Table 3

Comparison of indel and SNP density by ENCODE experimental features

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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