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