Table 12

Comparing four algorithms using different coverage cutoffs for dbSNPs and non-dbSNPs
A. dbSNPs
Coverage cutoffs Total By 1 By 2 By 3 By 4
≥ 3X 592 108 (18.24%) 82 (13.85%) 125 (21.11%) 277 (46.79%)
≥ 4X 276 68 (24.64%) 32 (11.59%) 50 (18.12%) 126 (45.65%)
≥ 5X 201 61 (30.35%) 20 (9.95%) 33 (16.42%) 87 (43.28%)
≥ 6X 169 54 (31.95%) 15 (8.88%) 33 (19.53%) 67 (39.64%)
≥ 7X 153 53 (34.64%) 15 (9.80%) 29 (18.95%) 56 (36.60%)
≥ 8X 134 43 (32.09%) 12 (8.96%) 29 (21.64%) 50 (37.31%)
≥ 9X 123 38 (30.89%) 15 (12.20%) 25 (20.33%) 45 (36.59%)
≥ 10X 110 34 (30.91%) 11 (10.00%) 27 (24.55%) 38 (34.55%)
B. non-dbSNPs
Coverage cutoffs Total By 1 By 2 By 3 By 4
≥ 3X 402 151 (37.56%) 99 (24.63%) 76 (18.91%) 76 (18.91%)
≥ 4X 211 76 (36.02%) 41 (19.43%) 53 (25.12%) 41 (19.43%)
≥ 5X 161 57 (35.04%) 30 (18.63%) 37 (22.98%) 37 (22.98%)
≥ 6X 127 38 (29.92%) 27 (21.26%) 29 (22.83%) 33 (25.98%)
≥ 7X 106 33 (31.13%) 21 (19.81%) 22 (20.75%) 30 (28.30%)
≥ 8X 93 32 (34.41%) 17 (18.28%) 22 (23.66%) 22 (23.66%)
≥ 9X 87 28 (32.18%) 16 (18.39%) 23 (26.44%) 20 (22.99%)
≥ 10X 79 25 (31.65%) 18 (22.78%) 20 (25.32%) 16 (20.25%)

“Total” means the total number of SNVs called by four algorithms. “By 1” means the number (percentage) of SNVs called by only one of the four algorithms. “By 2” means the number (percentage) of SNVs called by any two algorithms. “By 3” means the number (percentage) of SNVs called by any three algorithms. “By 4” means the number (percentage) of SNVs called by four algorithms.

Yu and Sun

Yu and Sun BMC Bioinformatics 2013 14:274   doi:10.1186/1471-2105-14-274

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