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Table 2 Quality assessment of the discovered SNPs. Pilot 2 SNPs are identified by the 1000 Genomes Project

From: Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

cell line

factor

total SNPs

overlap with Pilot 2

Pilot 2 SNPs recovered by ChlP

Pilot 2 SNPs in Ht5 region

Pilot 2 SNPs in Ht5 regions recovered by ChlP

validated/tested G1000 SNPs

Validated/Tested novel SNPs

GM12878

CTCF

112,999

94.14%

3.85%

11,908

75.37%

15/17

4/5

GM12891

CTCF

137,056

90.39%

4.55%

12,837

74.12%

13/13

4/4

GM12892

CTCF

206,349

92.23%

6.95%

20,772

76.54%

13/13

7/7

GM19238

CTCF

154,211

92.25%

4.47%

18,863

74.50%

11/11

3/3

GM19239

CTCF

153,092

94.33%

4.43%

14,844

70.37%

15/15

2/2

GM19240

CTCF

144,088

94.48%

4.08%

17,143

74.09%

10/10

3/3

GM12878

RNAPII

152,071

93.45%

5.14%

8,368

77.84%

5/6

2/2

GM12878

H3K4me3

200,675

93.19%

6.76%

44,755

79.40%

1/1

1/1

FB8470

CTCF

173,336

N/A

N/A

N/A

N/A

N/A

0/0

H1 ESC

CTCF

94,398

N/A

N/A

N/A

N/A

N/A

0/0

Progeria

CTCF

220,871

N/A

N/A

N/A

N/A

N/A

7/7

HUVEC

CTCF

55,492

N/A

N/A

N/A

N/A

N/A

7/7

Progeria

RNAPII

150,157

N/A

N/A

N/A

N/A

N/A

5/7

  1. G1000 SNPs are ChIP-seq discovered SNPs that overlap with Pilot 2 SNPs. N/A is not applicable, as these cells were not genotyped by the 1000 Genomes Project.
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BMC Genomic Data

ISSN: 2730-6844

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