Table 2

Indel density for annotation features (across all 44 ENCODE regions)

Indels

Rate (number per 100 kb)

Rate (bp per 100 kb)


n

bp

n

99% CI

bp

99% CI

Feature length (kb)


Manual

2,186

6,504

14.6

11.7 to 18.2

43.4

34.4 to 54.7

14,998

Random

2,300

6,506

15.3

13.6 to 17.3

43.4

37.5 to 50.2

15,000

Overall

4,486

13,010

15.0

13.4 to 16.7

43.4

38.3 to 49.1

29,998

RNA transcription

CDS

5

5

0.7

0.1 to 8.6

0.7

0.1 to 8.6

675

TSS

2

2

3.3

3.3

61

RACEfrags

9

28

2.1

0.8 to 5.4

6.6

1.3 to 33.9

425

TARs/transfrags

37

78

5.8

3.5 to 9.6

12.3

6.8 to 22.3

634

Pseudo-exons

9

26

6.6

2.6 to 16.6

19.1

5.8 to 63.3

136

3' UTR

48

103

11.0

7.2 to 16.7

23.6

13.5 to 41.3

436

5' UTR

7

32

6.0

1.6 to 22.3

27.4

3.8 to 198.7

117

TUF

53

160

12.2

7.8 to 19.2

36.9

20.2 to 67.6

433

Open chromatin

FAIRE-sites

106

327

7.7

5.6 to 10.6

23.8

15.5 to 36.7

1,372

DHS (NHGRI)

19

61

6.1

3.3 to 11.3

19.7

8.3 to 46.9

310

DHS (Regulome)

43

135

8.6

5.3 to 14.0

27.0

13.4 to 54.4

499

DNA-protein intreraction/transcript regulation

HisPolTAF

141

348

13.1

10.0 to 17.2

32.4

22.5 to 46.5

1,076

Seq_specific (all motifs)

131

420

11.2

8.3 to 15.0

35.8

23.1 to 55.3

1,174

SeqSp (sequence specific factors)

54

225

10.2

6.2 to 16.7

42.5

20.1 to 89.5

530

Ancestral repeats

532

1,592

7.9

6.7 to 9.2

26.5

21.7 to 32.5

5,998

Evolutionary constraint

MCS strict

19

31

2.5

1.3 to 5.1

4.1

1.6 to 10.4

748

MCS moderate

78

170

5.1

3.5 to 7.6

11.2

6.8 to 18.5

1,515

MCS loose

356

960

9.8

8.2 to 11.7

26.4

20.9 to 33.4

3,637

Cell cycle

EarlyRepSeg

1,124

2,989

16.4

13.8 to 19.4

43.5

33.3 to 56.9

6,868

MidRepSeg

1,190

3,352

15.4

13.5 to 17.5

43.2

35.3 to 53.0

7,751

LateRepSeg

1,110

3,345

13.9

12.1 to 15.9

41.9

32.9 to 53.3

7,991


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; 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

Open Data