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

Clark, Taane G; Andrew, Toby; Cooper, Gregory M; Margulies, Elliott H; Mullikin, James C; Balding, David J

doi:10.1186/gb-2007-8-9-r180

Table 1 Indel density (for all 44 ENCODE regions)

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

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.

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ISSN: 1474-760X

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