d":"0.002"},1.103,{"v":1E-3,"d":"0.0010"},0.0309,{"v":0.1,"d":"0.10"},0.1538,0.0667,{"v":0.1,"d":"0.1000"},{"v":0.125,"d":"0.1250"},51.26,{"v":49,"d":"49.0"},49.46]
[null,"AGU007.A0102.SG1.1","UDG",8703769,8513304,"N/A","N/A",507,91,13,78,0.006,{"v":1E-3,"d":"0.001"},1.167,0.0008,0.0285,0.08,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},48.54,{"v":46,"d":"46.0"},49.84]
[null,"AGU008.A0101.SG1.1","non-UDG",12028758,3571855,3571759,59.387,405,11,1,10,0.011,{"v":0,"d":"0.000"},{"v":1.1,"d":"1.100"},{"v":1E-4,"d":"0.0001"},0.0138,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":41.9,"d":"41.90"},40.5,64.35]
[null,"AGU009.A0101.SG1.1","non-UDG",9220186,3118792,3118703,67.649,207,9,3,6,0.007,{"v":0,"d":"0.000"},{"v":1.5,"d":"1.500"},{"v":1E-4,"d":"0.0001"},0.0084,0.01,{"v":0,"d":"0.0000"},{"v":0.5,"d":"0.5000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},44.83,{"v":42,"d":"42.0"},52.79]
[null,"AGU009.A0102.SG1.1","UDG",13749514,4251728,4251547,61.843,273,13,0,13,0.006,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":1E-4,"d":"0.0001"},0.0117,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},43.23,{"v":39,"d":"39.0"},58.01]
[null,"AGU010.A0101.SG1.1","non-UDG",12078670,4153366,4152992,68.766,732,63,8,55,0.018,{"v":2E-3,"d":"0.002"},1.145,0.0006,0.0264,0.06,{"v":0,"d":"0.0000"},0.0833,0.0909,{"v":0,"d":"0.0000"},{"v":52,"d":"52.00"},{"v":49,"d":"49.0"},49.55]
[null,"AGU010.A0102.SG1.1","UDG",11309862,3605200,3605136,63.752,573,49,4,45,0.016,{"v":1E-3,"d":"0.001"},1.089,0.0005,0.0218,0.05,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.33,{"v":47,"d":"47.0"},46.17]
[null,"AGU011.A0101.SG1.1","non-UDG",10736338,4029125,4028993,75.053,454,12,0,12,0.011,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":1E-4,"d":"0.0001"},0.0144,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0.2,"d":"0.2000"},{"v":0,"d":"0.0000"},38.92,{"v":32,"d":"32.0"},63.81]
[null,"AGU012.A0101.SG1.1","non-UDG",9999868,3356477,3356346,67.128,468,22,4,18,0.014,{"v":1E-3,"d":"0.001"},1.222,0.0002,0.0144,0.01,0.1667,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":39,"d":"39.00"},35.5,59.69]
[null,"AGU013.A0101.SG1.1","non-UDG",11320298,3460522,3460451,61.137,418,10,1,9,0.012,{"v":0,"d":"0.000"},1.111,{"v":1E-4,"d":"0.0001"},{"v":0.01,"d":"0.0100"},0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},36.78,{"v":37,"d":"37.0"},63.03]
[null,"AGU013.A0102.SG1.1","UDG",19962938,6104039,6103876,61.152,692,26,3,23,0.011,{"v":0,"d":"0.000"},{"v":1.13,"d":"1.130"},0.0002,0.0212,0.01,0.1111,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},40.39,{"v":42,"d":"42.0"},60.93]
[null,"AGU014.A0101.SG1.1","non-UDG",12847184,4049172,4049057,63.034,260,10,2,8,0.006,{"v":0,"d":"0.000"},{"v":1.25,"d":"1.250"},{"v":1E-4,"d":"0.0001"},{"v":0.01,"d":"0.0100"},0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},41.38,{"v":42,"d":"42.0"},55.02]
[null,"AGU015.A0101.SG1.1","non-UDG",9233100,3455702,3455638,74.853,439,41,4,37,0.013,{"v":1E-3,"d":"0.001"},1.108,0.0004,0.0237,0.04,{"v":0.1,"d":"0.1000"},{"v":0.25,"d":"0.2500"},0.1667,{"v":0,"d":"0.0000"},49.86,{"v":45,"d":"45.0"},52.25]
[null,"AGU016.A0101.SG1.1","non-UDG",8803024,3539607,3539563,80.417,297,20,2,18,0.008,{"v":1E-3,"d":"0.001"},1.111,0.0002,{"v":0.015,"d":"0.0150"},0.01,{"v":0.25,"d":"0.2500"},{"v":0,"d":"0.0000"},{"v":0.4,"d":"0.4000"},0.1111,39.56,{"v":38,"d":"38.0"},57.52]
[null,"AGU017.A0101.SG1.1","non-UDG",10628088,3034036,3033897,57.092,523,18,1,17,0.017,{"v":1E-3,"d":"0.001"},1.059,0.0002,0.0129,0.01,{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},0.1429,{"v":0,"d":"0.0000"},41.59,{"v":38,"d":"38.0"},58.92]
[null,"AGU018.A0101.SG1.1","non-UDG",8902716,2194559,2194497,49.299,148,2,0,2,0.007,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":0,"d":"0.0000"},0.0047,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":52.5,"d":"52.50"},52.5,56.19]
[null,"AGU019.A0101.SG1.1","non-UDG",11534596,4045826,4045658,70.148,673,17,3,14,0.017,{"v":0,"d":"0.000"},1.214,{"v":1E-4,"d":"0.0001"},0.0128,0.01,{"v":0.2,"d":"0.2000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},43.43,{"v":44,"d":"44.0"},57.43]
[null,"AGU020.A0101.SG1.1","non-UDG",11277678,3218890,3218776,57.082,824,61,7,54,0.026,{"v":2E-3,"d":"0.002"},{"v":1.13,"d":"1.130"},0.0006,0.0243,0.06,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.0556,0.2143,48.72,{"v":48,"d":"48.0"},49.54]
[null,"AGU020.A0102.SG1.1","UDG",12627960,2870365,2870222,45.458,722,59,2,57,0.025,{"v":2E-3,"d":"0.002"},1.035,0.0006,0.0256,0.06,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.79,{"v":47,"d":"47.0"},46.09]
[null,"AGU021.A0101.SG1.1","non-UDG",10880300,3810449,3810361,70.041,330,2,0,2,0.009,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":0,"d":"0.0000"},0.0044,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":46,"d":"46.00"},{"v":46,"d":"46.0"},54.35]
[null,"AGU022.A0101.SG1.1","non-UDG",8594676,3406047,3405485,79.246,411,19,4,15,0.012,{"v":1E-3,"d":"0.001"},1.267,{"v":1E-4,"d":"0.0001"},0.0161,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0.2,"d":"0.2000"},40.87,{"v":37,"d":"37.0"},56.28]
[null,"AGU023.A0101.SG1.1","non-UDG",9783000,4042304,4042225,82.638,679,23,3,20,0.017,{"v":1E-3,"d":"0.001"},{"v":1.15,"d":"1.150"},0.0002,0.0208,0.01,{"v":0,"d":"0.0000"},0.3333,{"v":0,"d":"0.0000"},{"v":0.2,"d":"0.2000"},38.95,35.5,64.86]
[null,"AGU024.A0101.SG1.1","non-UDG",10580150,3245282,3245209,61.345,510,12,1,11,0.016,{"v":0,"d":"0.000"},1.091,{"v":1E-4,"d":"0.0001"},0.0181,0.01,{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},47.82,{"v":43,"d":"43.0"},60.84]
[null,"AGU025.A0101.SG1.1","non-UDG",11195430,3411987,3411914,60.952,365,40,4,36,0.011,{"v":1E-3,"d":"0.001"},1.111,0.0004,0.0193,0.04,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0.2,"d":"0.2000"},{"v":48,"d":"48.00"},{"v":46,"d":"46.0"},46.24]
[null,"AGU025.A0102.SG1.1","UDG",10100378,2857664,2857556,56.583,383,40,1,39,0.013,{"v":1E-3,"d":"0.001"},1.026,0.0004,0.0208,0.04,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.38,{"v":47,"d":"47.0"},47.61]
[null,"AGU026.A0101.SG1.1","non-UDG",10115554,2899616,2899553,57.329,437,19,2,17,0.015,{"v":1E-3,"d":"0.001"},1.118,0.0002,0.0134,0.02,{"v":0,"d":"0.0000"},{"v":0.2,"d":"0.2000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.29,{"v":49,"d":"49.0"},50.84]
["Blank","EXB035.A0101.SG1.1","non-UDG",2827756,833228,149470,17.939,52,2,1,1,0.006,{"v":0,"d":"0.000"},{"v":2,"d":"2.000"},{"v":0,"d":"0.0000"},{"v":0.004,"d":"0.0040"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":75,"d":"75.00"},{"v":75,"d":"75.0"},{"v":36,"d":"36.00"}]
[null,"EXB035.A0102.SG1.1","UDG",2964614,1388401,644556,46.424,361,36,18,18,0.026,0.003,{"v":2,"d":"2.000"},0.0002,{"v":0.013,"d":"0.0130"},0.02,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":44,"d":"44.00"},43.5,55.56]
[null,"EXB035.A0201.SG1.1","non-UDG",2043384,656612,172133,26.215,41,1,0,1,0.006,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":0,"d":"0.0000"},0.0026,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":32,"d":"32.00"},{"v":32,"d":"32.0"},34.38]
[null,"EXB035.A0202.SG1.1","UDG",3318168,1628809,848935,52.12,279,40,20,20,0.017,{"v":2E-3,"d":"0.002"},{"v":2,"d":"2.000"},0.0002,0.0137,0.02,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},44.05,{"v":42,"d":"42.0"},52.39]
[null,"EXB035.A0301.SG1.1","non-UDG",2481204,794238,194965,24.547,89,9,5,4,0.011,{"v":1E-3,"d":"0.001"},{"v":2.25,"d":"2.250"},{"v":1E-4,"d":"0.0001"},0.0071,0.01,{"v":0.5,"d":"0.5000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},58.25,{"v":57,"d":"57.0"},52.79]
[null,"EXB035.A0401.SG1.1","non-UDG",2386704,735260,175783,23.908,70,7,3,4,{"v":0.01,"d":"0.010"},{"v":1E-3,"d":"0.001"},{"v":1.75,"d":"1.750"},{"v":0,"d":"0.0000"},0.0057,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},37.25,37.5,{"v":60.4,"d":"60.40"}]
[null,"EXB035.A0501.SG1.1","non-UDG",2457000,780935,261167,33.443,91,7,3,4,0.012,{"v":1E-3,"d":"0.001"},{"v":1.75,"d":"1.750"},{"v":1E-4,"d":"0.0001"},0.0078,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},70.75,55.5,55.48]
[null,"EXB035.A0502.SG1.1","UDG",4203044,1754381,1271185,72.458,494,68,38,30,0.028,0.004,2.267,0.0003,0.0189,0.03,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.0833,{"v":51.9,"d":"51.90"},{"v":46,"d":"46.0"},54.08]
[null,"EXB035.A0601.SG1.1","non-UDG",2523692,780534,309474,39.649,92,13,10,3,0.012,{"v":2E-3,"d":"0.002"},4.333,{"v":0,"d":"0.0000"},0.0049,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},37.67,{"v":32,"d":"32.0"},56.64]
[null,"EXB035.A0602.SG1.1","UDG",4009468,1853784,1316016,70.991,425,55,26,29,0.023,0.003,1.897,0.0003,0.0171,0.03,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0.125,"d":"0.1250"},{"v":0,"d":"0.0000"},47.14,{"v":44,"d":"44.0"},52.16]
[null,"EXB035.A0701.SG1.1","non-UDG",1875594,587466,136569,23.247,38,6,3,3,0.006,{"v":1E-3,"d":"0.001"},{"v":2,"d":"2.000"},{"v":0,"d":"0.0000"},0.0054,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},44.67,{"v":42,"d":"42.0"},{"v":59.7,"d":"59.70"}]
[null,"EXB035.A0801.SG1.1","non-UDG",935084,264934,66579,25.13,18,0,0,0,0.007,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A0802.SG1.1","UDG",2475512,823510,333554,40.504,235,41,25,16,0.029,0.005,2.563,0.0002,0.0129,0.02,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},47.31,{"v":42,"d":"42.0"},{"v":53.5,"d":"53.50"}]
[null,"LIB035.A0109.SG1.1","non-UDG",2077232,629214,97864,15.553,29,5,1,4,0.005,{"v":1E-3,"d":"0.001"},{"v":1.25,"d":"1.250"},{"v":0,"d":"0.0000"},0.0069,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":55,"d":"55.00"},50.5,53.64]
[null,"LIB035.A0110.SG1.1","non-UDG",3050928,893276,198521,22.224,84,20,13,7,0.009,{"v":2E-3,"d":"0.002"},2.857,{"v":1E-4,"d":"0.0001"},{"v":7.6E-3,"d":"0.0076"},0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},38.43,{"v":36,"d":"36.0"},52.04]
[null,"LIB035.A0111.SG1.1","non-UDG",2477328,668331,115057,17.216,44,15,12,3,0.007,{"v":2E-3,"d":"0.002"},{"v":5,"d":"5.000"},{"v":0,"d":"0.0000"},0.0048,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":36,"d":"36.00"},{"v":35,"d":"35.0"},54.63]
[null,"LIB035.A0112.SG1.1","non-UDG",2176626,584509,127865,21.876,62,11,5,6,0.011,{"v":2E-3,"d":"0.002"},1.833,{"v":1E-4,"d":"0.0001"},0.0104,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},42.83,{"v":43,"d":"43.0"},40.86]
[null,"LIB035.A0115.SG1.1","UDG",1801938,424950,86739,20.412,101,15,4,11,0.024,0.004,1.364,{"v":1E-4,"d":"0.0001"},0.0097,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},40.09,{"v":37,"d":"37.0"},50.79]
[null,"LIB035.A0116.SG1.1","UDG",42114,11389,2935,25.77,1,0,0,0,0.009,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0130.SG1.1","UDG",2017266,902083,201810,22.372,201,40,24,16,0.022,0.004,{"v":2.5,"d":"2.500"},{"v":1E-4,"d":"0.0001"},0.0114,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},37.88,{"v":37,"d":"37.0"},52.81]
[null,"LIB035.A0131.SG1.1","UDG",2625802,1144135,413828,36.17,255,38,21,17,0.022,0.003,2.235,0.0002,0.0134,0.02,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},44.29,{"v":36,"d":"36.0"},55.32]

{"sheet":"Supplementary Table 4","index":3,"n_rows":32,"n_cols":28,"rows_kept":32,"merged":[[3,0,14,0],[15,0,31,0]]}
["Table S4 - Mapping Capture Products from first tooth to Y. pestis CO92 for the six putative plague victims identified via PCR "]
[]
["Sample Type","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU003.A0101.YP1.1","non-UDG",8298136,5513613,2731924,65.844,29207,454,207,247,1.069,0.017,1.838,0.0025,0.1737,{"v":0.1,"d":"0.10"},0.03,0.02,0.01,0.01,{"v":0,"d":"0.0000"},0.0429,0.0267,{"v":0,"d":"0.0000"},46.24,{"v":42,"d":"42.0"},57.66]
[null,"AGU003.A0102.YP1.1","UDG",6630532,4540294,2057560,62.063,24072,393,177,216,{"v":1.17,"d":"1.170"},0.019,1.819,0.0021,0.1501,0.09,0.03,0.02,0.01,0.01,0.0323,0.0161,0.0192,0.0408,46.19,42.5,58.32]
[null,"AGU009.A0101.YP1.1","non-UDG",7025172,4472335,2511160,71.49,27132,2849,1836,1013,{"v":1.08,"d":"1.080"},0.113,2.812,0.0119,0.2346,1.01,0.06,0.02,0.01,0.01,0.0847,0.0249,0.0875,0.0496,54.75,{"v":54,"d":"54.0"},49.54]
[null,"AGU009.A0102.YP1.1","UDG",9127138,5865168,3222041,70.604,34481,3402,2085,1317,{"v":1.07,"d":"1.070"},0.106,2.583,0.0153,0.2484,1.31,0.07,0.02,0.01,0.01,{"v":3.3E-3,"d":"0.0033"},{"v":0.007,"d":"0.0070"},0.0031,0.0067,53.99,{"v":53,"d":"53.0"},50.02]
[null,"AGU010.A0101.YP1.1","non-UDG",12836042,8510632,4264957,66.453,172478,87923,40676,47247,4.044,2.061,1.861,0.6132,1.6647,38.21,11.78,3.58,1.41,0.82,0.0961,0.0569,0.1053,0.0553,{"v":60.4,"d":"60.40"},{"v":59,"d":"59.0"},48.06]
[null,"AGU010.A0102.YP1.1","UDG",8970962,6012611,2932976,65.388,99556,48423,25585,22838,3.394,1.651,{"v":2.12,"d":"2.120"},0.2847,0.9444,20.89,3.94,1.05,0.48,0.31,0.0013,{"v":1.9E-3,"d":"0.0019"},0.0039,0.0032,58.02,{"v":56,"d":"56.0"},47.99]
[null,"AGU013.A0101.YP1.1","non-UDG",9806196,6399527,3330385,67.924,32495,364,213,151,0.976,0.011,2.411,1.4E-3,0.1171,0.06,0.01,0.01,0.01,0.01,0.1373,0.1351,0.0612,{"v":0.027,"d":"0.0270"},42.38,{"v":37,"d":"37.0"},{"v":57.9,"d":"57.90"}]
[null,"AGU013.A0102.YP1.1","UDG",10545600,6902416,3603171,68.335,34482,307,188,119,0.957,0.009,{"v":2.58,"d":"2.580"},0.0011,0.1052,0.04,0.01,0.01,0.01,0.01,{"v":0.15,"d":"0.1500"},0.1379,0.0606,{"v":0.069,"d":"0.0690"},42.03,{"v":37,"d":"37.0"},59.36]
[null,"AGU020.A0101.YP1.1","non-UDG",7687974,5135798,2490065,64.778,166661,108696,55209,53487,6.693,4.365,2.032,{"v":0.664,"d":"0.6640"},1.0103,43.61,15.17,4.69,1.46,0.53,0.1321,0.0648,0.1347,0.0614,57.78,{"v":57,"d":"57.0"},{"v":47.6,"d":"47.60"}]
[null,"AGU020.A0102.YP1.1","UDG",6573866,4532676,2009875,61.147,138807,87921,37897,50024,6.906,4.374,1.758,0.6171,0.9831,{"v":41.2,"d":"41.20"},13.79,4.12,1.24,0.45,{"v":2.8E-3,"d":"0.0028"},{"v":2.3E-3,"d":"0.0023"},{"v":1.5E-3,"d":"0.0015"},0.0017,57.41,{"v":56,"d":"56.0"},48.21]
[null,"AGU025.A0101.YP1.1","non-UDG",7638670,5045398,2549819,66.761,188874,141142,108892,32250,7.407,5.535,4.376,0.3837,0.7115,29.29,7.14,1.47,0.28,0.06,0.1015,0.0508,0.1083,0.0501,55.37,{"v":53,"d":"53.0"},47.07]
[null,"AGU025.A0102.YP1.1","UDG",8165586,5290641,2823036,69.145,190612,140459,78449,62010,6.752,4.975,2.265,0.7688,1.0086,49.22,18.97,6.13,1.77,0.46,{"v":1.4E-3,"d":"0.0014"},0.0005,0.0013,0.0005,{"v":57.7,"d":"57.70"},{"v":56,"d":"56.0"},47.48]
["Blank","EXB035.A0101.YP1.1","non-UDG",1216611,957197,0,0,14521,37,21,16,1.517,0.004,2.313,0.0002,0.0147,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},56.94,{"v":58,"d":"58.0"},51.81]
[null,"EXB035.A0201.YP1.1","non-UDG",2186447,1835863,0,0,26889,90,78,12,1.465,0.005,{"v":7.5,"d":"7.500"},1E-4,0.0115,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},50.92,{"v":45,"d":"45.0"},{"v":52.7,"d":"52.70"}]
[null,"EXB035.A0301.YP1.1","non-UDG",2111434,1748132,0,0,85280,44800,44783,17,4.878,2.563,2635.294,0.0002,0.0162,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0.2,"d":"0.2000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":57,"d":"57.00"},{"v":57,"d":"57.0"},52.75]
[null,"EXB035.A0401.YP1.1","non-UDG",972836,762103,0,0,57744,13669,13658,11,7.577,1.794,1242.636,1E-4,0.0113,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":54,"d":"54.00"},{"v":56,"d":"56.0"},49.83]
[null,"EXB035.A0501.YP1.1","non-UDG",1557719,1296501,0,0,82619,39685,39670,15,6.372,3.061,2645.667,0.0002,0.0164,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},57.13,{"v":59,"d":"59.0"},56.59]
[null,"EXB035.A0502.YP1.1","UDG",6126859,5540697,0,0,308133,106773,106683,90,5.561,1.927,1186.367,1E-3,0.0359,0.09,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},0.0385,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.0357,51.96,46.5,53.22]
[null,"EXB035.A0601.YP1.1","non-UDG",1578302,1336464,0,0,50382,5274,5254,20,{"v":3.77,"d":"3.770"},0.395,{"v":263.7,"d":"263.700"},0.0002,0.0164,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},55.95,53.5,53.98]
[null,"EXB035.A0602.YP2.1","UDG",4905334,2553718,1897160,74.29,37136,3566,3548,18,1.454,{"v":0.14,"d":"0.140"},198.111,0.0002,0.0161,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.3333,{"v":0,"d":"0.0000"},54.33,58.5,50.31]
[null,"EXB035.A0701.YP1.1","non-UDG",1034521,841791,0,0,36800,2191,2178,13,4.372,{"v":0.26,"d":"0.260"},168.538,1E-4,0.0119,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},0.1667,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},50.62,{"v":49,"d":"49.0"},53.12]
[null,"EXB035.A0801.YP1.1","non-UDG",860495,716339,0,0,20648,1050,1041,9,2.882,0.147,116.667,1E-4,{"v":0.01,"d":"0.0100"},0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.56,{"v":49,"d":"49.0"},54.48]
[null,"EXB035.A0802.YP1.1","UDG",3445598,3062921,0,0,130006,44061,44022,39,4.245,1.439,1129.769,0.0004,0.0227,0.04,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},50.62,{"v":45,"d":"45.0"},52.16]
[null,"LIB035.A0109.YP1.1","non-UDG",530058,413351,0,0,16934,7665,7656,9,4.097,1.854,851.667,1E-4,0.0101,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},52.44,{"v":46,"d":"46.0"},52.97]
[null,"LIB035.A0110.YP1.1","non-UDG",1357250,1099452,0,0,40432,13552,13532,20,3.677,1.233,{"v":677.6,"d":"677.600"},0.0002,{"v":0.016,"d":"0.0160"},0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0.125,"d":"0.1250"},0.1111,{"v":0,"d":"0.0000"},49.55,43.5,52.17]
[null,"LIB035.A0111.YP1.1","non-UDG",1562948,1279409,0,0,10889,948,939,9,0.851,0.074,105.333,1E-4,0.0099,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},50.56,{"v":42,"d":"42.0"},49.23]
[null,"LIB035.A0112.YP1.1","non-UDG",1758205,1535402,0,0,30700,4762,4747,15,1.999,{"v":0.31,"d":"0.310"},317.467,0.0002,0.0153,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},56.13,{"v":55,"d":"55.0"},47.44]
[null,"LIB035.A0115.YP1.1","UDG",1558138,1346279,0,0,104939,24603,24564,39,7.795,1.827,630.846,0.0004,0.0242,0.03,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.2143,45.64,{"v":40,"d":"40.0"},56.52]
[null,"LIB035.A0116.YP1.1","UDG",172901,166515,0,0,12523,5175,5160,15,7.521,3.108,{"v":345,"d":"345.000"},1E-4,0.0128,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0.5,"d":"0.5000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},46.13,{"v":45,"d":"45.0"},58.96]

{"sheet":"Supplementary Table 5","index":4,"n_rows":9,"n_cols":28,"rows_kept":9,"merged":[[3,0,4,0],[5,0,8,0]]}
["Table S5 - Mapping of AGU007 Capture Products from first tooth to Y. pestis CO92 in EAGER"]
[]
["Sample Type","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.A0101.YP1.1","nonUDG",10289812,5280755,4900738,92.804,283180,204297,144565,59732,5.362,3.869,{"v":3.42,"d":"3.420"},0.7422,1.0823,48.28,17.61,5.31,1.48,0.46,0.1268,0.0598,0.1298,{"v":0.063,"d":"0.0630"},57.82,{"v":55,"d":"55.0"},47.62]
[null,"AGU007.A0102.YP2.1","UDG",17223958,9100997,7906679,86.877,486298,324631,168508,156123,5.343,3.567,2.079,1.9779,2.1695,75.99,52.06,31.53,17.41,9.09,0.0017,{"v":1E-3,"d":"0.0010"},0.0016,0.0012,58.96,{"v":55,"d":"55.0"},{"v":48.2,"d":"48.20"}]
["Blank","EXB035.A0102.YP2.1","UDG",7510166,4006033,2674045,66.75,55804,602,597,5,1.393,0.015,{"v":120.4,"d":"120.400"},0,0.0064,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":38,"d":"38.00"},{"v":34,"d":"34.0"},57.37]
[null,"EXB035.A0202.YP2.1","UDG",9632910,5396589,3267728,60.552,34951,1177,1160,17,0.648,0.022,69.235,0.0002,{"v":0.013,"d":"0.0130"},0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},46.18,{"v":42,"d":"42.0"},50.83]
[null,"LIB035.A0130.YP2.1","UDG",1921036,1006201,615909,61.211,23505,2051,2043,8,2.336,0.204,256.375,1E-4,0.0092,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":39.38,"d":"39.4"},{"v":38.5,"d":"38.50"},51.43]
[null,"LIB035.A0131.YP2.1","UDG",2576078,1318799,834276,63.26,34791,2301,2294,7,2.638,0.174,328.714,1E-4,0.0087,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":50.86,"d":"50.9"},{"v":45,"d":"45.00"},54.08]

{"sheet":"Supplementary Table 6","index":5,"n_rows":19,"n_cols":27,"rows_kept":19,"merged":[[3,0,10,0],[11,0,18,0]]}
["Table S6 - Shotgun Mapping of Libraries from the second tooth to Hg19 in EAGER"]
[]
["Sample Type","Sample ID","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","# of reads on mitochondrion","Average coverage on mitochondron","MT/NUC Ratio","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.SG1.1","non-UDG",12853927,12683203,"N/A","N/A",8876815,7492473,977529,6514944,69.989,59.074,{"v":1.15,"d":"1.150"},0.1305,0.4146,11.79,4882,{"v":19.2785322,"d":"19.279"},{"v":147.81,"d":"148"},0.1222,0.0638,0.1603,0.0864,62.02,{"v":65,"d":"65.0"},45.01]
[null,"AGU007.B0102.SG1.1","UDG",14325984,14139405,"N/A","N/A",9509934,7709954,723487,6986467,67.258,54.528,1.104,0.1383,0.4036,12.47,4202,{"v":16.3056309976462,"d":"16.306"},{"v":117.95,"d":"118"},0.0196,{"v":0.01,"d":"0.0100"},0.0125,0.0068,61.29,{"v":63,"d":"63.0"},45.3]
[null,"AGU010.B0101.SG1.1","non-UDG",11676387,11481364,"N/A","N/A",604047,492534,49908,442626,5.261,{"v":4.29,"d":"4.290"},1.113,{"v":0.008,"d":"0.0080"},0.0971,0.79,1311,{"v":4.987386082,"d":"4.987"},{"v":622.55,"d":"623"},0.1215,{"v":0.068,"d":"0.0680"},0.1294,0.0707,56.22,{"v":55,"d":"55.0"},43.43]
[null,"AGU010.B0102.SG1.1","UDG",12934357,12790224,"N/A","N/A",497809,396598,33337,363261,3.892,3.101,1.092,0.0067,0.0842,0.66,994,{"v":3.74796306355241,"d":"3.748"},{"v":563.49,"d":"563"},0.0182,{"v":0.01,"d":"0.0100"},0.0094,0.0067,56.85,{"v":56,"d":"56.0"},43.59]
[null,"AGU020.B0101.SG1.1","non-UDG",13368330,13086050,"N/A","N/A",8916,7196,815,6381,0.068,0.055,1.128,{"v":1E-4,"d":"0.0001"},0.0172,0.01,1291,{"v":5.17617237,"d":"5.176"},{"v":53224.4,"d":"53224"},0.1576,0.0799,0.1812,0.1194,60.61,{"v":65,"d":"65.0"},44.19]
[null,"AGU020.B0102.SG1.1","UDG",13323315,13011915,"N/A","N/A",9834,7207,551,6656,0.076,0.055,1.083,{"v":1E-4,"d":"0.0001"},0.0158,0.01,1112,{"v":4.14847003440159,"d":"4.148"},{"v":40799.68,"d":"40800"},0.0221,0.0127,0.0106,{"v":0.003,"d":"0.0030"},57.62,{"v":58,"d":"58.0"},44.12]
[null,"AGU025.B0101.SG1.1","non-UDG",12215744,12066446,"N/A","N/A",48238,41709,5089,36620,{"v":0.4,"d":"0.400"},0.346,1.139,0.0008,{"v":0.035,"d":"0.0350"},0.08,1911,{"v":7.871989861,"d":"7.872"},{"v":10270.06,"d":"10270"},0.0506,{"v":0.022,"d":"0.0220"},0.0665,0.0427,68.36,{"v":76,"d":"76.0"},42.99]
[null,"AGU025.B0102.SG1.1","UDG",13261592,13073620,"N/A","N/A",53498,44068,4030,40038,0.409,0.337,1.101,0.0009,0.0368,0.08,2069,{"v":8.03047860462309,"d":"8.030"},{"v":9765.36,"d":"9765"},{"v":0.013,"d":"0.0130"},{"v":0.005,"d":"0.0050"},{"v":6.3E-3,"d":"0.0063"},{"v":2.8E-3,"d":"0.0028"},66.91,{"v":75,"d":"75.0"},42.9]
["Blank","EXB035.A3901.SG1.1","non-UDG",2259404,890713,281980,31.658,261580,7225,4229,2996,29.367,0.811,2.412,{"v":1E-4,"d":"0.0001"},0.0181,0.01,0,{"v":0,"d":"0.000"},0,{"v":0.015,"d":"0.0150"},0.0071,{"v":0.005,"d":"0.0050"},0.0047,72.97,{"v":75,"d":"75.0"},49]
[null,"EXB035.A3902.SG1.1","UDG",1167984,385973,136304,35.314,116954,9706,3329,6377,30.301,2.515,1.522,{"v":1E-4,"d":"0.0001"},0.0164,0.01,2,{"v":0.00597501357957631,"d":"0.006"},{"v":40.66,"d":"41"},{"v":0.008,"d":"0.0080"},0.0095,{"v":0.006,"d":"0.0060"},{"v":1.5E-3,"d":"0.0015"},71.35,{"v":75,"d":"75.0"},44.83]
[null,"EXB035.A4001.SG1.1","non-UDG",2320538,843079,280527,33.274,240441,6500,3841,2659,28.519,0.771,2.445,{"v":1E-4,"d":"0.0001"},0.0179,0.01,5,{"v":0.0211841390548614,"d":"0.021"},{"v":347.81,"d":"348"},0.0122,0.0194,{"v":0,"d":"0.0000"},0.0095,71.01,{"v":75,"d":"75.0"},49.75]
[null,"EXB035.A4002.SG1.1","UDG",1433192,551779,273101,49.495,122148,11178,4312,6866,22.137,2.026,1.628,0.0002,0.0166,0.01,8,{"v":0.0347637153720803,"d":"0.035"},{"v":228.41,"d":"228"},0.0049,0.0044,{"v":1.4E-3,"d":"0.0014"},0.0007,68.71,{"v":72,"d":"72.0"},45.04]
[null,"LIB035.A0138.SG1.1","non-UDG",2555718,992871,325166,32.75,282467,2503,1820,683,{"v":28.45,"d":"28.450"},0.252,3.665,{"v":0,"d":"0.0000"},0.0174,{"v":0,"d":"0.00"},0,{"v":0,"d":"0.000"},0,0.0338,0.0401,{"v":0,"d":"0.0000"},{"v":0.012,"d":"0.0120"},63.01,{"v":70,"d":"70.0"},65.03]
[null,"LIB035.A0139.SG1.1","non-UDG",2624356,1011126,319251,31.574,289647,2892,2147,745,28.646,0.286,3.882,{"v":0,"d":"0.0000"},0.0166,{"v":0,"d":"0.00"},0,{"v":0,"d":"0.000"},0,{"v":0.043,"d":"0.0430"},0.0387,0.0377,0.0204,61.26,{"v":67,"d":"67.0"},63.07]
[null,"LIB035.A0144.SG1.1","UDG",1240598,407734,69908,17.145,153476,3427,1605,1822,37.641,{"v":0.84,"d":"0.840"},1.881,{"v":0,"d":"0.0000"},0.0137,{"v":0,"d":"0.00"},1,{"v":0.00410404973142615,"d":"0.004"},{"v":104.39,"d":"104"},0.0259,0.0216,{"v":0,"d":"0.0000"},0.0061,66.81,{"v":70,"d":"70.0"},47.96]
[null,"LIB035.A0145.SG1.1","UDG",846752,311663,69838,22.408,113098,7948,3409,4539,36.289,{"v":2.55,"d":"2.550"},1.751,{"v":1E-4,"d":"0.0001"},0.0147,0.01,1,{"v":0.00458687911159394,"d":"0.005"},{"v":44.4,"d":"44"},0.0131,0.0068,0.0099,{"v":3.3E-3,"d":"0.0033"},70.48,{"v":73,"d":"73.0"},45.92]

{"sheet":"Supplementary Table 7","index":6,"n_rows":19,"n_cols":24,"rows_kept":19,"merged":[[3,0,10,0],[11,0,18,0]]}
["Table S7 - Shotgun Mapping of Libraries from the second tooth to Y. pestis CO92 in EAGER"]
[]
["Sample Type","Sample ID","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.SG1.1","non-UDG",12853927,12683203,"N/A","N/A",8027,6824,852,5972,0.063,0.054,1.143,0.0744,0.2752,7.11,0.1439,0.0657,0.1556,0.0757,57.99,{"v":58,"d":"58.0"},48.28]
[null,"AGU007.B0102.SG1.1","UDG",14325984,14139405,"N/A","N/A",8069,6989,595,6394,0.057,0.049,1.093,0.0792,0.2835,7.55,0.0096,0.0074,0.0006,0.0007,57.64,{"v":57,"d":"57.0"},48.87]
[null,"AGU010.B0101.SG1.1","non-UDG",11676387,11481364,"N/A","N/A",4840,3004,309,2695,0.042,0.026,1.115,0.0307,0.1778,2.99,0.1248,0.0569,0.1053,0.0557,52.96,{"v":51,"d":"51.0"},46.99]
[null,"AGU010.B0102.SG1.1","UDG",12934357,12790224,"N/A","N/A",3391,2423,229,2194,0.027,0.019,1.104,0.0255,0.1607,{"v":2.5,"d":"2.50"},{"v":4.3E-3,"d":"0.0043"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":54,"d":"54.00"},{"v":53,"d":"53.0"},47.14]
[null,"AGU020.B0101.SG1.1","non-UDG",13368330,13086050,"N/A","N/A",1538,61,7,54,0.012,{"v":0,"d":"0.000"},{"v":1.13,"d":"1.130"},0.0005,0.0363,0.04,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.0526,0.0833,43.54,39.5,55.83]
[null,"AGU020.B0102.SG1.1","UDG",13323315,13011915,"N/A","N/A",796,24,2,22,0.006,{"v":0,"d":"0.000"},1.091,0.0002,0.0281,0.01,{"v":0,"d":"0.0000"},{"v":0.2,"d":"0.2000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},46.95,46.5,59.54]
[null,"AGU025.B0101.SG1.1","non-UDG",12215744,12066446,"N/A","N/A",1885,753,72,681,0.016,0.006,1.106,{"v":8.6E-3,"d":"0.0086"},0.0938,0.85,0.1227,0.0488,0.1224,0.0533,58.78,{"v":60,"d":"60.0"},46.85]
[null,"AGU025.B0102.SG1.1","UDG",13261592,13073620,"N/A","N/A",1610,925,77,848,0.012,0.007,1.091,0.0106,0.1037,1.05,0.0249,0.0049,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},58.28,{"v":58,"d":"58.0"},47.62]
["Blank","EXB035.A3901.SG1.1","non-UDG",2259404,890713,281980,31.658,42,8,3,5,0.005,{"v":1E-3,"d":"0.001"},{"v":1.6,"d":"1.600"},{"v":1E-4,"d":"0.0001"},0.0075,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":52.6,"d":"52.60"},{"v":57,"d":"57.0"},48.67]
[null,"EXB035.A3902.SG1.1","UDG",1167984,385973,136304,35.314,78,22,11,11,{"v":0.02,"d":"0.020"},0.006,{"v":2,"d":"2.000"},{"v":1E-4,"d":"0.0001"},0.0108,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.27,{"v":42,"d":"42.0"},49.08]
[null,"EXB035.A4001.SG1.1","non-UDG",2320538,843079,280527,33.274,59,7,3,4,0.007,{"v":1E-3,"d":"0.001"},{"v":1.75,"d":"1.750"},{"v":0,"d":"0.0000"},{"v":6.3E-3,"d":"0.0063"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":47,"d":"47.00"},37.5,39.57]
[null,"EXB035.A4002.SG1.1","UDG",1433192,551779,273101,49.495,139,21,10,11,0.025,0.004,1.909,{"v":1E-4,"d":"0.0001"},0.0108,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},49.36,{"v":36,"d":"36.0"},55.25]
[null,"LIB035.A0138.SG1.1","non-UDG",2555718,992871,325166,32.75,35,5,3,2,0.004,{"v":1E-3,"d":"0.001"},{"v":2.5,"d":"2.500"},{"v":0,"d":"0.0000"},{"v":4.3E-3,"d":"0.0043"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":43,"d":"43.00"},{"v":43,"d":"43.0"},34.88]
[null,"LIB035.A0139.SG1.1","non-UDG",2624356,1011126,319251,31.574,35,4,2,2,0.003,{"v":0,"d":"0.000"},{"v":2,"d":"2.000"},{"v":0,"d":"0.0000"},{"v":0.004,"d":"0.0040"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":37,"d":"37.00"},{"v":37,"d":"37.0"},43.24]
[null,"LIB035.A0144.SG1.1","UDG",1240598,407734,69908,17.145,53,10,4,6,0.013,{"v":2E-3,"d":"0.002"},1.667,{"v":1E-4,"d":"0.0001"},0.0087,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":58.5,"d":"58.50"},{"v":56,"d":"56.0"},51]
[null,"LIB035.A0145.SG1.1","UDG",846752,311663,69838,22.408,64,20,13,7,0.021,0.006,2.857,{"v":1E-4,"d":"0.0001"},{"v":0.009,"d":"0.0090"},0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},53.86,{"v":51,"d":"51.0"},50.4]

{"sheet":"Supplementary Table 8","index":7,"n_rows":21,"n_cols":28,"rows_kept":21,"merged":[[3,0,11,0],[12,0,19,0]]}
["Table S8 - Mapping capture products of libraries from the second tooth to Y. pestis CO92 in EAGER"]
[]
["Source","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.YP1.2","non-UDG",20901682,10866805,9851118,90.653,4296670,3935478,2231051,1704427,39.539,36.216,2.309,26.8114,12.7978,95.04,94.54,94.1,93.68,93.22,0.1448,0.0696,0.1519,{"v":0.073,"d":"0.0730"},73.21,{"v":71,"d":"71.0"},{"v":48.4,"d":"48.40"}]
[null,"AGU007.B0102.YP1.2","UDG",23998414,12421542,11380294,91.617,4981046,4636358,2291663,2344695,{"v":40.1,"d":"40.100"},37.325,1.977,38.0124,18.2057,95.08,94.67,94.32,94.01,93.67,0.0025,0.0006,{"v":2.3E-3,"d":"0.0023"},0.0004,75.45,{"v":74,"d":"74.0"},48.88]
[null,"AGU010.B0101.YP1.2","non-UDG",24499218,12649825,11587266,91.6,4249212,3818186,2847862,970324,33.591,30.184,3.935,{"v":12.516,"d":"12.5160"},6.5899,94.53,93.66,92.57,91.11,89.08,0.1079,0.0531,0.1108,0.0539,60.03,{"v":57,"d":"57.0"},47.41]
[null,"AGU010.B0102.YP1.2","UDG",24725162,12914715,11607635,89.879,3619969,3286859,1806578,1480281,{"v":28.03,"d":"28.030"},{"v":25.45,"d":"25.450"},{"v":2.22,"d":"2.220"},20.7597,10.8568,94.72,94.11,93.51,92.81,92,{"v":1.9E-3,"d":"0.0019"},0.0006,{"v":2E-3,"d":"0.0020"},0.0005,65.26,{"v":63,"d":"63.0"},47.88]
[null,"AGU020.A0102*","UDG",14397991,14397991,"N/A","N/A",700706,367280,235021,132259,4.867,2.551,2.777,1.6823,2.3468,70.96,43.75,23.66,11.66,5.49,{"v":2.8E-3,"d":"0.0028"},0.0024,0.0021,{"v":1.8E-3,"d":"0.0018"},{"v":59.2,"d":"59.20"},{"v":56,"d":"56.0"},48.33]
[null,"AGU020.B0101.YP1.2","non-UDG",19136670,10069794,8763386,87.026,134647,19546,15568,3978,1.337,0.194,4.914,0.0411,0.3853,3.52,0.16,0.06,0.04,0.04,0.1151,0.0506,0.0913,0.0327,48.04,{"v":45,"d":"45.0"},49.12]
[null,"AGU020.B0102.YP1.2","UDG",19925684,10564534,9026546,85.442,142409,17942,9707,8235,1.348,{"v":0.17,"d":"0.170"},2.179,0.0881,0.5205,7.59,0.52,0.09,0.06,0.05,0.0065,0.0078,{"v":0.005,"d":"0.0050"},0.0051,49.77,{"v":47,"d":"47.0"},48.74]
[null,"AGU025.B0101.YP1.2","non-UDG",19964532,11086218,8693279,78.415,2865593,2570320,2304033,266287,25.848,23.185,9.652,4.1658,2.4712,92.54,85.97,74.3,58.8,42.26,0.0891,0.0423,0.1079,0.0529,{"v":72.8,"d":"72.80"},{"v":76,"d":"76.0"},47.29]
[null,"AGU025.B0102.YP1.2","UDG",23621324,13043931,10325228,79.157,3541500,3253735,2403961,849774,27.151,24.944,3.829,14.3636,6.2117,{"v":94.9,"d":"94.90"},94.28,93.65,92.96,92.14,{"v":1.5E-3,"d":"0.0015"},0.0005,{"v":1.8E-3,"d":"0.0018"},0.0005,78.66,{"v":76,"d":"76.0"},47.76]
["Blank","EXB035.A3901.YP1.1","non-UDG",1741416,964085,587730,60.962,22797,6132,6120,12,2.365,0.636,{"v":511,"d":"511.000"},0.0002,0.0138,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},60.92,60.5,53.42]
[null,"EXB035.A3902.YP1.1","UDG",1548816,842285,486063,57.708,34406,9636,9620,16,4.085,1.144,{"v":602.25,"d":"602.250"},0.0002,0.0151,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},66.38,66.5,52.97]
[null,"EXB035.A4001.YP1.1","non-UDG",3388494,1923672,1113235,57.87,17989,4935,4925,10,0.935,0.257,{"v":493.5,"d":"493.500"},{"v":1E-4,"d":"0.0001"},0.0113,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":59.6,"d":"59.60"},50.5,51.51]
[null,"EXB035.A4002.YP1.1","UDG",3623442,1906910,1313399,68.876,33530,5958,5934,24,1.758,0.312,{"v":248.25,"d":"248.250"},0.0003,0.0169,0.03,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":53.5,"d":"53.50"},50.5,52.34]
[null,"LIB035.A0138.YP1.1","non-UDG",655976,359968,211718,58.816,10324,38,30,8,2.868,0.011,{"v":4.75,"d":"4.750"},{"v":1E-4,"d":"0.0001"},0.0105,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},56.63,53.5,47.79]
[null,"LIB035.A0139.YP1.1","non-UDG",645770,338907,218999,64.619,8367,3,0,3,2.469,{"v":1E-3,"d":"0.001"},{"v":1,"d":"1.000"},{"v":0,"d":"0.0000"},0.0052,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},{"v":42,"d":"42.00"},{"v":46,"d":"46.0"},50.79]
[null,"LIB035.A0144.YP1.1","UDG",1348848,693031,345638,49.873,24496,2155,2142,13,3.535,0.311,165.769,0.0002,0.0131,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":62,"d":"62.00"},{"v":73,"d":"73.0"},51.62]
[null,"LIB035.A0145.YP1.1","UDG",1210120,614053,387818,63.157,39229,20743,20724,19,6.389,3.378,1091.737,0.0002,0.0177,0.02,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},61.21,{"v":52,"d":"52.0"},{"v":53.7,"d":"53.70"}]
["*merged data of two sequencing efforts from one UDG library"]

{"sheet":"Supplementary Table 9","index":8,"n_rows":19,"n_cols":28,"rows_kept":19,"merged":[[3,0,9,0],[10,0,17,0]]}
["Table S9 - Mapping of capture products for libraries from the second tooth to Y. pestis pMT1 plasmid in EAGER"]
[]
["Sample Type","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.YP1.2","non-UDG",20901682,10866805,9851118,90.653,293210,183485,123059,60426,2.698,1.688,3.037,47.0292,{"v":25.914,"d":"25.9140"},96.32,96.18,96.11,96.01,95.92,{"v":0.146,"d":"0.1460"},0.0718,0.1568,{"v":0.076,"d":"0.0760"},74.88,{"v":73,"d":"73.0"},50.38]
[null,"AGU007.B0102.YP1.2","UDG",23998414,12421542,11380294,91.617,349448,218366,139261,79105,2.813,1.758,{"v":2.76,"d":"2.760"},63.7513,30.2758,96.32,96.27,96.23,96.19,96.13,{"v":2.8E-3,"d":"0.0028"},0.0009,{"v":0.003,"d":"0.0030"},0.0004,77.54,{"v":76,"d":"76.0"},50.88]
[null,"AGU010.B0101.YP1.2","non-UDG",24499218,12649825,11587266,91.6,314028,175933,140861,35072,2.482,1.391,5.016,22.3887,17.9898,96.17,96,95.85,95.47,95.04,0.1073,0.0528,0.1122,0.0582,61.42,{"v":58,"d":"58.0"},49.45]
[null,"AGU010.B0102.YP1.2","UDG",24725162,12914715,11607635,89.879,277122,156256,105006,51250,2.146,{"v":1.21,"d":"1.210"},3.049,35.6534,22.6921,96.19,96.07,95.95,95.77,95.53,0.0024,{"v":1.8E-3,"d":"0.0018"},0.0026,0.0005,66.93,{"v":64,"d":"64.0"},{"v":50,"d":"50.00"}]
[null,"AGU020.A0102*","UDG",14397991,14397991,"N/A","N/A",46236,28728,22444,6284,0.321,0.2,4.572,4.0249,9.8084,85.02,66.73,47.39,32.44,20.84,0.0057,0.0021,0.0025,0.0029,61.62,{"v":58,"d":"58.0"},50.69]
[null,"AGU025.B0101.YP1.2","non-UDG",19964532,11086218,8693279,78.415,194135,104196,94339,9857,1.751,{"v":0.94,"d":"0.940"},10.571,7.5767,11.6726,95.58,93.76,89.14,81.15,70.1,0.0953,0.0426,0.0994,0.0611,73.95,{"v":76,"d":"76.0"},48.77]
[null,"AGU025.B0102.YP1.2","UDG",23621324,13043931,10325228,79.157,237686,132236,104432,27804,1.822,1.014,4.756,23.1856,20.4015,96.33,96.24,96.08,95.9,95.63,0.0017,{"v":1E-3,"d":"0.0010"},{"v":2.3E-3,"d":"0.0023"},{"v":1E-3,"d":"0.0010"},80.23,{"v":76,"d":"76.0"},49.58]
["Blank","EXB035.A3901.YP1.1","non-UDG",1741416,964085,587730,60.962,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},0,0]
[null,"EXB035.A3902.YP1.1","UDG",1548816,842285,486063,57.708,132,120,117,3,0.016,0.014,{"v":40,"d":"40.000"},0.0025,0.0496,0.25,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":79,"d":"79.00"},76,52.32]
[null,"EXB035.A4001.YP1.1","non-UDG",3388494,1923672,1113235,57.87,3,0,0,3,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},0.0025,0.0496,0.25,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":79,"d":"79.00"},76,52.74]
[null,"EXB035.A4002.YP1.1","UDG",3623442,1906910,1313399,68.876,132,129,126,3,0.007,0.007,{"v":43,"d":"43.000"},0.0025,0.0496,0.25,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":79,"d":"79.00"},76,52.74]
[null,"LIB035.A0138.YP1.1","non-UDG",655976,359968,211718,58.816,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},0,0]
[null,"LIB035.A0139.YP1.1","non-UDG",645770,338907,218999,64.619,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},0,0]
[null,"LIB035.A0144.YP1.1","UDG",1348848,693031,345638,49.873,260,254,251,3,0.038,0.037,84.667,{"v":1.9E-3,"d":"0.0019"},0.0436,0.19,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":61,"d":"61.00"},76,56.28]
[null,"LIB035.A0145.YP1.1","UDG",1210120,614053,387818,63.157,332,331,327,4,0.054,0.054,{"v":82.75,"d":"82.750"},0.0031,0.0554,0.31,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":74,"d":"74.00"},76,53.38]
["*merged UDG library data"]

{"sheet":"Supplementary Table 10","index":9,"n_rows":19,"n_cols":28,"rows_kept":19,"merged":[[3,0,9,0],[10,0,17,0]]}
["Table S10 - Mapping of capture products of libraries for the second tooth to Y. pestis pCD1 plasmid in EAGER"]
[]
["Sample Type","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.YP1.2","non-UDG",20901682,10866805,9851118,90.653,272424,252887,197477,55410,2.507,2.327,4.564,62.8254,36.9519,97.66,97.2,96.79,96.46,96.07,0.1503,{"v":0.076,"d":"0.0760"},0.1582,0.0767,79.71,{"v":76,"d":"76.0"},46.36]
[null,"AGU007.B0102.YP1.2","UDG",23998414,12421542,11380294,91.617,325482,309312,240371,68941,{"v":2.62,"d":"2.620"},{"v":2.49,"d":"2.490"},4.487,80.9008,41.9058,97.53,97.19,96.84,96.54,96.29,{"v":0.003,"d":"0.0030"},0.0005,{"v":2E-3,"d":"0.0020"},0.0002,{"v":82.5,"d":"82.50"},{"v":79,"d":"79.0"},{"v":46.8,"d":"46.80"}]
[null,"AGU010.B0101.YP1.2","non-UDG",24499218,12649825,11587266,91.6,300882,280105,243595,36510,2.379,2.214,7.672,33.5887,{"v":26.578,"d":"26.5780"},96.57,95.67,95.01,94.46,93.91,0.1099,0.0585,0.1159,0.0568,64.68,{"v":61,"d":"61.0"},45.78]
[null,"AGU010.B0102.YP1.2","UDG",24725162,12914715,11607635,89.879,259588,247273,197068,50205,{"v":2.01,"d":"2.010"},1.915,4.925,50.2608,32.1633,97.05,96.38,95.82,95.11,94.58,{"v":1.9E-3,"d":"0.0019"},0.0005,{"v":1.9E-3,"d":"0.0019"},0.0006,70.38,{"v":68,"d":"68.0"},46.17]
[null,"AGU020.A0102*","UDG",14397991,14397991,"N/A","N/A",28985,27231,20248,6983,0.201,0.189,3.9,6.0776,12.8783,86.99,75.54,63.01,51.16,39.1,0.0011,{"v":1.4E-3,"d":"0.0014"},0.0006,0.0007,61.19,{"v":58,"d":"58.0"},48.44]
[null,"AGU025.B0101.YP1.2","non-UDG",19964532,11086218,8693279,78.415,190265,179005,166310,12695,1.716,1.615,{"v":14.1,"d":"14.100"},13.8301,20.1825,96.45,94.83,93.28,91.82,89.46,0.0907,0.0433,0.1068,0.0532,76.59,{"v":76,"d":"76.0"},46.28]
[null,"AGU025.B0102.YP1.2","UDG",23621324,13043931,10325228,79.157,233252,224131,191722,32409,1.788,1.718,6.916,38.6146,30.9933,97.25,96.52,96.22,95.74,95.11,{"v":2.3E-3,"d":"0.0023"},0.0007,0.0016,0.0007,83.77,{"v":76,"d":"76.0"},46.25]
["Blank","EXB035.A3901.YP1.1","non-UDG",1741416,964085,587730,60.962,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A3902.YP1.1","UDG",1548816,842285,486063,57.708,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A4001.YP1.1","non-UDG",3388494,1923672,1113235,57.87,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A4002.YP1.1","UDG",3623442,1906910,1313399,68.876,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0138.YP1.1","non-UDG",655976,359968,211718,58.816,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0139.YP1.1","non-UDG",645770,338907,218999,64.619,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0144.YP1.1","UDG",1348848,693031,345638,49.873,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0145.YP1.1","UDG",1210120,614053,387818,63.157,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
["*merged UDG library data"]

{"sheet":"Supplementary Table 11","index":10,"n_rows":57,"n_cols":23,"rows_kept":57,"merged":[[3,0,35,0],[36,0,56,0]]}
["Table S11 - Shotgun Mapping of Libraries from the first tooth to Nichols NC_021490.2 in EAGER"]
[]
["Sample Type","Sample ID","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
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[null,"LIB035.A0110.SG1.1",3050928,893276,198521,22.224,43,0,0,0,0.005,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0111.SG1.1",2477328,668331,115057,17.216,9,0,0,0,{"v":1E-3,"d":"0.001"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0112.SG1.1",2176626,584509,127865,21.876,6,0,0,0,{"v":1E-3,"d":"0.001"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0115.SG1.1",1801938,424950,86739,20.412,18,0,0,0,0.004,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0116.SG1.1",42114,11389,2935,25.77,0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0130.SG1.1",2017266,902083,201810,22.372,33,2,1,1,0.004,{"v":0,"d":"0.000"},{"v":2,"d":"2.000"},{"v":0,"d":"0.0000"},0.0052,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":31,"d":"31.00"},{"v":31,"d":"31.0"},61.29]
[null,"LIB035.A0131.SG1.1",2625802,1144135,413828,36.17,46,0,0,0,0.004,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]

{"sheet":"Supplementary Table 12","index":11,"n_rows":13,"n_cols":28,"rows_kept":13,"merged":[[3,0,4,0],[5,0,12,0]]}
["Table S12 - Mapping of T. pallidum capture products of AGU007 (first tooth only) to Nichols NC_021490.2 in EAGER"]
[]
["Sample Type","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.A0101.TP2.1","nonUDG",47202724,25079309,21748234,86.718,1052023,775407,743525,31882,4.195,3.092,24.321,1.7751,1.4696,80.24,51.68,26.88,11.75,4.42,0.1592,0.0899,0.1758,0.0961,63.45,{"v":59,"d":"59.0"},52.56]
[null,"AGU007.A0102.TP2.1","UDG",41012302,21895713,18522599,84.595,926076,744375,617823,126552,4.23,3.4,5.882,6.6661,3.086,97.43,96.09,92.64,86.13,76.1,0.0024,0.0011,0.0016,0.0008,60.03,{"v":55,"d":"55.0"},53.13]
["Blank","EXB035.A0101.TP1.1","nonUDG",930508,595091,"N/A","N/A",3426,0,0,0,0.576,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A0102.TP1.1","UDG",2749182,2328482,"N/A","N/A",17822,870,866,4,0.765,0.037,{"v":217.5,"d":"217.500"},1E-4,0.0133,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},35.75,{"v":36,"d":"36.0"},60.99]
[null,"EXB035.A0201.TP1.1","nonUDG",1767841,1166620,"N/A","N/A",6789,1312,1309,3,0.582,0.112,437.333,1E-4,0.0121,0.01,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},35.33,{"v":35,"d":"35.0"},61.54]
[null,"EXB035.A0202.TP1.1","UDG",3283023,2864145,"N/A","N/A",12509,1,0,1,0.437,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},0,0.0052,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":31,"d":"31.00"},{"v":31,"d":"31.0"},58.06]
[null,"LIB035.A0109.TP1.1","nonUDG",839407,516407,"N/A","N/A",4138,0,0,0,0.801,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0110.TP1.1","nonUDG",1258281,815852,"N/A","N/A",12004,0,0,0,1.471,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0130.TP1.1","UDG",1127832,880609,"N/A","N/A",8386,186,185,1,0.952,0.021,{"v":186,"d":"186.000"},0,0.0052,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":32,"d":"32.00"},{"v":32,"d":"32.0"},61.29]
[null,"LIB035.A0131.TP1.1","UDG",2015389,1609007,"N/A","N/A",0,0,0,0,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]

{"sheet":"Supplementary Table 13","index":12,"n_rows":19,"n_cols":24,"rows_kept":19,"merged":[[3,0,10,0],[11,0,18,0]]}
["Table S13 - Shotgun Mapping of Libraries from the second tooth to Nichols NC_021490.2 in EAGER"]
[]
["Sample Type","Sample ID","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.SG1.1","non-UDG",12853927,12683203,"N/A","N/A",445,194,21,173,0.004,{"v":2E-3,"d":"0.002"},1.121,0.0093,0.0979,0.92,0.1636,{"v":0.04,"d":"0.0400"},0.1132,0.1321,61.42,{"v":66,"d":"66.0"},53.41]
[null,"AGU007.B0102.SG1.1","UDG",14325984,14139405,"N/A","N/A",330,193,12,181,{"v":2E-3,"d":"0.002"},{"v":1E-3,"d":"0.001"},1.066,0.0097,0.0993,0.96,{"v":0,"d":"0.0000"},0.0189,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},61.36,{"v":64,"d":"64.0"},53.75]
[null,"AGU010.B0101.SG1.1","non-UDG",11676387,11481364,"N/A","N/A",697,13,1,12,0.006,{"v":0,"d":"0.000"},1.083,0.0004,{"v":0.027,"d":"0.0270"},0.02,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},35.67,{"v":33,"d":"33.0"},59.58]
[null,"AGU010.B0102.SG1.1","UDG",12934357,12790224,"N/A","N/A",248,3,2,1,{"v":2E-3,"d":"0.002"},{"v":0,"d":"0.000"},{"v":3,"d":"3.000"},{"v":0,"d":"0.0000"},0.0054,{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":33,"d":"33.00"},{"v":33,"d":"33.0"},51.52]
[null,"AGU020.B0101.SG1.1","non-UDG",13368330,13086050,"N/A","N/A",514,12,0,12,0.004,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},0.0004,0.0321,0.02,{"v":0,"d":"0.0000"},{"v":0.5,"d":"0.5000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},36.75,36.5,59.55]
[null,"AGU020.B0102.SG1.1","UDG",13323315,13011915,"N/A","N/A",261,4,0,4,{"v":2E-3,"d":"0.002"},{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":1E-4,"d":"0.0001"},{"v":0.013,"d":"0.0130"},0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},0.3333,{"v":0,"d":"0.0000"},{"v":32.5,"d":"32.50"},{"v":33,"d":"33.0"},60]
[null,"AGU025.B0101.SG1.1","non-UDG",12215744,12066446,"N/A","N/A",453,11,1,10,0.004,{"v":0,"d":"0.000"},{"v":1.1,"d":"1.100"},0.0003,0.0205,0.03,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":35.2,"d":"35.20"},35.5,61.36]
[null,"AGU025.B0102.SG1.1","UDG",13261592,13073620,"N/A","N/A",221,3,0,3,{"v":2E-3,"d":"0.002"},{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},{"v":1E-4,"d":"0.0001"},0.0095,0.01,{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},34.33,{"v":34,"d":"34.0"},60.19]
["Blank","EXB035.A3901.SG1.1","non-UDG",2259404,890713,281980,31.658,6,0,0,0,{"v":1E-3,"d":"0.001"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"EXB035.A3902.SG1.1","UDG",1167984,385973,136304,35.314,9,0,0,0,{"v":2E-3,"d":"0.002"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"EXB035.A4001.SG1.1","non-UDG",2320538,843079,280527,33.274,30,0,0,0,0.004,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"EXB035.A4002.SG1.1","UDG",1433192,551779,273101,49.495,32,0,0,0,0.006,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"LIB035.A0138.SG1.1","non-UDG",2555718,992871,325166,32.75,6,0,0,0,{"v":1E-3,"d":"0.001"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"LIB035.A0139.SG1.1","non-UDG",2624356,1011126,319251,31.574,11,0,0,0,{"v":1E-3,"d":"0.001"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"LIB035.A0144.SG1.1","UDG",1240598,407734,69908,17.145,17,0,0,0,0.004,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]
[null,"LIB035.A0145.SG1.1","UDG",846752,311663,69838,22.408,13,0,0,0,0.004,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},0]

{"sheet":"Supplementary Table 14","index":13,"n_rows":13,"n_cols":28,"rows_kept":13,"merged":[[3,0,4,0],[5,0,12,0]]}
["Table S14 - Mapping of T. pallidum capture products from libraries from the second tooth to Nichols NC_021490.2 in EAGER"]
[]
["Source","Sample Name","Library Type","# of raw reads ","# of reads after Clip & Merge prior to mapping","# of merged reads","% merged reads","# mapped reads prior to duplicate removal","# quality filtered mapped reads prior to duplicate removal","# of duplicates removed","Mapped reads after duplicate removal","Endogenous DNA (%)","Quality filtered endogenous DNA (%)","Cluster factor","Mean coverage","Standard deviation in coverage","Coverage >= 1X (%)","Coverage >= 2X (%)","Coverage >= 3X (%)","Coverage >= 4X (%)","Coverage >= 5X (%)","% damage of first 3-prime base","% damage of second 3-prime base","% damage of first 5-prime base","% damage of second 5-prime base","Average fragment length","Median fragment length","GC content (%)"]
["Tooth","AGU007.B0101.YP1.1","non-UDG",46614028,24931617,21199812,85.032,2147243,1903634,1757236,146398,8.613,7.635,13.003,9.3116,3.6836,{"v":97.7,"d":"97.70"},97.37,96.68,95.17,92.13,0.1251,0.0681,0.1452,0.0783,72.49,{"v":76,"d":"76.0"},52.71]
[null,"AGU007.B0102.YP1.1","UDG",45771712,24333697,21016531,86.368,2081210,1969907,1639402,330505,8.553,8.095,{"v":5.96,"d":"5.960"},21.3584,6.3869,97.86,97.75,97.69,97.62,97.56,{"v":2.3E-3,"d":"0.0023"},0.0012,0.0024,0.0009,73.65,{"v":76,"d":"76.0"},53.21]
["Blank","EXB035.A3901.TP1.1","non-UDG",2040770,1112629,667594,60.001,21561,162,161,1,1.938,0.015,{"v":162,"d":"162.000"},0,{"v":0.005,"d":"0.0050"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":29,"d":"29.00"},{"v":29,"d":"29.0"},62.07]
[null,"EXB035.A3902.TP1.1","UDG",1005988,498104,364298,73.137,3341,0,0,0,0.671,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A4001.TP1.1","non-UDG",2573024,1351031,917107,67.882,35013,0,0,0,2.592,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"EXB035.A4002.TP1.1","UDG",2453350,1236805,940387,76.034,25638,0,0,0,2.073,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0138.TP1.1","non-UDG",1911852,1042405,626893,60.139,6094,0,0,0,0.585,{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0139.TP1.1","non-UDG",1465736,774816,440647,56.871,14031,3,2,1,1.811,{"v":0,"d":"0.000"},{"v":3,"d":"3.000"},0,0.0054,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":34,"d":"34.00"},{"v":34,"d":"34.0"},42.42]
[null,"LIB035.A0144.TP1.1","UDG",1037642,521307,299310,57.415,29504,0,0,0,{"v":5.66,"d":"5.660"},{"v":0,"d":"0.000"},{"v":0,"d":"0.000"},0,{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0"},{"v":0,"d":"0.00"}]
[null,"LIB035.A0145.TP1.1","UDG",775740,397020,245501,61.836,6382,1,0,1,1.607,{"v":0,"d":"0.000"},{"v":1,"d":"1.000"},0,0.0057,{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.00"},{"v":0,"d":"0.0000"},{"v":0,"d":"0.0000"},{"v":1,"d":"1.0000"},{"v":0,"d":"0.0000"},{"v":37,"d":"37.00"},{"v":37,"d":"37.0"},62.16]

{"sheet":"Supplementary Table 15","index":14,"n_rows":275,"n_cols":2,"rows_kept":275}
["Table S15- Yersinia pestis genomes used for phylogenetic analysis"]
["Genome","Source (Publication / NCBI accession)"]
["STN021.A0101                          ","Spyrou et al. 2019"]
["STN020.A0101                          ","Spyrou et al. 2019"]
["STN019.A0101                          ","Spyrou et al. 2019"]
["STN014.A0101                          ","Spyrou et al. 2019"]
["STN013.A0101                          ","Spyrou et al. 2019"]
["STN008.A0101                          ","Spyrou et al. 2019"]
["STN007.A0101                          ","Spyrou et al. 2019"]
["STN002.A0101                          ","Spyrou et al. 2019"]
["STA001.A0101                          ","Spyrou et al. 2019"]
["RT5                                   ","Spyrou et al. 2018"]
["RISE509                               ","Rasmussen et al. 2015"]
["RISE505                               ","Rasmussen et al. 2015"]
["OBS137                                ","Bos et al. 2016"]
["OBS124                                ","Bos et al. 2016"]
["OBS116                                ","Bos et al. 2016"]
["OBS110                                ","Bos et al. 2016"]
["OBS107                                ","Bos et al. 2016"]
["NMS002.A0101                          ","Spyrou et al. 2019"]
["NAB003.B0101                          ","Spyrou et al. 2019"]
["MAN008.B0101                          ","Spyrou et al. 2019"]
["London St. Mary Graces 6330              ","Bos et al. 2011"]
["London EastSmithfield 8124/8291/11972 (n=3)","Bos et al. 2011"]
["LBG002.A0101                          ","Spyrou et al. 2019"]
["LAI009.A0101                          ","Spyrou et al. 2019"]
["ELW098.A0101                           ","Spyrou et al. 2016; Spyrou et al. 2019"]
["DA101                                 ","Damgaard et al. 2018"]
["BRA001.A0101                          ","Spyrou et al. 2019"]
["Bolgar 2370                             ","Spyrou et al. 2016"]
["Ber45                                 ","Namouchi et al. 2018"]
["Ber37                                 ","Namouchi et al. 2018"]
["BED034.A0102                          ","Spyrou et al. 2019"]
["BED030.A0102                          ","Spyrou et al. 2019"]
["BED028.A0102                          ","Spyrou et al. 2019"]
["BED024.A0102                          ","Spyrou et al. 2019"]
["Barcelona 3031                      ","Spyrou et al. 2016"]
["Altenerding_2148                      ","Feldman et al. 2016"]
["AGU025.B0101_02                       ","this study"]
["AGU010.B0101_02                       ","this study"]
["AGU007.B0101_02                       ","this study"]
["4.ANT1a_MGJZ12                        ","Cui et al. 2013"]
["4.ANT_M-1944                          ","Kutyrev et al. 2018"]
["4.ANT_KM932                           ","Kutyrev et al. 2018"]
["4.ANT_517                             ","Kutyrev et al. 2018"]
["4.ANT_338                             ","Kutyrev et al. 2018"]
["4.ANT_1454                            ","Kutyrev et al. 2018"]
["3.ANT2e_MGJZ3                         ","Cui et al. 2013"]
["3.ANT2d_MGJZ11                        ","Cui et al. 2013"]
["3.ANT2c_MGJZ9                         ","Cui et al. 2013"]
["3.ANT2b_MGJZ7                         ","Cui et al. 2013"]
["3.ANT2a_MGJZ6                         ","Cui et al. 2013"]
["3.ANT1d_71021                         ","Cui et al. 2013"]
["3.ANT1c_C1976001                      ","Cui et al. 2013"]
["3.ANT1b_CMCC71001                     ","Cui et al. 2013"]
["3.ANT1a_7b                            ","Cui et al. 2013"]
["2.MED0_C-627                          ","Kutyrev et al. 2018"]
["2.MED1_1045                           ","Zhgenti et al. 2015"]
["2.MED1_1116-D                         ","Kutyrev et al. 2018"]
["2.MED1_1240                           ","Kutyrev et al. 2018"]
["2.MED1_139                            ","Kutyrev et al. 2018"]
["2.MED1_173                            ","Kutyrev et al. 2018"]
["2.MED1_1906                           ","Kutyrev et al. 2018"]
["2.MED1_244                            ","Kutyrev et al. 2018"]
["2.MED1_261                            ","Kutyrev et al. 2018"]
["2.MED1_2944                           ","Zhgenti et al. 2015"]
["2.MED1_44                             ","Kutyrev et al. 2018"]
["2.MED1_A-1763                         ","Kutyrev et al. 2018"]
["2.MED1_A-1809                         ","Eroshenko et al. 2017"]
["2.MED1_A-1825                         ","Kutyrev et al. 2018"]
["2.MED1_A-1920                         ","Kutyrev et al. 2018"]
["2.MED1_C-791                          ","Kutyrev et al. 2018"]
["2.MED1_K1973002                       ","Eppinger et al. 2009"]
["2.MED1_KIM10                          ","Deng et al. 2002"]
["2.MED1_KM816                          ","Kutyrev et al. 2018"]
["2.MED1_KM918                          ","Kutyrev et al. 2018"]
["2.MED1_M-1448                         ","Kutyrev et al. 2018"]
["2.MED1_M-1453                         ","Kutyrev et al. 2018"]
["2.MED1_M-1484                         ","Kutyrev et al. 2018"]
["2.MED1_M-1524                         ","Kutyrev et al. 2018"]
["2.MED1_M-1773                         ","Kutyrev et al. 2018"]
["2.MED1_M-1864                         ","Kutyrev et al. 2018"]
["2.MED1_M-519                          ","Kutyrev et al. 2018"]
["2.MED1_M-549                          ","Kutyrev et al. 2018"]
["2.MED1_M-595                          ","Kutyrev et al. 2018"]
["2.MED1_M-978                          ","Kutyrev et al. 2018"]
["2.MED1b_2506                          ","Cui et al. 2013"]
["2.MED1c_2654                          ","Cui et al. 2013"]
["2.MED1d_2504                          ","Cui et al. 2013"]
["2.MED2b_91                            ","Cui et al. 2013"]
["2.MED2c_K11973002                     ","Cui et al. 2013"]
["2.MED2d_A1973001                      ","Cui et al. 2013"]
["2.MED2e_7338                          ","Cui et al. 2013"]
["2.MED3a_J1963002                      ","Cui et al. 2013"]
["2.MED3b_CMCC125002b                   ","Cui et al. 2013"]
["2.MED3c_I1969003                      ","Cui et al. 2013"]
["2.MED3d_J1978002                      ","Cui et al. 2013"]
["2.MED3f_I1970005                      ","Cui et al. 2013"]
["2.MED3g_CMCC99103                     ","Cui et al. 2013"]
["2.MED3h_CMCC90027                     ","Cui et al. 2013"]
["2.MED3i_CMCC92004                     ","Cui et al. 2013"]
["2.MED3j_I2001001                      ","Cui et al. 2013"]
["2.MED3k_CMCC12003                     ","Cui et al. 2013"]
["2.MED3l_I1994006                      ","Cui et al. 2013"]
["2.MED3m_SHAN11                        ","Cui et al. 2013"]
["2.MED3n_SHAN12                        ","Cui et al. 2013"]
["2.MED3o_I1991001                      ","Cui et al. 2013"]
["2.MED3p_CMCC107004                    ","Cui et al. 2013"]
["2.ANT1_Nepal516                       ","NZ_ACNQ00000000.1"]
["2.ANT1a_34008                         ","Cui et al. 2013"]
["2.ANT1b_34202                         ","Cui et al. 2013"]
["2.ANT2a_2                             ","Cui et al. 2013"]
["2.ANT2b_351001                        ","Cui et al. 2013"]
["2.ANT2c_CMCC347001                    ","Cui et al. 2013"]
["2.ANT2d_G1996006                      ","Cui et al. 2013"]
["2.ANT2e_G1996010                      ","Cui et al. 2013"]
["2.ANT2f_CMCC348002                    ","Cui et al. 2013"]
["2.ANT3_KM682                          ","Kutyrev et al. 2018"]
["2.ANT3a_CMCC92010                     ","Cui et al. 2013"]
["2.ANT3b_CMCC95001                     ","Cui et al. 2013"]
["2.ANT3c_CMCC96001                     ","Cui et al. 2013"]
["2.ANT3d_CMCC96007                     ","Cui et al. 2013"]
["2.ANT3e_CMCC67001                     ","Cui et al. 2013"]
["2.ANT3f_CMCC104003                    ","Cui et al. 2013"]
["2.ANT3g_CMCC51020                     ","Cui et al. 2013"]
["2.ANT3h_CMCC106002                    ","Cui et al. 2013"]
["2.ANT3i_CMCC64001                     ","Cui et al. 2013"]
["2.ANT3j_H1959004                      ","Cui et al. 2013"]
["2.ANT3k_5761                          ","Cui et al. 2013"]
["2.ANT3l_735                           ","Cui et al. 2013"]
["1.ORI1_CA88                           ","Auerbach et al. 2007"]
["1.ORI1_CO92                           ","Parkhill et al. 2001"]
["1.ORI1a_CMCC114001                    ","Cui et al. 2013"]
["1.ORI1b_India195                      ","NZ_ACNR00000000.1"]
["1.ORI1c_F1946001                      ","Cui et al. 2013"]
["1.ORI2_F1991016                       ","Eppinger et al. 2009"]
["1.ORI2a_YN2179                        ","Cui et al. 2013"]
["1.ORI2c_YN2551b                       ","Cui et al. 2013"]
["1.ORI2d_YN2588                        ","Cui et al. 2013"]
["1.ORI2f_CMCC87001                     ","Cui et al. 2013"]
["1.ORI2g_F1984001                      ","Cui et al. 2013"]
["1.ORI2h_YN663                         ","Cui et al. 2013"]
["1.ORI2i_CMCCK100001a                  ","Cui et al. 2013"]
["1.ORI2i_CMCCK110001b                  ","Cui et al. 2013"]
["1.ORI3_IP275                          ","Morelli et al. 2010"]
["1.ORI3_MG05-1020                      ","Morelli et al. 2010"]
["1.ORI3a_EV76                          ","Cui et al. 2013"]
["1.ANT1_Antiqua                        ","Cui et al. 2013"]
["1.ANT1_UG05-0454                      ","Morelli et al. 2010"]
["1.IN1a_CMCC11001                      ","Cui et al. 2013"]
["1.IN1b_780441                         ","Cui et al. 2013"]
["1.IN1c_K21985002                      ","Cui et al. 2013"]
["1.IN2a_CMCC640047                     ","Cui et al. 2013"]
["1.IN2b_30017                          ","Cui et al. 2013"]
["1.IN2c_CMCC31004                      ","Cui et al. 2013"]
["1.IN2d_C1975003                       ","Cui et al. 2013"]
["1.IN2e_C1989001                       ","Cui et al. 2013"]
["1.IN2f_710317                         ","Cui et al. 2013"]
["1.IN2g_CMCC05013                      ","Cui et al. 2013"]
["1.IN2h_5                              ","Cui et al. 2013"]
["1.IN2i_CMCC10012                      ","Cui et al. 2013"]
["1.IN2j_CMCC27002                      ","Cui et al. 2013"]
["1.IN2k_970754                         ","Cui et al. 2013"]
["1.IN2l_D1991004                       ","Cui et al. 2013"]
["1.IN2m_D1964002b                      ","Cui et al. 2013"]
["1.IN2n_CMCC02041                      ","Cui et al. 2013"]
["1.IN2o_CMCC03001                      ","Cui et al. 2013"]
["1.IN2p_D1982001                       ","Cui et al. 2013"]
["1.IN2q_D1964001                       ","Cui et al. 2013"]
["1.IN3a_F1954001                       ","Cui et al. 2013"]
["1.IN3b_E1979001                       ","Cui et al. 2013"]
["1.IN3c_CMCC84038b                     ","Cui et al. 2013"]
["1.IN3d_YN1683                         ","Cui et al. 2013"]
["1.IN3e_YN472                          ","Cui et al. 2013"]
["1.IN3f_YN1065                         ","Cui et al. 2013"]
["1.IN3g_E1977001                       ","Cui et al. 2013"]
["1.IN3h_CMCC84033                      ","Cui et al. 2013"]
["1.IN3i_CMCC84046                      ","Cui et al. 2013"]
["0.PE7b_620024                         ","Cui et al. 2013"]
["0.PE2_1412                            ","Zhgenti et al. 2015"]
["0.PE2_1413                            ","Zhgenti et al. 2015"]
["0.PE2_14735                           ","Zhgenti et al. 2015"]
["0.PE2_1522                            ","Zhgenti et al. 2015"]
["0.PE2_1670                            ","Zhgenti et al. 2015"]
["0.PE2_3067                            ","Zhgenti et al. 2015"]
["0.PE2_3544                            ","Kutyrev et al. 2018"]
["0.PE2_3551                            ","Kutyrev et al. 2018"]
["0.PE2_3770                            ","Zhgenti et al. 2015"]
["0.PE2_835_BPC                         ","Kutyrev et al. 2018"]
["0.PE2_8787                            ","Zhgenti et al. 2015"]
["0.PE2_C-197                           ","Kislichkina et al. 2015"]
["0.PE2_C-235                           ","Kislichkina et al. 2015"]
["0.PE2_C-267                           ","Kislichkina et al. 2015"]
["0.PE2_C-290                           ","Kislichkina et al. 2015"]
["0.PE2_C-291                           ","Kislichkina et al. 2015"]
["0.PE2_C-346                           ","Kislichkina et al. 2015"]
["0.PE2_C-359                           ","Kislichkina et al. 2015"]
["0.PE2_C-370                           ","Kislichkina et al. 2017"]
["0.PE2_C-535                           ","Kislichkina et al. 2017"]
["0.PE2_C-537                           ","Kislichkina et al. 2015"]
["0.PE2_C-590                           ","Kislichkina et al. 2015"]
["0.PE2_C-666                           ","Kislichkina et al. 2015"]
["0.PE2_C-678                           ","Kislichkina et al. 2017"]
["0.PE2_C-700                           ","Kislichkina et al. 2017"]
["0.PE2_C-712                           ","Kislichkina et al. 2017"]
["0.PE2_C-739                           ","Kislichkina et al. 2017"]
["0.PE2_C-741                           ","Kutyrev et al. 2018"]
["0.PE2_C-746                           ","Kislichkina et al. 2017"]
["0.PE2_C-824                           ","Kislichkina et al. 2017"]
["0.PE2_KM874                           ","Kutyrev et al. 2018"]
["0.PE2_M-986                           ","Kutyrev et al. 2018"]
["0.PE2_PEST-F                          ","Garcia et al. 2007"]
["0.PE2b_G8786                          ","Cui et al. 2013"]
["0.PE4_5307-Gis                        ","Kislichkina et al. 2015"]
["0.PE4_A-1804                          ","Kislichkina et al. 2015"]
["0.PE4_A-1807                          ","Kislichkina et al. 2015"]
["0.PE4_A-513                           ","Kislichkina et al. 2015"]
["0.PE4_I-3134                          ","Kislichkina et al. 2015"]
["0.PE4_I-3442                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3443                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3446                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3447                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3455                          ","Kislichkina et al. 2015"]
["0.PE4_I-3515                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3516                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3517                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3518                          ","Kislichkina et al. 2018a"]
["0.PE4_I-3519                          ","Kislichkina et al. 2018a"]
["0.PE4_M0000002                        ","Cui et al. 2013"]
["0.PE4_Microtus91001                   ","Zhou et al. 2004 / NC_005810.1"]
["0.PE4a_B1313                          ","Kutyrev et al. 2018"]
["0.PE4a_I-2751-55                      ","Kutyrev et al. 2018"]
["0.PE4a_I-2998                         ","Kutyrev et al. 2018"]
["0.PE4Aa_12                            ","Cui et al. 2013"]
["0.PE4Ab_9                             ","Cui et al. 2013"]
["0.PE4Ba_PestoidesA                    ","NZ_ACNT00000000"]
["0.PE4Ca_CMCCN010025                   ","Cui et al. 2013"]
["0.PE4Cc_CMCC18019                     ","Cui et al. 2013"]
["0.PE4Cd_CMCC93014                     ","Cui et al. 2013"]
["0.PE4Ce_CMCC91090                     ","Cui et al. 2013"]
["0.PE4h_A-1249                         ","Eroshenko et al. 2017"]
["0.PE4m_I-3086                         ","Kutyrev et al. 2018"]
["0.PE4t_A-1815                         ","Eroshenko et al. 2017"]
["0.PE5_I-2231                          ","Kislichkina et al. 2018b"]
["0.PE5_I-2236                          ","Kislichkina et al. 2018b"]
["0.PE5_I-2238                          ","Kislichkina et al. 2018b"]
["0.PE5_I-2239                          ","Kislichkina et al. 2015"]
["0.PE5_I-2422a                         ","Kislichkina et al. 2015"]
["0.PE5_I-2422b                         ","Kutyrev et al. 2018"]
["0.PE5_I-2457                          ","Kislichkina et al. 2018b"]
["0.PE5_I-3189                          ","Kislichkina et al. 2015"]
["0.PE5_I-3190                          ","Kislichkina et al. 2018b"]
["0.ANT1a_42013                         ","Cui et al. 2013"]
["0.ANT1b_CMCC49003                     ","Cui et al. 2013"]
["0.ANT1c_945                           ","Cui et al. 2013"]
["0.ANT1d_164                           ","Cui et al. 2013"]
["0.ANT1e_CMCC8211                      ","Cui et al. 2013"]
["0.ANT1f_42095                         ","Cui et al. 2013"]
["0.ANT1g_CMCC42007                     ","Cui et al. 2013"]
["0.ANT1h_CMCC43032                     ","Cui et al. 2013"]
["0.ANT2_B42003004                      ","Eppinger et al. 2009"]
["0.ANT2a_2330                          ","Cui et al. 2013"]
["0.ANT3_231                            ","Eroshenko et al. 2017"]
["0.ANT3_790                            ","Zhgenti et al. 2015"]
["0.ANT3_A-1486                         ","Eroshenko et al. 2017"]
["0.ANT3a_CMCC38001                     ","Cui et al. 2013"]
["0.ANT3b_A1956001                      ","Cui et al. 2013"]
["0.ANT3c_42082                         ","Cui et al. 2013"]
["0.ANT3d_CMCC21106                     ","Cui et al. 2013"]
["0.ANT3e_42091b                        ","Cui et al. 2013"]
["0.ANT5_262                            ","Kutyrev et al. 2018"]
["0.ANT5_5M                             ","Kutyrev et al. 2018"]
["0.ANT5_A-1691                         ","Eroshenko et al. 2017"]
["0.ANT5_A-1836                         ","Eroshenko et al. 2017"]
["Y. pseudotuberculosis (IP32953) outgroup                     ","Chain et al. 2004"]

{"sheet":"Supplementary Table 16","index":15,"n_rows":6952,"n_cols":277,"rows_kept":281,"cut":true,"bounds":{"rows_first":125,"rows_last":31,"rows_between":125,"halvings":4}}
["Table S16 - SNP Table of Y. pestis genomes generated by MultivcfAnalyzer"]
[]
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{"sheet":"Supplementary Table 17","index":16,"n_rows":7,"n_cols":256,"rows_kept":7}
["Table S17 - Private Y. pestis SNPs of AGU025 and AGU020"]
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{"sheet":"Supplementary Table 18","index":17,"n_rows":7,"n_cols":10,"rows_kept":7}
["Table S18 - SNP effects for Y. pestis SNPs located on the branch between AGU025 and AGU007 & AGU010 strains"]
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{"sheet":"Supplementary Table 19","index":18,"n_rows":37,"n_cols":7,"rows_kept":37}
["Table S19 - T. pallidum genomes used in phylogenetic analyses"]
[]
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["Table S20 - SNP Table of T. pallidum genomes produced by MultiVCFAnalyzer"]
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["Table S21 - Homoplastic positions removed for Treponema phylogenetic assessment"]
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{"sheet":"Supplementary Table 22","index":21,"n_rows":8,"n_cols":32,"rows_kept":8}
["Table S22 - Positions that distinguish AGU007 from the inferred yaws MRCA"]
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{"sheet":"Supplementary Table 23","index":22,"n_rows":5,"n_cols":9,"rows_kept":5}
["Table S23 - SNP effects for positions that distinguish AGU007 from the inferred yaws MRCA"]
[]
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