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 |