Table 12 Comparing four algorithms using different coverage cutoffs for dbSNPs and non-dbSNPs
From: Comparing a few SNP calling algorithms using low-coverage sequencing data
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%) |