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Table 1 Samples and sequence data statistics

From: Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment

Sample or poola

Average sequence depth

Cumulative depth at variants (%)

Mapped reads (%)d

Mapped on target (%)e

Designb

Variantsc

≥1x

≥30x

ALL1_gDNA

1385

1940

99.4

96.5

92.4

67.1

Normal1_gDNA

1280

1588

99.6

96.2

91.4

60.8

ALL2_gDNA

1466

1791

99.4

95.7

92.2

64.7

Normal2_gDNA

792

1008

99.2

95.2

91.8

64.0

ALL1_wgaDNA

1564

1831

99.2

94.2

92.6

73.5

ALL2_wgaDNA

1569

1706

99.1

94.0

92.5

73.0

ALL1_pool2

1752

2254

99.7

97.4

91.8

67.7

ALL2_pool5

1502

1710

99.4

96.9

93.1

68.8

ALL1_pool10

1044

1445

99.6

96.8

89.4

63.0

ALL1_pool2_rep

1150

1614

99.4

95.9

84.5

42.4

ALL2_pool5_rep

1021

1503

99.3

91.6

85.5

49.9

ALL1_pool10_rep

1386

1837

99.5

96.3

85.9

58.5

  1. a Pools are named with the whole genome sequenced ALL sample included and the total number of samples in the pool.
  2. a Average sequence depth in the complete region covered by the HaloPlex design.
  3. c Average sequence depth at the 1528 candidate SNVs and SNPs covered by the HaloPlex design.
  4. d Percentage of sequence reads that map to the human genome.
  5. e Percentage of the sequence reads mapping to the genome that map to the regions covered by the HaloPlex design.