Table 1 Missing rate and Inconsistency between whole genome sequencing and genome-wide association studies
Family ID | Total number of individuals | Missing rate | Genotype inconsistency between GWAS and WGS | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Â | All | GWAS | WGS | GWAS | WGS | GWAS and WGS | Cause of genotype inconsistency | ||
| Â | Â | Â | Â | 65,500 | 1,697,985 | 63,803 | Missing in GWAS | Missing in WGS | Mismatch |
2 | 107 | 86 | 43 | 1.18% | 2.31% | 3.20% | 67.55% | 29.72% | 2.73% |
3 | 98 | 77 | 38 | 0.17% | 1.66% | 0.84% | 19.98% | 72.31% | 7.71% |
4 | 97 | 64 | 39 | 0.17% | 2.34% | 1.38% | 15.80% | 73.59% | 10.60% |
5 | 91 | 68 | 40 | 0.13% | 1.56% | 0.82% | 20.41% | 72.47% | 7.12% |
6 | 88 | 64 | 39 | 0.84% | 2.06% | 2.07% | 59.85% | 36.38% | 3.77% |
7 | 89 | 36 | 30 | 14.59% | 1.58% | 17.58% | 96.60% | 2.95% | 0.45% |
8 | 84 | 68 | 25 | 3.31% | 2.18% | 9.23% | 89.44% | 9.33% | 1.23% |
9 | 81 | 33 | 27 | 13.34% | 1.50% | 16.38% | 96.63% | 2.90% | 0.47% |
10 | 83 | 64 | 40 | 2.42% | 1.86% | 4.43% | 81.79% | 16.71% | 1.50% |
11 | 76 | 35 | 29 | 20.57% | 1.88% | 24.81% | 96.92% | 2.63% | 0.45% |
16 | 59 | 48 | 26 | 0.10% | 1.62% | 0.82% | 14.04% | 78.04% | 7.93% |
17 | 57 | 42 | 20 | 0.30% | 2.58% | 1.45% | 18.22% | 75.43% | 6.35% |
20 | 51 | 36 | 20 | 0.36% | 2.12% | 1.43% | 28.55% | 65.70% | 5.76% |
21 | 50 | 35 | 19 | 0.11% | 2.49% | 1.26% | 4.83% | 90.21% | 4.96% |
27 | 44 | 35 | 17 | 0.16% | 2.22% | 1.27% | 14.98% | 77.98% | 7.04% |
47 | 27 | 22 | 12 | 0.09% | 2.06% | 1.04% | 9.89% | 84.35% | 5.76% |
| Â | 1182 | 813 | 464 | *3.61% | *2.00% | *5.50% | *45.97% | *49.42% | *4.61% |
| Â | Â | Â | Â | ^0.72% | ^2.08% | ^2.25% | ^34.26% | ^60.17% | ^5.57% |