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.