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.

Sulonen et al. Genome Biology 2011 12:R94   doi:10.1186/gb-2011-12-9-r94

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