BMC Genomic Data

Table 1 Haplotype frequency estimates in the MGLL region using data from 148 obese individuals

From: An EM algorithm based on an internal list for estimating haplotype distributions of rare variants from pooled genotype data

	k=1, n=148				k=2, n=74
Position of ‘1’s	CDMLE	EML	EM-CDL	EM-ATCDL		CDMLE	EML	EM-CDL	EM-ATCDL
None	0.7927	0.7941	0.7995	0.7984		0.7912	0.8202	0.8169	0.7898
1	0.0536	0.0505	0.0509	0.0544		0.0497	0.0397	0.0398	0.0494
2	0.0043	0.0034	0.0034	0.0034					0.0034
3	0.0456	0.0433	0.0436	0.0441		0.0381	0.0291	0.0291	0.0440
5	0.0043	0.0034	0.0034	0.0034					0.0034
6	0.0043	0.0034	0.0034	0.0034		0.0067	0.0034	0.0034	0.0034
9	0.0085	0.0072	0.0073	0.0103		0.0133	0.0079	0.0079	0.0101
11	0.0043	0.0034	0.0034	0.0034					0.0034
14									0.0034
15	0.0043	0.0034	0.0034	0.0034					0.0034
19	0.0043	0.0068	0.0068	0.0068		0.0067	0.0069	0.0101	0.0101
20	0.0043	0.0068	0.0068	0.0068		0.0067	0.0069	0.0101	0.0101
21	0.0043	0.0034	0.0034	0.0034					0.0034
22	0.0127	0.0101	0.0102	0.0103		0.0197	0.0101	0.0101	0.0101
23	0.0043	0.0034	0.0034	0.0034		0.0067	0.0034	0.0034	0.0034
24	0.0127	0.0101	0.0102	0.0103		0.0067	0.0040	0.0040	0.0040
1, 3	0.0048	0.0040	0.0040	0.0038		0.0090	0.0059	0.0059	0.0020
1, 9	0.0034	0.0029	0.0029			0.0032	0.0022	0.0022
1, 15						0.0056	0.0034	0.0034
1, 24						0.0098	0.0064	0.0064	0.0095
2, 3						0.0059	0.0034	0.0034
3, 14	0.0040	0.0034	0.0034			0.0059	0.0034	0.0034
3, 11						0.0059	0.0034	0.0034
5, 21						0.0067	0.0034	0.0034
6, 7	0.0250	0.0203	0.0204	0.0205		0.0314	0.0182	0.0181	0.0189
19, 20		0.0017					0.0033
3, 6, 7	0.0026	0.0034	0.0034	0.0034		0.0066	0.0057	0.0057	0.0081
6, 19, 20		0.0017
7, 19, 20		0.0017
1, 6, 7, 24	0.0039	0.0034	0.0034	0.0034
6, 7, 19, 20	0.0041	0.0017				0.0057	0.0033	0.0034	0.0034
1, 3, 6, 7, 24						0.0041	0.0032	0.0032
1, 12, 13, 22, 25	0.0039	0.0034	0.0034	0.0034		0.0053	0.0034	0.0034	0.0034

Estimates of haplotype frequencies for the 25 rare variants in the MGLL region obtained by CDMLE (collapsed data maximum likelihood estimation), EML (EM with combinatorially determined list), EM-CDL (EM with CD list) and EM-ATCDL (EM with augmented and trimmed CD list with adaptive threshold) based on n=148/k pools of k individuals each.

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