Table 1.
Summary of data of sequencing and of mutation identification, for the different combinations of library-building techniques and analysis software.
| Sequencing and mapping stats | Haloplex | SeqCap EZ |
|---|---|---|
| Total sequenced reads | 485,210 (154,231) | 469,283 (273,083) |
| Total sequenced bases | 7.97E + 07 (± 1.85E + 07) | 10.31E + 07 (± 4.95E + 07) |
| Mean read length | 135 (± 7) | 199 (± 9) |
| Bases ≥ Q20 | 88.78% (± 1.23) | 89.04% (± 0.49) |
| Bases ≥ Q30 | 52.50% (± 1.78) | 48.98% (± 1.00) |
| %GC | 50.9% (± 1.1) | 43.2% (± 0.9) |
| Mapping rate | 97.79% (± 1.45) | 99.61% (± 0.06) |
| Duplicate rate | NS | 50.50% (± 8.24) |
| Aligned reads ≥ mapQ20 | 90.22% (± 4.53) | 93.23% (± 0.35) |
| Aligned reads ≥ mapQ30 | 88.98% (± 4.65) | 91.52% (± 0.43) |
| Capture efficiency | 76.50% (± 0.50) | 81.08% (± 7.03) |
| Mean target coverage | 159 ± 37 | 125 ± 53 |
| Not sequenced target regions | 2.67% (± 0.55) | 2.35% (± 1.2) |
| Target regions covered > 20 × | 88.67% (± 3.53) | 90.08% (± 6.04( |
| Target regions covered > 30 × | 84.21% (± 4.87) | 85.85% (± 11.74) |
| Variant calling stats | NextGene | Ion Reporter | NextGene | Ion Reporter |
|---|---|---|---|---|
| Total (filtered) | 214 (± 38) | 203 (± 16) | 99 (± 8) | 169 (± 14) |
| Indels | 77.3% (± 3.3) | 26.3% (± 5.1) | 58.7% (± 3.3) | 7.5% (± 1.2) |
| Known SNV (dbSnp144) | 83.0% (± 7.2) | 97.3% (± 1.1) | 94.3% (± 6.4) | 97.8% (± 1.1) |
| Ti/Tv | 2.66 (± 0.83) | 3.17 (± 0.33) | 3.74 (± 1.85) | 2.85 (± 0.26) |
| Mutation identification | NextGene | Ion Reporter | NextGene | Ion Reporter |
|---|---|---|---|---|
| SNV (n = 15) | 10 | 12 | 11 | 13 |
| Indel (n = 4) | 0 | 3 | 0 | 1 |
| CNV (n = 2) | 0 | 0 | 0 | 0 |
| Total (n = 21) | 10 (48%) | 15 (71%) | 11 (52%) | 14 (67%) |