Table 1.
Genotype concordance metrics
| Genotype concordance | Non-reference sensitivity | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GATK | Freebayes | SAMtools | GATK | Freebayes | SAMtools | |||||||
| No.SNPs | Mean ± SD | No.SNPs | Mean ± SD | No.SNPs | Mean ± SD | No.SNPs | Mean ± SD | No.SNPs | Mean ± SD | No.SNPs | Mean ± SD | |
| ≤0.1 | 23 | 0.03 ± 0.03 | 9 | 0.03 ± 0.03 | 3 | 0.08 ± 0.00 | 3 | 0.01 ± 0.02 | 9 | 0.04 ± 0.04 | 5 | 0.04 ± 0.04 |
| ≤0.2 | 18 | 0.14 ± 0.03 | 6 | 0.15 ± 0.03 | 6 | 0.15 ± 0.02 | 13 | 0.15 ± 0.03 | 10 | 0.14 ± 0.03 | 15 | 0.14 ± 0.03 |
| ≤0.3 | 12 | 0.25 ± 0.02 | 9 | 0.27 ± 0.02 | 9 | 0.25 ± 0.03 | 25 | 0.25 ± 0.03 | 7 | 0.24 ± 0.03 | 20 | 0.24 ± 0.03 |
| ≤0.4 | 13 | 0.33 ± 0.02 | 5 | 0.33 ± 0.01 | 18 | 0.35 ± 0.03 | 20 | 0.34 ± 0.02 | 11 | 0.34 ± 0.03 | 19 | 0.34 ± 0.03 |
| ≤0.5 | 22 | 0.45 ± 0.03 | 18 | 0.45 ± 0.03 | 24 | 0.45 ± 0.03 | 20 | 0.45 ± 0.02 | 14 | 0.45 ± 0.03 | 24 | 0.44 ± 0.03 |
| ≤0.6 | 42 | 0.55 ± 0.03 | 39 | 0.55 ± 0.04 | 43 | 0.55 ± 0.03 | 59 | 0.52 ± 0.03 | 89 | 0.51 ± 0.02 | 82 | 0.51 ± 0.03 |
| ≤0.7 | 73 | 0.65 ± 0.03 | 64 | 0.66 ± 0.03 | 62 | 0.66 ± 0.03 | 96 | 0.66 ± 0.02 | 105 | 0.66 ± 0.02 | 158 | 0.66 ± 0.03 |
| ≤0.8 | 110 | 0.76 ± 0.03 | 183 | 0.76 ± 0.03 | 123 | 0.76 ± 0.03 | 152 | 0.75 ± 0.02 | 150 | 0.75 ± 0.02 | 215 | 0.75 ± 0.02 |
| ≤0.9 | 679 | 0.87 ± 0.03 | 3828 | 0.88 ± 0.02 | 738 | 0.87 ± 0.03 | 1206 | 0.86 ± 0.03 | 1171 | 0.86 ± 0.03 | 1561 | 0.86 ± 0.03 |
| ≤1 | 50441 | 0.98 ± 0.02 | 46725 | 0.97 ± 0.02 | 50334 | 0.98 ± 0.02 | 49732 | 0.99 ± 0.02 | 49206 | 0.99 ± 0.02 | 49148 | 0.99 ± 0.02 |
| Non-reference genotype concordance | Precision | |||||||||||
| ≤0.1 | 55 | 0.02 ± 0.03 | 34 | 0.02 ± 0.03 | 35 | 0.02 ± 0.03 | 46 | 0.02 ± 0.04 | 28 | 0.01 ± 0.03 | 28 | 0.01 ± 0.03 |
| ≤0.2 | 18 | 0.13 ± 0.03 | 10 | 0.14 ± 0.03 | 23 | 0.14 ± 0.03 | 11 | 0.14 ± 0.03 | 12 | 0.15 ± 0.03 | 11 | 0.16 ± 0.03 |
| ≤0.3 | 24 | 0.26 ± 0.03 | 20 | 0.25 ± 0.03 | 24 | 0.25 ± 0.03 | 22 | 0.25 ± 0.03 | 22 | 0.25 ± 0.03 | 17 | 0.25 ± 0.03 |
| ≤0.4 | 32 | 0.34 ± 0.02 | 35 | 0.34 ± 0.02 | 43 | 0.35 ± 0.02 | 26 | 0.35 ± 0.03 | 21 | 0.34 ± 0.02 | 20 | 0.35 ± 0.03 |
| ≤0.5 | 32 | 0.43 ± 0.03 | 41 | 0.43 ± 0.03 | 38 | 0.43 ± 0.03 | 15 | 0.42 ± 0.02 | 36 | 0.43 ± 0.03 | 21 | 0.44 ± 0.03 |
| ≤0.6 | 144 | 0.52 ± 0.03 | 249 | 0.52 ± 0.03 | 168 | 0.52 ± 0.03 | 99 | 0.52 ± 0.03 | 161 | 0.52 ± 0.03 | 99 | 0.53 ± 0.03 |
| ≤0.7 | 245 | 0.66 ± 0.03 | 540 | 0.66 ± 0.03 | 297 | 0.65 ± 0.03 | 157 | 0.66 ± 0.03 | 499 | 0.66 ± 0.03 | 156 | 0.66 ± 0.03 |
| ≤0.8 | 445 | 0.75 ± 0.02 | 1725 | 0.76 ± 0.03 | 584 | 0.76 ± 0.02 | 270 | 0.75 ± 0.02 | 2246 | 0.76 ± 0.02 | 240 | 0.75 ± 0.02 |
| ≤0.9 | 3019 | 0.86 ± 0.03 | 6607 | 0.86 ± 0.03 | 3720 | 0.86 ± 0.03 | 1644 | 0.86 ± 0.03 | 6808 | 0.85 ± 0.03 | 1964 | 0.86 ± 0.03 |
| ≤1 | 47312 | 0.98 ± 0.03 | 41511 | 0.97 ± 0.03 | 46315 | 0.98 ± 0.03 | 49038 | 0.99 ± 0.02 | 40941 | 0.97 ± 0.03 | 48692 | 0.98 ± 0.03 |
The calculation based on array genotypes and corresponding sequence-based genotypes obtained with different variant callers at positions where SNPs from the array were available on chromosomes 3, 6 and 28