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Table 1 Statistics of SNP discovery

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

Cell line

factor

aligned reads

Ht5 regions

total SNPs

novel SNPs

Ti/Tv

GM12878

CTCF

30,400,254

0.40%

112,999

2989(2.6%)

2.04

GM12891

CTCF

28,282,066

0.45%

137,056

3443(2.5%)

2.18

GM12892

CTCF

41,857,998

0.75%

206,349

5439(2.6%)

2.13

GM19238

CTCF

31,125,372

0.53%

154,211

7474(4.8%)

2.11

GM19239

CTCF

24,857,361

0.41%

153,092

7034(4.6%)

2.13

GM19240

CTCF

32,009,059

0.45%

144,088

7832(5.4%)

2.11

GM12878

RNAPII

85,763,827

0.55%

152,071

5720(3.8%)

2.03

GM12878

H3K4me3

74,464,458

1.95%

200,675

8231(4.1%)

1.99

FB8470

CTCF

39,394,358

0.47%

173,336

4344(2.5%)

2.11

H1 ESC

CTCF

14,462,504

0.28%

94,398

2308(2.4%)

2.18

Progeria

CTCF

46,925,953

0.47%

220,871

5328(2.4%)

2.06

HUVEC

CTCF

21,734,605

0.32%

55,492

1117(2.0%)

2.08

  1. GM lines are lymphoblastoid cells resequenced by the 1000 Genomes Project. FB8470 is a normal fibroblast line and Progeria refers to a fibroblast line obtained from patients with the disease. H1 ESCs are human embryonic stem cells and HUVECs are human vascular endothelial cells. Ht5 regions are regions covered by at least 5 reads in ChIP-seq data. The fraction of the genome represented in Ht5 regions is shown. Novel SNPs are with reference to dbSNP129. Ti/Tv is the transition to transversion ratio.