Comparison of measures of marker informativeness for ancestry and admixture mapping

BMC Genomics

Table 1 Chromosome length and number of SNP markers across the genome in CEU and YRI population of the HapMap Phase III dataset

		Number of SNPs			SNPs genotyped in both population^a
Chr #	length	in each population		SNPs genotyped	and fulfilling the filtering criteria^b
	(Mb)	CEU	YRI	in both populations^a	Delta	F_ST	FIC	SIC	I_n
1	246.6	111887	120349	103330	1663	1657	1653	1651	1654
2	242.7	113613	122377	106053	1742	1751	1742	1740	1749
3	199.3	94608	101070	88060	1464	1447	1448	1450	1450
4	191.2	85403	92052	79856	1390	1394	1387	1398	1392
5	180.6	87071	92350	81083	1310	1298	1314	1302	1304
6	170.7	91415	95108	84536	1241	1235	1239	1231	1236
7	158.7	75234	79231	69766	1139	1144	1152	1157	1148
8	146.2	74443	79368	69177	1053	1055	1053	1048	1054
9	140.2	63507	66437	58713	842	841	834	844	845
10	135.3	72846	76787	67388	979	988	980	980	988
11	134.3	69175	73942	64140	986	987	988	990	981
12	132.3	67486	70909	62018	988	981	973	972	977
13	96.2	51879	55392	48496	719	726	701	713	723
14	88.2	44570	47354	41434	646	646	650	648	650
15	82.0	40705	43837	37774	590	596	596	590	595
16	88.7	42738	46366	39616	568	559	554	555	557
17	78.6	36534	39075	33576	572	569	580	574	570
18	76.1	40153	43467	37669	562	568	564	561	572
19	63.6	25251	26798	23264	405	404	404	407	405
20	62.4	35252	37476	32870	447	447	446	448	443
21	37.1	19336	20556	18105	252	250	254	249	249
22	35.1	19617	20595	17817	249	253	253	252	249
Total		1362723	1450896	1264741	19807	19796	19765	19760	19791

^a Two inclusion criteria are in effective: 1) The SNP is shared by both YRI and CEU populations and 2) SNPs with missing frequency less than 10% of the samples.
^b Every SNP is at least 100 kb from its nearest neighbor.

ISSN: 1471-2164