Table 2.
Statistics of the sequencing lanes for the control I sample and mean values for the additional samples
| Percentage of base pairs in the target region covered ≥ 20×b | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Exome capture method | Read length (bp) | Number of high quality readsa | Mb of sequence | Percentage of reads removed in duplicate removal | Percentage of high quality reads aligned to hg19 | Percentage of high quality reads aligned to CTR | CTR | CTR + flank | CCDS | Common |
| Agilent SureSelect | ||||||||||
| Lane 1 | 60 | 32,943,000 | 1,980 | 6.45% | 90.27% | 54.71% | 45.31% | 29.05% | 42.04% | 46.57% |
| Lane 2 | 82 | 57,259,000 | 4,700 | 9.24% | 81.42% | 51.50% | 60.84% | 46.87% | 54.54% | 61.82% |
| Combined | 90,202,000 | 6,670 | 8.22% | 84.65% | 52.67% | 68.15% | 55.3% | 60.98% | 69.2% | |
| Agilent SureSelect 50 Mb | ||||||||||
| Lane 1 | 82 | 41,871,000 | 3,430 | 5.23% | 93.59% | 42.96% | 45.66% | 33.62% | 47.04% | 44.71% |
| Lane 2 | 82 | 56,407,000 | 4,630 | 6.15% | 92.37% | 42.25% | 53.72% | 42.83% | 54.54% | 53.81% |
| Conditionally combinedc | 82 | 67,755,000 | 5,560 | 4.44% | 94.15% | 43.17% | 60.25% | 50.05% | 60.95% | 60.82% |
| NimbleGen SeqCap | ||||||||||
| Lane 1 | 60 | 33,518,000 | 2,010 | 8.98% | 90.79% | 73.57% | 56.96% | 38.24% | 44.78% | 59.18% |
| Lane 2 | 82 | 62,141,000 | 5,100 | 14.92% | 84.42% | 71.27% | 75.41% | 57.52% | 59.69% | 77.1% |
| Combined | 95,659,000 | 7,110 | 12.84% | 86.65% | 72.08% | 82.33% | 66.65% | 65.45% | 83.74% | |
| NimbleGen SeqCap v2.0 | ||||||||||
| Lane 1 | 82d | 85,072,000 | 6,980 | 24.48% | 75.27% | 51.22% | 79.99% | 70.84% | 77.55% | 81.1% |
| Mean for the additional samplese | ||||||||||
| Agilent SureSelect (n = 2) | 82 | 71,201,000 | 5,840 | 10.37% | 88.72% | 51.84% | 73.63% | - | - | - |
| Agilent SureSelect 50 Mb (n = 2) | 82 | 67,089,000 | 5,500 | 8.65% | 90.41% | 46.03% | 60.30% | - | - | - |
| NimbleGen SeqCap (n = 19) | 82 | 67,626,000 | 5,550 | 14.66% | 81.98% | 61.25% | 78.94% | - | - | - |
| NimbleGen SeqCap v2.0 (n = 2) | 82f | 70,638,000 | 5,790 | 22.76% | 76.97% | 55.35% | 81.82% | - | - | - |
aNumber of reads after B block trimming. bTarget region abbreviations: CTR, own capture target region of the kit; CTR + flank, own capture target region ± 100 bp; CCDS, exon annotated regions from CCDS, Ensembl v59; Common, regions captured by all the kits in comparison. cData from the sequencing lanes combined and randomly down-sampled to meet comparable read amounts after filtering. dSequenced with 100 bp, reads trimmed to 82 bp prior to any other action. eThe additional exome samples were aligned only against the whole genome and own capture target region. fSequenced with 110 bp, reads trimmed to 82 bp prior to any other action.