Table 1.
SNV identified by replicated ES of CMT proband.
| Platform | GAII-1 | GAII-2 | HiSeq-1 | HiSeq-2 | PGM | Proton | WGS-SOLID | WGS-HiSeq |
|---|---|---|---|---|---|---|---|---|
| Total reads produced | 117,685,348 | 107,207,362 | 119,508,046 | 118,716,380 | 41,268,598 | 71,113,537 | 2,469,936,140 | 1,479,177,846 |
| Duplicate reads (%) | 4.98 | 3.63 | 5.86 | 5.74 | 25.10 | 19.34 | 5.00 | 2.29 |
| Total reads aligned (%) | 97.80 | 98.66 | 96.76 | 97.09 | 99.16 | 98.83 | 58.12 | 96.57 |
| Aligned reads on target (%) | 64.90 | 69.70 | 70.59 | 70.66 | 60.81 | 71.66 | N/A | N/A |
| Average coverage | 138x | 137x | 170x | 169x | 65x | 93x | 29.6x | 47.6x |
| Median coverage | 110x | 111x | 140x | 139x | 60x | 80x | N/A | 40x |
| Targets hit (%) | 99.42 | 99.32 | 99.42 | 99.40 | 99.22 | 99.29 | N/A | N/A |
| Bases targeted | 35,432,211 | 35,432,211 | 35,432,211 | 35,432,211 | 35,432,211 | 35,432,211 | N/A | N/A |
| Targeted bases with 10+ coverage (%) | 97.58 | 97.49 | 97.98 | 97.99 | 95.84 | 94.64 | N/A | N/A |
| Targeted bases with 20+ coverage (%) | 96.19 | 96.18 | 97.23 | 97.21 | 92.28 | 91.28 | N/A | N/A |
| Targeted bases with 40+ coverage (%) | 90.60 | 91.08 | 94.59 | 94.53 | 75.19 | 80.75 | N/A | N/A |
| Total SNPs | 102,444 | 91,661 | 92,553 | 91,484 | 41,958 | 57,243 | 3,420,306 | 4,016,486 |
| cSNPs (n) | 23,321 | 22,869 | 23,017 | 22,980 | 20,372 | 22,079 | 18,829 | 24,475 |
| nsSNPs (n) | 11,491 | 11,217 | 11,288 | 11,252 | 11,363 | 10,821 | 9,069 | 12,370 |
| Total c_inDels | 8,879 | 8,249 | 9,576 | 9,375 | N/A | N/A | N/A | 10,439 |