From: Comparison of solution-based exome capture methods for next generation sequencing
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% | - | - | - |