Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits

Huang, Yu S.; Ramensky, Vasily; Service, Susan K.; Jasinska, Anna J.; Jung, Yoon; Choi, Oi-Wa; Cantor, Rita M.; Juretic, Nikoleta; Wasserscheid, Jessica; Kaplan, Jay R.; Jorgensen, Matthew J.; Dyer, Thomas D.; Dewar, Ken; Blangero, John; Wilson, Richard K.; Warren, Wesley; Weinstock, George M.; Freimer, Nelson B.

doi:10.1186/s12915-015-0152-2

Table 3 Characteristics of the two mapping sets of markers derived in Stage 4

From: Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits

	Approx. 500K mapping set					Approx. 150K mapping set
CHR	N	SNP/Mb^a	Max Gap^b (BP)	Mean Gap^b (BP)	Mean R2^c	N	SNP/Mb^a	Max Gap^b (BP)	Mean Gap^b (BP)	Mean R2^c
1	25863	205.2	1074224	4873	0.38	7695	61.1	1112341	16380	0.31
2	16774	185.7	3730217	5385	0.40	4403	48.8	3731818	20515	0.34
3	18390	199.7	1144078	5007	0.38	5653	61.4	1176302	16291	0.33
4	15560	209.3	1663269	4777	0.39	5476	73.7	1689958	13576	0.34
5	15940	211.4	1150416	4730	0.38	4674	62.0	1275087	16132	0.32
6	10112	198.7	1020214	5032	0.36	2792	54.9	1030612	18227	0.29
7	24288	178.9	1518445	5590	0.40	7026	51.8	1631219	19310	0.35
8	28272	220.8	2004329	4530	0.37	9192	71.8	2598031	13933	0.33
9	21550	171.6	1066472	5828	0.38	6456	51.4	1089666	19453	0.33
10	20112	156.4	1043042	6393	0.39	6104	47.5	1050307	21054	0.37
11	25512	198.5	2199143	5038	0.39	7530	58.6	2424911	17072	0.32
12	17587	162.0	1420166	6171	0.39	5615	51.7	1520086	19331	0.34
13	18794	191.1	1516380	5234	0.38	5934	60.4	1518768	16573	0.33
14	19105	177.6	1817866	5632	0.44	5943	55.3	1830044	18099	0.39
15	18395	200.5	1542801	4988	0.39	5110	55.7	1545377	17952	0.32
16	14040	186.9	1023476	5350	0.36	3698	49.3	1026661	20304	0.30
17	15640	217.3	1093222	4602	0.39	4292	59.7	1122085	16754	0.34
18	15291	211.6	1330661	4726	0.41	4623	64.0	1542198	15620	0.35
19	5596	173.5	476395	5765	0.41	1416	43.9	554050	22793	0.35
20	27113	209.3	459070	4778	0.35	8034	62.1	711003	16094	0.28
21	18878	149.6	1477644	6685	0.41	6175	48.9	1502779	20435	0.37
22	15859	158.4	258174	6314	0.43	5064	50.6	422458	19777	0.40
23	16564	202.4	391245	4940	0.38	5118	62.6	732327	15985	0.32
24	18746	223.4	225900	4476	0.37	4889	58.3	325648	17162	0.32
25	18731	221.2	238967	4522	0.37	5563	65.7	421038	15228	0.30
26	12435	217.8	215585	4593	0.38	3324	58.3	270040	17166	0.31
27	12055	259.1	284037	3860	0.37	3470	74.8	425185	13379	0.31
28	4122	207.4	199874	4822	0.43	1046	52.7	379794	19003	0.37
29	5839	252.6	112574	3960	0.35	1652	71.5	211468	13998	0.29

^aNumber of SNPs per Mb
^bMax and mean distance between consecutive SNPs, in basepairs
^cAverage of pairwise estimates of windows of five markers

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ISSN: 1741-7007

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