Skip to main content

Table 1 Sample throughput and sequence capacity- general sequencing and enrichment metrics

From: Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing

HapMap sample ID

Sample type

Library ID

Reads

Mapped

On-target %

ADoC

C1

C20

Coverage 0.2X mean

NA12003

gDNA

759L

36,453,208

33.50%

65.30%

2,121

99.50%

98.00%

86.10%

 

WGA

765L

42,752,716

36.30%

63.20%

2,588

99.60%

98.10%

86.40%

 

gDNA-pB

770L_BC1

10,031,809

36.40%

64.10%

621

99.00%

96.50%

86.50%

 

gDNA-pA

792L_BC1

5,221,822

31.60%

64.20%

280

98.40%

93.50%

85.70%

NA12004

gDNA

760L

39,005,646

31.00%

73.30%

2,356

99.40%

98.00%

86.30%

 

WGA

766L

43,079,257

17.50%

64.40%

1,273

99.40%

97.20%

84.80%

 

gDNA-pB

770L_BC2

3,272,424

39.30%

72.70%

249

98.30%

93.60%

87.10%

 

gDNA-pA

792L_BC2

6,023,113

32.50%

72.90%

380

98.50%

94.60%

85.70%

NA10838

gDNA

761L

35,573,703

21.10%

66.00%

1,309

99.40%

97.50%

85.90%

 

WGA

767L

43,140,968

30.60%

57.80%

2,014

99.60%

98.20%

86.50%

 

gDNA-pB

770L_BC3

7,114,637

35.80%

67.50%

456

98.60%

95.30%

85.80%

 

gDNA-pA

792L_BC3

6,587,601

34.00%

67.60%

401

98.60%

94.90%

85.80%

NA11829

gDNA

762L

39,864,620

29.20%

63.90%

1,961

99.60%

97.90%

85.50%

 

gDNA-pB

770L_BC4*

638,985

36.40%

66.00%

41

95.40%

63.40%

84.60%

 

gDNA-pA

792L_BC4*

677,767

28.50%

66.40%

34

94.50%

55.40%

84.90%

NA11830

gDNA

763L

38,654,830

34.10%

68.50%

2,404

99.70%

98.10%

85.80%

 

gDNA-pB

770L_BC5

Insufficient amount of material to run sample

 

gDNA-pA

792L_BC5

5,403,560

32.80%

68.10%

320

98.40%

94.10%

85.60%

NA10856

gDNA

764L

43,185,707

34.60%

61.10%

2,418

99.50%

98.00%

85.80%

 

gDNA-pB

770L_BC6

9,255,333

36.30%

61.30%

545

98.90%

96.00%

85.90%

 

gDNA-pA

792L_BC6

6,435,690

33.90%

62.00%

357

98.50%

94.40%

85.00%

Pooled Samples

gDNA

768L_1

41,913,860

32.40%

67.00%

2,406

99.80%

98.30%

84.90%

 

gDNA

768L_2

41,958,628

33.40%

66.70%

2,474

99.60%

98.30%

85.30%

  1. - Reads: Total sequencing reads per sample.
  2. - Mapped: Percentage of total reads that could be aligned to the human genome (hg18/NCBI).
  3. - On-Target: Percentage of mapped reads that align to the target regions.
  4. - ADoC: Average depth of coverage of target base.
  5. - C1: Percentage of target bases that are covered by at least one sequencing read.
  6. - C20: Percentage of target bases that are covered by at least 20 sequencing reads.
  7. - Coverage 0.2× Mean: Percentage of target bases that are covered by at least 0.2× of ADoC. Note that one barcode (BC4) was underrepresented (assigned with “*” in this Table; see also Results and Discussion sections).
  8. - gDNA: genomic DNA; WGA: whole-genome amplification; emPCR: emulsion PCR; BC: barcode.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us