Table 2 Indel density for annotation features (across all 44 ENCODE regions)

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