Table 2.
Sequencing coverage
| Trio | R18AA922 | R18AA923 | R18AA924 | Units |
|---|---|---|---|---|
| Date sample was run | Jun 4 2018 | Jun 1 2018 | Jun 1 2018 | |
| Sex | F | F (mother) | M (father) | |
| Yield: raw/bulk | 179.5 | 116.2 | 125.4 | |
| % mapped | 98.50% | 98.50% | 98.20% | % |
| % duplicates | 7.90% | 7.10% | 8.10% | % |
| Yield | 176.8 | 114.4 | 123.1 | Gbp |
| Insert size: mean | 423.6 | 413.1 | 407.3 | bp |
| Average and median coverage across genome | 49.6 | 32.3 | 34.3 | × |
| Average coverage over OMIM genes | 46.7 | 31.0 | 32.6 | × |
| # of OMIM genes with coverage at <10× | 314 | 703 | 977 | |
| # of OMIM genes with 100% coverage at ≥10× | 97.8% | 95.0% | 93.1% | % |
| # of OMIM genes with 100% coverage at ≥20× | 90.0% | 21.2% | 35.0% | % |
| # of OMIM genes with 100% coverage at ≥30× | 37.3% | 2.3% | 2.7% | % |
| # of genes with 100% coverage at ≥40× | 4.0% | 0.5% | 0.9% | |
| Variation (VCF) metrics | ||||
| # of calls total | 4,968,231 | 4,962,138 | 4,837,935 | |
| # of PASS calls | 4,887,184 | 4,903,387 | 4,775,895 | |
| # of calls total coding | 24,742 | 24,702 | 24,319 | |
| Total # of SNVs | 3,969,838 | 4,008,954 | 3,897,489 | |
| Total # of Indels | 917,346 | 894,433 | 878,406 | |
| Hom/Het ratio (in coding regions) | 0.55 | 0.54 | 0.60 | ratio |
| Ti/Tv ratio (in coding regions) | 1.96 | 1.97 | 1.97 | ratio |
| # of het calls (# of hom call) | 3,186,900 (1,781,331) | 3,208,560 (1,753,578) | 3,007,910 (1,830,025) | units |