Table 2.
Data | No. of SNP |
Ti/Tva |
Concordanceb | |||||
---|---|---|---|---|---|---|---|---|
All | Known | Novel | dbSNP% | All | Known | Novel | TP/P (%) | |
Autism (pooled) | ||||||||
Case | ||||||||
CRISP | 2182 | 1791 | 391 | 82.1 | 1.68 | 1.79 | 1.26 | 101/101 (100) |
SNVer | 2182 | 1795 | 387 | 82.3 | 1.71 | 1.81 | 1.35 | 102/102 (100) |
SAMtools | 261 | 260 | 1 | 99.6 | 2.26 | 2.29 | 0/1 | 16/16 (100) |
Control | ||||||||
CRISP | 2063 | 1610 | 453 | 78.0 | 1.68 | 1.83 | 1.27 | 96/96 (100) |
SNVer | 2063 | 1617 | 446 | 78.4 | 1.78 | 1.89 | 1.45 | 95/95 (100) |
SAMtools | 239 | 238 | 1 | 99.6 | 2.06 | 2.05 | 1/0 | 16/16 (100) |
T1D (pooled) | ||||||||
Case | ||||||||
CRISP | 306 | 93 | 213 | 30.3 | 0.95 | 2.58 | 0.63 | N/A |
SNVer | 306 | 126 | 180 | 41.2 | 1.71 | 2.15 | 1.47 | |
SAMtools | 14 | 9 | 5 | 64.3 | 10/4 | 8/1 | 2/3 | |
Control | ||||||||
CRISP | 167 | 110 | 57 | 65.9 | 1.49 | 2.93 | 0.46 | |
SNVer | 167 | 120 | 47 | 71.9 | 2.34 | 3.00 | 1.35 | |
SAMtools | 18 | 12 | 6 | 66.7 | 14/4 | 11/1 | 3/3 | |
ADHD (Individual) | ||||||||
84 060 | ||||||||
SNVer | 18 001 | 17 535 | 466 | 97.4 | 2.89 | 2.89 | 2.73 | 4158/4183 (99.4) |
SAMtools | 48 988 | 47 513 | 1475 | 97.0 | 2.66 | 2.68 | 2.16 | 4437/8116 (54.7) |
SAMtools20× | 15 038 | 14 538 | 500 | 96.7 | 2.70 | 2.72 | 2.11 | 2034/3158 (64.4) |
GATK | 19 655 | 19 713 | 482 | 97.6 | 2.91 | 2.94 | 2.15 | 4649/4657 (99.8) |
84 615 | ||||||||
SNVer | 17 436 | 16 914 | 522 | 97.0 | 2.85 | 2.87 | 2.22 | 4032/4063 (99.2) |
SAMtools | 46 037 | 44 489 | 1548 | 96.6 | 2.64 | 2.67 | 1.94 | 4173/7643 (54.4) |
SAMtools20× | 15 510 | 14 942 | 568 | 96.3 | 2.74 | 2.77 | 2.02 | 2062/3247 (63.5) |
GATK | 18 892 | 18 419 | 473 | 97.5 | 2.89 | 2.92 | 2.03 | 4537/4566 (99.4) |
92 157 | ||||||||
SNVer | 18 676 | 18 208 | 468 | 97.5 | 2.90 | 2.92 | 2.37 | 4192/4224 (99.2) |
SAMtools | 49 729 | 47 693 | 2036 | 95.9 | 2.69 | 2.73 | 2.03 | 4251/7996 (53.2) |
SAMtools20× | 15 881 | 15 370 | 511 | 96.8 | 2.80 | 2.83 | 1.99 | 2028/3259 (62.2) |
GATK | 20 100 | 19 631 | 469 | 97.7 | 2.98 | 3.00 | 2.35 | 4700/4710 (99.8) |
aTransition and transversion ratio for the identified variants. When the number of variants is small we just report the numbers but not calculate the ratio, e.g. 10/4 for all variants in T1D case by SAMtools means 10 transitions and 4 transversions.
bGenotype concordance. P represents the number of variants called by each program and also genotyped. TP represents the number of variant calls concordant between sequencing data and individual genotyping data.
20×: Additional filtering of sequencing depth ≥20 is applied.