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{"sheet":"Performance validation","index":0,"n_rows":47,"n_cols":15,"rows_kept":47,"merged":[[0,3,0,5],[0,6,0,8],[0,9,0,11],[1,3,1,5],[1,6,1,8],[1,9,1,11],[3,1,4,1],[5,1,6,1],[7,1,8,1],[10,1,11,1],[12,1,13,1],[15,1,16,1],[17,3,17,5],[17,6,17,8],[17,9,17,11],[18,3,18,5],[18,6,18,8],[18,9,18,11],[19,3,19,5],[19,6,19,8],[19,9,19,11],[21,1,22,1],[23,1,24,1],[25,1,26,1],[28,1,29,1],[30,1,31,1],[32,3,32,5],[32,6,32,8],[32,9,32,11],[33,3,33,5],[33,6,33,8],[33,9,33,11],[34,3,34,5],[34,6,34,8],[34,9,34,11],[36,1,37,1],[38,1,39,1],[40,1,41,1],[43,1,44,1],[45,1,46,1]],"flags":["formulas_cached_only"]}
[]
[null,"Program","Benchmark","k = 1",null,null,"k = 2",null,null,"k = 3"]
[{"$nulls":3},"TPR","FDR","N","TPR","FDR","N","TPR","FDR","N",null,"Avg. TP","Avg. FP"]
["Q≥90","Sniper (ALL)","Sanger",0.7355,0.0156,"(253|0,4,91/17/50)",0.7878,0.0144,"(271|2,4,71/20/36)",0.7558,0.0114,"(260|1,3,83/22/40)",null,0.7613222222222222,0.014566666666666665]
[null,null,"Sanger \\ NGS",0.9051,{"v":0,"d":"0.0000"},"(229|0,0,24)",0.9684,{"v":0,"d":"0.0000"},"(245|1,0,7)",{"v":0.917,"d":"0.9170"},{"v":0,"d":"0.0000"},"(232|0,0,21)",null,0.9297222222222222,0]
["Q≥90","Sniper (UNI)","Sanger",0.7326,0.0156,"(252|0,4,92/27/45)",0.7733,0.0148,"(266|1,4,77/29/38)",0.7442,0.0153,"(256|1,4,87/32/38) "]
[null,null,"Sanger \\ NGS",0.8972,{"v":0,"d":"0.0000"},"(227|0,0,26)",0.9486,{"v":0,"d":"0.0000"},"(240|0,0,13)",0.9051,{"v":0,"d":"0.0000"},"(229|0,0,24)"]
["Q≥90","Sniper (BEST)","Sanger",0.7384,0.0152,"(254|0,4,90/22/47)",0.7994,0.0143,"(275|1,4,68/20/37)",0.7849,0.0145,"(270|1,4,73/20/36)"]
[null,null,"Sanger \\ NGS",0.9012,{"v":0,"d":"0.0000"},"(228|0,0,25)",0.9763,{"v":0,"d":"0.0000"},"(247|0,0,6)",0.9486,{"v":0,"d":"0.0000"},"(240|0,0,13)"]
[]
["90/60","Maq (UNI)","Sanger",0.7093,{"v":0.012,"d":"0.0120"},"(244|4,3,96)",0.7791,0.0144,"(268|6,4,70)",0.7762,0.0144,"(267|6,4,71)",null,0.7640500000000001,0.013466666666666667]
[null,null,"Sanger \\ NGS",0.8577,{"v":0,"d":"0.0000"},"(217|0,0,36)",0.9328,{"v":0,"d":"0.0000"},"(236|0,0,17)",0.9368,{"v":0,"d":"0.0000"},"(237|0,0,16)",null,0.9143500000000001,0]
["90/60","Maq (BEST)","Sanger",0.7122,{"v":0.012,"d":"0.0120"},"(245|3,3,96)",0.7994,0.0141,"(275|5,4,64)",0.8081,0.0139,"(278|6,4,60)"]
[null,null,"Sanger \\ NGS",0.8458,{"v":0,"d":"0.0000"},"(214|0,0,39)",0.9486,{"v":0,"d":"0.0000"},"(240|0,0,13)",0.9644,{"v":0,"d":"0.0000"},"(244|0,0,9)"]
[]
["-t -u- n","SOAPsnp (BEST)","Sanger",0.8401,0.0136,"(289|2,4,53)",0.8401,0.0136,"(289|2,4,53)",0.8401,0.0136,"(289|2,4,53)",null,0.8401,0.0136]
[null,null,"Sanger \\ NGS",0.9881,{"v":0,"d":"0.0000"},"(250|0,0,3)",0.9881,{"v":0,"d":"0.0000"},"(250|0,0,3)",0.9881,{"v":0,"d":"0.0000"},"(250|0,0,3)",null,0.9881,{"v":0,"d":"0.0000"}]
[]
[]
[null,"Program","Benchmark","k = 1",null,null,"k = 2",null,null,"k = 3"]
[{"$nulls":3},"TPR","FDR","N","TPR","FDR","N","TPR","FDR","N",null,"Avg. TP","Avg. FP"]
["Q≥40","Sniper (ALL)","Sanger",0.7994,0.0143,"(275|1,4,68/17/43)",0.8169,0.0138,"(281|4,4,59/20/35)",0.7936,0.0108,"(273|1,3,70/22/35) ",null,0.8039444444444445,0.014199999999999999]
[null,null,"Sanger \\ NGS",0.9605,{"v":0,"d":"0.0000"},"(243|0,0,10)",0.9802,{"v":0,"d":"0.0000"},"(248|2,0,3)",0.9526,{"v":0,"d":"0.0000"},"(241|1,0,11)",null,0.9618,0]
["Q≥40","Sniper (UNI)","Sanger",0.7965,0.0144,"(274|0,4,70/27/37)",0.8052,0.0142,"(277|1,4,66/29/35)",0.7762,0.0183,"(267|1,5,76/32/35) "]
[null,null,"Sanger \\ NGS",0.9526,{"v":0,"d":"0.0000"},"(241|0,0,12)",0.9644,{"v":0,"d":"0.0000"},"(244|0,0,9)",0.9289,{"v":0,"d":"0.0000"},"(235|0,0,18)"]
["Q≥40","Sniper (BEST)","Sanger",0.8052,0.0142,"(277|0,4,67/22/38)  ",0.8285,0.0138,"(285|1,4,58/20/36) ",{"v":0.814,"d":"0.8140"},{"v":0.014,"d":"0.0140"},"(280|1,4,63/20/33)  "]
[null,null,"Sanger \\ NGS",0.9605,{"v":0,"d":"0.0000"},"(243|0,0,10)",0.9881,{"v":0,"d":"0.0000"},"(250|0,0,3)",0.9684,{"v":0,"d":"0.0000"},"(245|0,0,8) "]
[]
["40/40","Maq (UNI)","Sanger",0.782,0.0144,"(269|4,4,71)  ",0.7994,{"v":0.014,"d":"0.0140"},"(275|6,4,63)  ",0.7878,0.0142,"(271|6,4,67)",null,{"v":0.8028166666666666,"d":"0.8028"},{"v":0.014016666666666669,"d":"0.0140"}]
[null,null,"Sanger \\ NGS",0.9289,{"v":0,"d":"0.0000"},"(235|0,0,18) ",0.9605,{"v":0,"d":"0.0000"},"(243|0,0,10) ",0.9486,{"v":0,"d":"0.0000"},"(240|0,0,13) ",null,{"v":0.95785,"d":"0.9579"},{"v":0,"d":"0.0000"}]
["40/40","Maq (BEST)","Sanger",0.7907,0.0143,"(272|3,4,69) ",0.8314,0.0136,"(286|5,4,53) ",0.8256,0.0136,"(284|6,4,54)"]
[null,null,"Sanger \\ NGS",0.9289,{"v":0,"d":"0.0000"},"(235|0,0,18)   ",0.9921,{"v":0,"d":"0.0000"},"(251|0,0,2)  ",0.9881,{"v":0,"d":"0.0000"},"(250|0,0,3)"]
[]
[]
[null,"Program","Benchmark","k = 1",null,null,"k = 2",null,null,"k = 3"]
[{"$nulls":3},"TPR","FDR","N","TPR","FDR","N","TPR","FDR","N",null,"Avg. TP","Avg. FP"]
["Q≥13","Sniper (ALL)","Sanger",0.8169,0.0139,"(281|3,4,60/17/39)",0.8256,0.0136,"(284|7,4,53/20/32)",0.8052,0.0139,"(277|7,4,60/22/31)",null,0.8149222222222223,0.014299999999999998]
[null,null,"Sanger \\ NGS",0.9723,{"v":0,"d":"0.0000"},"(246|0,0,7)",0.9842,{"v":0,"d":"0.0000"},"(249|2,0,2)",0.9644,{"v":0,"d":"0.0000"},"(244|3,0,6)",null,0.9718777777777778,0]
["Q≥13","Sniper (UNI)","Sanger",0.8081,0.0141,"(278|2,4,64/27/34)",{"v":0.811,"d":"0.8110"},{"v":0.014,"d":"0.0140"},"(279|3,4,62/29/32)",0.7936,0.0178,"(273|3,5,68/32/31)"]
[null,null,"Sanger \\ NGS",0.9644,{"v":0,"d":"0.0000"},"(244|0,0,9)",0.9684,{"v":0,"d":"0.0000"},"(245|0,0,8)",0.9486,{"v":0,"d":"0.0000"},"(240|0,0,13)"]
["Q≥13","Sniper (BEST)","Sanger",0.8198,0.0139,"(282|2,4,60/22/34)  ",0.8314,0.0137,"286|3,4,55/20/34)",0.8227,0.0138,"(283|3,4,58/20/32)"]
[null,null,"Sanger \\ NGS",0.9723,{"v":0,"d":"0.0000"},"(246|0,0,7)",0.9921,{"v":0,"d":"0.0000"},"(251|0,0,2)",0.9802,{"v":0,"d":"0.0000"},"(248|0,0,5)"]
[]
["13/13","Maq (UNI)","Sanger",0.7994,0.0141,"(275|4,4,65) ",0.8081,0.0138,"(278|7,4,59) ",0.7965,0.0141,"(274|6,4,64)",null,{"v":0.81345,"d":"0.8135"},{"v":0.013833333333333331,"d":"0.0138"}]
[null,null,"Sanger \\ NGS",0.9526,{"v":0,"d":"0.0000"},"(241|0,0,12) ",0.9684,{"v":0,"d":"0.0000"},"(245|1,0,7)  ",0.9565,{"v":0,"d":"0.0000"},"(242|0,0,11)",null,{"v":0.9716666666666667,"d":"0.9717"},{"v":0,"d":"0.0000"}]
["13/13","Maq (BEST)","Sanger",{"v":0.811,"d":"0.8110"},{"v":0.014,"d":"0.0140"},"(279|3,4,62)   ",0.8343,0.0135,"(287|5,4,52) ",0.8314,0.0135,"(286|6,4,52)"]
[null,null,"Sanger \\ NGS",0.9605,{"v":0,"d":"0.0000"},"(243|0,0,10) ",{"v":0.996,"d":"0.9960"},{"v":0,"d":"0.0000"},"(252|0,0,1)   ",{"v":0.996,"d":"0.9960"},{"v":0,"d":"0.0000"},"(252|0,0,1) "]

{"sheet":"Total SNP calls and novel SNPs","index":1,"n_rows":38,"n_cols":10,"rows_kept":38,"merged":[[16,1,17,1],[16,2,17,2],[16,3,17,3],[16,4,17,4],[26,0,26,9],[29,0,29,9],[34,0,34,3],[35,0,35,2],[36,0,36,3],[37,0,37,4]],"flags":["formulas_cached_only"]}
["Program","Stringency","k = 1","k = 2","k = 3"]
["Sniper","Q ≥ 90",1166,1243,1219]
["(ALL)","Q ≥ 40",1301,1434,1482]
[null,"Q ≥ 13",1389,1630,1793]
["Sniper","Q ≥ 90",1151,1266,1258]
["(UNI)","Q ≥ 40",1310,1513,1615]
[null,"Q ≥ 13",1457,1801,2100]
["Sniper","Q ≥ 90",1151,1279,1316]
["(BEST)","Q ≥ 40",1269,1434,1535]
[null,"Q ≥ 13",1339,1575,1757]
["Maq","Q ≥ 90, Qadj ≥ 60",1045,1188,1153]
["(UNI)","Q ≥ 40, Qadj ≥ 40",1180,1276,1220]
[null,"Q ≥ 13, Qadj ≥ 13",1255,1384,1392]
["Maq","Q ≥ 90, Qadj ≥ 60",1046,1249,1252]
["(BEST)","Q ≥ 40, Qadj ≥ 40",1187,1333,1314]
[null,"Q ≥ 13, Qadj ≥ 13",1253,1379,1384]
["SOAPsnp",{"$error":"#NAME?"},1845,1845,1845]
["(BEST)"]
[]
["Total significant SNP calls produced by each program and read map approach, using the specified number of mismatches k and stringency thresholds Q. "]
["For Sniper, –10 log10(1–P), where P is the posterior probability of the SNP. For Maq, Q indicates the minimum consensus quality and Qadj indicates the minimum adjacent quality."]
[]
[]
[]
[]
["Chr","Position","Ref","SNP","Qa","Depthb","Rdegc","Ndegd","Ndeg/Depth","Allele frequency"]
["Individual NA17156"]
[3,38639167,"T","GT",160,109,1,1,0.01,"T:0.46, G:0.52"]
[7,150293189,"T","GT",160,220,0,0,0,"T:0.44, G:0.55"]
["Individual NA17275"]
[7,150293044,"A","AG",160,395,27,121,0.31,"A:0.48, G:0.52"]
[21,34759675,"C","CT",160,53,0,0,0,"T:0.43, C:0.57"]
[]
[]
["aphred-like posterior probability, Q = –10 log10(1–P). "]
["bnumber of reads overlapping the locus. "]
["cnumber of reads with more than 1 alignment. "]
["dnumber of alignments for these reads mapping elsewhere."]