|
Comparison of indel and SNP density by ENCODE experimental features |
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| Indels |
Validated SNPs |
|||
|
|
||||
| bp/100 kb |
99% CI |
bp |
bp/100 kb |
|
|
|
||||
| Manual |
43.4 |
34.4 to 54.7 |
14,390 |
95.9 |
| Random |
43.4 |
37.5 to 50.2 |
16,343 |
109.0 |
| Overall |
43.4 |
38.3 to 49.1 |
30,733 |
102.4 |
| RNA transcription |
||||
| CDS |
0.7 |
0.1 to 8.6 |
421 |
62.4 |
| TSS |
3.3 |
42 |
68.7 |
|
| RACEfrags |
6.6 |
1.3 to 33.9 |
278 |
65.4 |
| TARs/transfrags |
12.3 |
6.8 to 22.3 |
591 |
93.1 |
| Pseudo-exons |
19.1 |
5.8 to 63.3 |
132 |
96.9 |
| 3' UTR |
23.6 |
13.5 to 41.3 |
370 |
84.8 |
| 3' UTR |
27.4 |
3.8 to 198.7 |
97 |
83.2 |
| TUF |
36.9 |
20.2 to 67.6 |
423 |
97.6 |
| Open chromatin |
||||
| FAIRE-sites |
23.8 |
15.5 to 36.7 |
1,232 |
89.8 |
| DHS (NHGRI) |
19.7 |
8.3 to 46.9 |
297 |
95.9 |
| DHS (Regulome) |
27.0 |
13.4 to 54.4 |
450 |
90.1 |
| DNA-protein interaction/transcript regulation |
||||
| HisPolTAF |
32.4 |
22.5 to 46.5 |
850 |
79.0 |
| Seq_specific (all motifs) |
35.8 |
23.1 to 55.3 |
1,098 |
93.5 |
| SeqSp (sequence specific factors) |
42.5 |
20.1 to 89.5 |
421 |
79.4 |
| Ancestral repeats |
26.5 |
21.7 to 32.5 |
5,749 |
95.9 |
| Evolutionary constraint |
||||
| MCS strict |
4.1 |
1.6 to 10.4 |
229 |
30.6 |
| MCS moderate |
11.2 |
6.8 to 18.5 |
667 |
44.0 |
| MCS loose |
26.4 |
20.9 to 33.4 |
2,052 |
56.4 |
| Cell cycle |
||||
| EarlyRepSeg |
43.5 |
33.3 to 56.9 |
6,165 |
89.8 |
| MidRepSeg |
43.2 |
35.3 to 53.0 |
7,418 |
95.7 |
| LateRepSeg |
41.9 |
32.9 to 53.3 |
8,896 |
111.3 |
|
bp, base pairs; CDS, coding sequence; CI, confidence interval; DHS, DNAse hypersensitive sites; ENCODE, Encyclopedia of DNA Elements; FAIRE, formaldehyde assisted isolation of regulatory elements; kb, kilobases; MCS, multi-species conserved sequence; NHGRI, National Human Genome Research Institute; transfrag, transcribed fragment; RACEfrag, rapid amplification of cDNA ends fragment; SNP, single nucleotide polymorphism; TAR, transcriptionally active region; TSS, transcription start site; TUF, transcripts of unknown function; UTR, untranslated region. | ||||
Clark et al. Genome Biology 2007 8:R180 doi:10.1186/gb-2007-8-9-r180 |
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