Skip to main content

Advertisement

Table 2 Statistics of the sequencing lanes for the control I sample and mean values for the additional samples

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% - - -
  1. 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.