Table 1

Indel density (for all 44 ENCODE regions)

ENCODE region

Chromosome

Number of indels

Indels (bp)

Size (bp)

Density (per 100 kb)

Density (bp per 100 kb)

Gene (bp%)

Val. SNP (per 100 kb)

SNP:indel


(per 100 kb)

(bp/100 kb)


Overall

4,486

13,010

29,998,060

15.0

43.4

2.2

102.4

6.7

2.4

1: ENm001 CFTR

7

189

533

1,877,426

10.1

28.4

1.2

64.5

5.8

2.3

2: ENm002 Interleukin

5

139

535

1,000,000

13.9

53.5

3.0

101.1

6.6

1.9

3: ENm003 ApoCluster

11

59

187

500,000

11.8

37.4

2.1

93.2

8.4

2.5

4: ENm004

22

289

789

1,700,000

17.0

46.4

2.1

89.7

4.9

1.9

5: ENm005

21

368

982

1,695,985

21.7

57.9

2.4

108.1

4.3

1.9

6: ENm006

X

97

249

1,338,447

7.2

18.6

5.5

34.5

7.4

1.9

7: ENm007

19

207

711

1,000,876

20.7

71.0

4.9

151.6

7.8

2.1

8: ENm008 AlphaGlobin

16

118

253

500,000

23.6

50.6

5.2

120.2

5.0

2.4

9: ENm009 BetaGlobin

11

168

545

1,001,592

16.8

54.4

4.2

181.4

10.9

3.3

10: ENm010 HOXACluster

7

95

317

500,000

19.0

63.4

2.4

89.4

4.5

1.4

11: ENm011 1GF2H19

11

62

228

606,048

10.2

37.6

2.1

102.3

13.4

2.7

12: ENm012 FOXP2

7

128

370

1,000,000

12.8

37.0

0.3

73.2

5.9

2.0

13: ENm013

7

139

483

1,114,424

12.5

43.3

1.0

105.7

7.7

2.4

14: ENm014

7

128

322

1,163,197

11.0

27.7

0.8

83.4

7.6

3.0

Manual

2,186

6,504

14,997,995

14.6

43.4

2.7

95.9

6.5

2.2

15: ENr111

13

96

364

500,000

19.2

72.8

0.3

128.2

5.7

1.8

16: ENr112

2

55

156

500,000

11.0

31.2

0.0

94.2

10.6

3.0

17: ENr113

4

56

152

500,000

11.2

30.4

0.1

104.0

9.6

3.4

18: ENr114

10

101

284

500,000

20.2

56.8

1.0

142.8

8.5

2.5

19: ENr121

2

108

270

500,000

21.6

54.0

0.8

140.0

6.1

2.6

20: ENr122

18

76

287

500,000

15.2

57.4

1.9

139.8

8.2

2.4

21: ENr123

12

65

136

500,000

13.0

27.2

2.5

122.0

9.2

4.5

22: ENr131

2

75

202

500,064

15.0

40.4

3.6

123.4

6.9

3.1

23: ENr132

13

43

169

500,000

8.6

33.8

1.9

123.8

14.5

3.7

24: ENr133

21

112

293

500,000

22.4

58.6

2.2

165.0

6.3

2.8

25: ENr211

16

68

251

500,001

13.6

50.2

0.1

114.8

8.8

2.3

26: ENr212

5

70

118

500,000

14.0

23.6

0.3

112.6

7.6

4.8

27: ENr213

18

74

165

500,000

14.8

33.0

0.6

91.8

6.0

2.8

28: ENr221

5

68

156

500,000

13.6

31.2

1.4

105.0

6.9

3.4

29: ENr222

6

73

201

500,000

14.6

40.2

0.9

104.0

6.4

2.6

30: ENr223

6

130

384

500,000

26.0

76.8

2.2

135.2

4.5

1.8

31: ENr231

1

91

178

500,000

18.2

35.6

4.8

94.6

4.9

2.7

32: ENr232

9

93

282

500,000

18.6

56.4

3.2

112.0

5.8

2.0

33: ENr233

15

47

126

500,000

9.4

25.2

7.3

59.8

7.4

2.4

34: ENr311

14

50

171

500,000

10.0

34.2

0.0

93.0

8.8

2.7

35: ENr312

11

54

176

500,000

10.8

35.2

0.0

142.0

12.2

4.0

36: ENr313

16

83

242

500,000

16.6

48.4

0.0

108.4

6.4

2.2

37: ENr321

8

84

257

500,000

16.8

51.4

0.4

94.0

4.6

1.8

38: ENr322

14

86

323

500,000

17.2

64.6

0.8

127.6

7.3

2.0

39: ENr323

6

77

176

500,000

15.4

35.2

0.7

78.8

4.7

2.2

40: ENr324

X

70

138

500,000

14.0

27.6

1.3

43.8

4.3

1.6

41: ENr331

2

67

204.0

500,000

13.4

40.8

6.4

118.8

8.4

2.9

42: ENr332

11

60

184

500,000

12.0

36.8

6.5

88.6

7.6

2.4

43: ENr333

20

89

226

500,000

17.8

45.2

6.1

77.2

4.0

1.7

44: ENr334

6

79

235

500,000

15.8

47.0

2.2

83.4

5.4

1.8


Random

2,300

6,506

15,000,065

15.3

43.4

2.0

109.0

6.9

2.5


Manual (regions 1-14; each approx. 500 kb-2 MB) and random (regions 15-44 each approx. 500 kb) selected ENCODE regions are defined [12] as:

Manual: genomic regions with well studied genes and availability of comparative sequence

Random: selected randomly across the genome, stratified by gene density and non-exonic conservation

The ten Encyclopedia of DNA Elements (ENCODE) regions with in-depth single nucleotide polymorphism (SNP) discovery are ENm010, ENm013, ENm014, ENr112, ENr113, ENr123, ENr131, ENr213, ENr232, and ENr321. bp, base pairs; kb, kilobases.

Clark et al. Genome Biology 2007 8:R180   doi:10.1186/gb-2007-8-9-r180

Open Data