Table 2. Concordance between low-coverage re-sequencing and 12X coverage for homozygous and heterozygous genotypes.
| Coverage (Genotype inference) | 1x (12x-calling) | 1x (GL) | 2x (12x-calling) | 2x (GL) | 5x (12x-calling) | 5x (GL) | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Species | Sheep | Goats | Sheep | Goats | Sheep | Goats | Sheep | Goats | Sheep | Goats | Sheep | Goats | |
| # of sites | 12,550,038 | 10,662,633 | 30,135,105 | 18,274,530 | 15,617,291 | 12,930,734 | 37,578,055 | 23,631,570 | 28,419,192 | 20,974,409 | 44,698,817 | 29,810,608 | |
| Genotypes for 100% of individuals | # of polymorphic variants | 259,177 | 249,056 | 30,134,708 | 18,274,238 | 1,783,255 | 1,737,328 | 37,577,014 | 23,630,719 | 15,847,527 | 11,296,131 | 44,691,747 | 29,805,099 |
| # of variants shared with 12x data | - | - | 17,109,335 | 10,936,768 | - | - | 20,760,524 | 13,951,043 | - | - | 24,647,380 | 17,543,844 | |
| Heterozygote genotypes | Matching 12x (%) | 0.12 ± 0.02 | 0.19 ± 0.03 | 28.6 ± 3.4 | 28.2 ± 2.9 | 6.20 ± 0.79 | 5.68 ± 0.72 | 40.6 ± 4.8 | 41.2 ± 4.1 | 74.1 ± 8.6 | 71.5 ± 7.1 | 60.0 ± 7.0 | 61.8 ± 6.1 |
| Mis-matching 12x (%) | 3.14 ± 0.33 | 4.38 ± 0.65 | 28.7 ± 3.3 | 28.1 ± 2.9 | 2.97 ± 0.30 | 3.66 ± 0.53 | 23.3 ± 2.6 | 22.9 ± 2.3 | 2.27 ± 0.24 | 2.16 ± 0.23 | 8.05 ± 0.92 | 7.80 ± 0.84 | |
| Missing (%) | 96.7 ± 11.1 | 95.4 ± 9.4 | 42.7 ± 4.9 | 43.7 ± 4.3 | 90.8 ± 10.3 | 90.7 ± 9.0 | 36.1 ± 4.1 | 36.0 ± 3.5 | 23.6 ± 2.6 | 26.4 ± 2.6 | 32.0 ± 3.7 | 30.4 ± 3.0 | |
| Homozygote genotypes | Matching 12x (%) | 34.1 ± 0.1 | 38.1 ± 0.1 | 23.6 ± 0.6 | 30.0 ± 0.4 | 49.2 ± 0.2 | 52.3 ± 0.2 | 33.5 ± 0.9 | 31.2 ± 0.6 | 87.8 ± 1.7 | 87.5 ± 1.1 | 44.9 ± 1.3 | 44.1 ± 0.9 |
| Mis-matching 12x (%) | 0.02 ± 0.02 | 0.02 ± 0.02 | 3.32 ± 0.62 | 2.45 ± 0.43 | 0.03 ± 0.01 | 0.02 ± 0.01 | 2.01 ± 0.51 | 1.50 ± 0.37 | 0.09 ± 0.10 | 0.07 ± 0.02 | 0.53 ± 0.22 | 0.39 ± 0.15 | |
| Missing (%) | 65.9 ± 2.1 | 61.9 ± 1.4 | 73.1 ± 0.9 | 76.6 ± 0.6 | 50.8 ± 1.9 | 47.7 ± 1.4 | 64.5 ± 0.8 | 67.3 ± 0.5 | 12.2 ± 0.4 | 12.5 ± 0.4 | 54.6 ± 0.7 | 55.5 ± 0.4 | |
| Correlations of Ho with 12X estimates | r (Pearson) | 0.642 | 0.173 | 0.972 | 0.877 | 0.989 | 0.507 | 0.989 | 0.953 | 0.999 | 0.989 | 0.990 | 0.980 |
| Slope (Pearson) | 0.149 | 0.176 | 0.118 | 0.128 | 0.329 | 0.281 | 0.287 | 0.305 | 0.864 | 0.818 | 0.609 | 0.628 | |
| r (Spearman) | 0.586 | 0.203 | 0.688 | 0.733 | 0.802 | 0.522 | 0.758 | 0.780 | 0.942 | 0.900 | 0.812 | 0.805 | |
For each depth, comparisons were made using for direct variant calling (12x-calling) and for variant discovery based on genotype likelihoods (GL). Ho correlations were estimated according to Pearson and Spearman to compare rankings of individuals. Slopes were estimated by forcing the intercept of the linear regression to be 0.