Functional constraint and small insertions and deletions in the ENCODE regions of the human genome

Table 3 Comparison of indel and SNP density by ENCODE experimental features

	Indels		Validated SNPs
	bp/100 kb	99% CI	bp	bp/100 kb
Manual	43.4	34.4 to 54.7	14,390	95.9
Random	43.4	37.5 to 50.2	16,343	109.0
Overall	43.4	38.3 to 49.1	30,733	102.4
RNA transcription
CDS	0.7	0.1 to 8.6	421	62.4
TSS	3.3		42	68.7
RACEfrags	6.6	1.3 to 33.9	278	65.4
TARs/transfrags	12.3	6.8 to 22.3	591	93.1
Pseudo-exons	19.1	5.8 to 63.3	132	96.9
3' UTR	23.6	13.5 to 41.3	370	84.8
3' UTR	27.4	3.8 to 198.7	97	83.2
TUF	36.9	20.2 to 67.6	423	97.6
Open chromatin
FAIRE-sites	23.8	15.5 to 36.7	1,232	89.8
DHS (NHGRI)	19.7	8.3 to 46.9	297	95.9
DHS (Regulome)	27.0	13.4 to 54.4	450	90.1
DNA-protein interaction/transcript regulation
HisPolTAF	32.4	22.5 to 46.5	850	79.0
Seq_specific (all motifs)	35.8	23.1 to 55.3	1,098	93.5
SeqSp (sequence specific factors)	42.5	20.1 to 89.5	421	79.4
Ancestral repeats	26.5	21.7 to 32.5	5,749	95.9
Evolutionary constraint
MCS strict	4.1	1.6 to 10.4	229	30.6
MCS moderate	11.2	6.8 to 18.5	667	44.0
MCS loose	26.4	20.9 to 33.4	2,052	56.4
Cell cycle
EarlyRepSeg	43.5	33.3 to 56.9	6,165	89.8
MidRepSeg	43.2	35.3 to 53.0	7,418	95.7
LateRepSeg	41.9	32.9 to 53.3	8,896	111.3

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; SNP, single nucleotide polymorphism; TAR, transcriptionally active region; TSS, transcription start site; TUF, transcripts of unknown function; UTR, untranslated region.

ISSN: 1474-760X