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