YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data

Zhang, Fan; Chen, Ruoyan; Liu, Dongbing; Yao, Xiaotian; Li, Guoqing; Jin, Yabin; Yu, Chang; Li, Yingrui; Coin, Lachlan JM

doi:10.1186/1471-2105-14-331

BMC Bioinformatics

Table 1 Assignment of individuals included in this study to haplogroups

From: YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data

Pop	ID	Hapmap¹	1KG²	Chip³	NGS⁴	Pop	ID	Hapmap¹	1KG²	Chip³	NGS⁴	Pop	ID	Hapmap¹	1KG²	Chip³	NGS⁴
CHB	NA18558	O	N	N1	N1c1c1	CEU	NA06994	HI	I1	I1	I1b1	YRI	NA18501	E3a	E1b1a8a	E1b1a	E1b1a
CHB	NA18561	O	O2b	O2	O2b	CEU	NA07357	R	R1b1b21	R1b1b2	R1b1b2	YRI	NA18504	E3a7	E1b1a	E1b1a	E1b1a
CHB	NA18562	O	O	O3a	O3a3b1	CEU	NA10851	R	R	R1b1b2	R1b1b2	YRI	NA18507	E3a7	E1b1a	E1b1a	E1b1a
CHB	NA18563	O	O2b	O2	O2b	CEU	NA11829	HI	I1	I1	I1b1	YRI	NA18516	E3a	E1b1a	E1b1a	E1b1a
CHB	NA18572	O	O	O3a	O3a3b1	CEU	NA11831	R	R	R1b1b2	R1b1b2	YRI	NA18522	E3a	E1b1a	E1b1a	E1b1a
CHB	NA18603	O	O	O2	O2a1a	CEU	NA11881	HI	I1	I1	I1b1	YRI	NA18853	E3a	E1b1a8a	E1b1a	E1b1a
CHB	NA18605	O	O	O	O3a3b1	CEU	NA11994	R	R1b1b21	R1b1b2	R1b1b2	YRI	NA18856	E1	E1	E1/E2	E1/E2
CHB	NA18608	O	N	N1	N1c1c	CEU	NA12003	HI	I2b	I2b	I2b	YRI	NA18871	E3a	E1b1a8a	E1b1a	E1b1a
CHB	NA18609	O	O	O3a	O3a3b1	CEU	NA12005	R	R1b1b2	R1b1b2	R1b1b2	YRI	NA19098	E3a	E1b1a	E1b1a	E1b1a
JPT	NA18940	D	D2 × D2b1	D2a	D2a	CEU	NA12043	R	R1	R1b1b2	R1b1b2	YRI	NA19119	E3a	E1b1a8a	E1b1a	E1b1a
JPT	NA18943	O	O2b	O2	O2b	CEU	NA12144	R	R1b1b21	R1b1b2	R1b1b2	YRI	NA19138	E3a	E1b1a8a	E1b1a	E1b1a
JPT	NA18944	D	D2b1	D2a	D2a	CEU	NA12154	R	R1	R1b1b2	R1b1b2	YRI	NA19141	E3a	E1b1a8a	E1b1a	E1b1a
JPT	NA18945	O	O	O3a	O2b	CEU	NA12155	R	R1	R1a1	R1a1c	YRI	NA19144	E3a	E1b1a8a	E1b1a	E1b1a
JPT	NA18948	D	D2b1	D2a	D2a	CEU	NA12716	R	R1	R1b1b2	R1b1b2	YRI	NA19153	E3a	E1b1a8a	E1b1a	E1b1a
JPT	NA18952	D	D	D2a	D2a	CEU	NA12750	HI	I1	I1	I1b1	YRI	NA19160	E3a	E1b1a8a	E1b1a	E1b1a
JPT	NA18953	O	O2b	O2	O2a	CEU	NA1760	R	R	R1b1b2	R1b1b2	YRI	NA19171	E3a7	E1b1a	E1b1a	E1b1a
JPT	NA18959	O	O	O3a	O3a3b1	CEU	NA12762	R	R1	R1b1b2	R1b1b2	YRI	NA19200	E3a7	E1b1a	E1b1a	E1b1a
JPT	NA18960	D	D2 × D2b1	D2a	D2a	CEU	NA12812	R	R1	R1b1b2	R1b1b2	YRI	NA19207	E3a	E1b1a	E1b1a	E1b1a
JPT	NA18961	D	D	D2a	D2a	CEU	NA12814	R	R1	R1b1b2	R1b1b2	YRI	NA19210	E3a7	E1b1a	E1b1a	E1b1a
JPT	NA18965	O	O2b	O2	O2b	CEU	NA12872	R	R1b1b2g	R1b1b2	R1b1b2
JPT	NA18967	D	D2b1	D2a	D2a	CEU	NA12874	R	R1	R	R1b1b2
JPT	NA18970	D	D2 × D2b1	D2a	D2a
JPT	NA18971	C	C1	C1a	C3
JPT	NA18974	C	C1	C1a	C3
JPT	NA19005	O	O2b	O2	O2b

*E1b1a was formerly known as E3a.
¹Hapmap indicates results from Hapmap consortium.
²IKG indicates results form 1000 genomes consortium.
³Chip indicates results from YHap applied to Hapmap genotype data.
⁴NGS indicates results from YHap applied to 1000 genomes consortium sequence data.
The resolution reported for YHap is the level at which a single assignment achieved greater than 90% posterior probability.

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ISSN: 1471-2105

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