Table 4.
Metrics of sequencing data
| Patient A | Patient B | Father | Mother | |
|---|---|---|---|---|
| Paired-end; read length | 99 | 99 | 99 | 99 |
| Number reads (M) | 46.4 | 35.9 | 43.4 | 48.4 |
| Number bases (G) | 4.6 | 3.6 | 4.3 | 4.8 |
| Mean coverage | 45.2 | 37.3 | 42.8 | 42.4 |
| Median coverage | 42 | 35 | 40 | 39 |
| PCR duplicates | 21.40% | 19.92% | 20.38% | 22.93% |
| Unmapped | 0.03% | 0.02% | 0.03% | 0.04% |
| Reads on-target | 56.47% | 58.79% | 56.40% | 51.59% |
| Bases on-target | 45.77% | 47.99% | 45.45% | 41.12% |
| Mean error rate | 0.26% | 0.24% | 0.27% | 0.30% |
| 8× target base coverage | 93.80% | 93.40% | 93.90% | 94.00% |
| 10× target base coverage | 93.30% | 92.60% | 93.40% | 93.40% |
| 15× target base coverage | 90.80% | 88.90% | 90.70% | 90.20% |
| 20× target base coverage | 86.00% | 82.20% | 85.50% | 84.40% |
| 30× target base coverage | 71.20% | 62.60% | 69.50% | 67.80% |
| 50× target base coverage | 38.00% | 23.70% | 34.00% | 33.10% |
| Variant allele #1 in AARS2 (NM_020745) | c.1774C>T, p.Arg592Trp | c.1774C>T, p.Arg592Trp | c.1774C>T, p.Arg592Trp | — |
| Variant #1 reads/total reads | 33/59 | 18/38 | 25/50 | 0/52 |
| Variant allele #2 in AARS2 (NM_020745) | c.647dupG, p.Cys218Leufs*6 | c.647dupG, p.Cys218Leufs*6 | — | c.647dupG, p.Cys218Leufs*6 |
| Variant #2 reads/total reads | 16/38 | 13/27 | 0/44 | 18/40 |
| Compound heterozygosity in USH2A (NM_206933) | c.14718G>T, p.Lys4906Asn | c.14718G>T, p.Lys4906Asn | — | c.14718G>T, p.Lys4906Asn |
| c.10202T>C, p.Ile3401Thr | c.10202T>C, p.Ile3401Thr | c.10202T>C, p.Ile3401Thr | ||
| De novo nonsynonymous Variant 1 | ABCF3:NM_018358, c.496C>T, p.Arg166Trp | KLHL36:NM_024731, c.916G>A, p.Glu306Lys | — | — |
| De novo nonsynonymous Variant 2 | GRHL2:NM_024915,c.1400A>G, p.Tyr467Cys | — | — | — |
Bold rows refer to the AARS2 gene.