Joint Open Genome and Omics Platform (JoGo)

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geneid	64591
ensemblid	ENSG00000168757.13
hgncid	23924
symbol	TSPY2
name	testis specific protein Y-linked 2
refseq_nuc	NM_022573.4
refseq_prot	NP_072095.2
ensembl_nuc	ENST00000320701.9
ensembl_prot	ENSP00000314077.4
mane_status	MANE Select
chr	chrY
start	6246223
end	6249018
strand	+
ver	v1.2
region	chrY:6246223-6249018
region5000	chrY:6241223-6254018
regionname0	TSPY2_chrY_6246223_6249018
regionname5000	TSPY2_chrY_6241223_6254018

ahapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	alen	total	AFR	AMR	EAS	EUR	SAS	JPT	regionname	genename	aa	chr	start	end
a0001	0/0	308	95	11	19	46	4	15	39	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0002	0/0	308	11	0	0	11	0	0	6	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0003	0/0	308	1	1	0	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0004	0/0	70	1	0	0	1	0	0	1	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018

chapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
c0001	0/0	927	95	11	19	46	4	15	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
c0002	0/0	927	11	0	0	11	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
c0003	0/0	929	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
c0004	0/0	927	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018

thapid	grch38 chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
t0001	0/0	240	104	11	19	55	4	15	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
t0002	0/0	241	3	0	0	3	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
t0003	0/0	240	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018

ghapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
g0001	0/0	93	12	14	48	4	15	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0002	0/0	5	0	5	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0003	0/0	3	0	0	3	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0004	0/0	2	0	0	2	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0005	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0006	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0007	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0008	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
g0009	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018

achapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	clen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	cseq	chr	start	end
a0001c0001	0/0	927	95	11	19	46	4	15	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0002c0002	0/0	927	11	0	0	11	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0003c0004	0/0	927	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0004c0003	0/0	929	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1166	91	10	19	43	4	15	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0001c0001t0002	0/0	1167	3	0	0	3	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0001c0001t0003	0/0	1166	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0002c0002t0001	0/0	1166	11	0	0	11	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0003c0004t0001	0/0	1166	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018
a0004c0003t0001	0/0	1168	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	copy fasta	chrY	6241223	6254018

actghapid	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	chr	start	end
a0001c0001t0001g0001	0/0	81	10	14	38	4	15	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0001g0002	0/0	5	0	5	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0001g0004	0/0	2	0	0	2	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0001g0007	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0001g0008	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0001g0009	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0002g0003	0/0	3	0	0	3	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0001c0001t0003g0001	0/0	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0002c0002t0001g0001	0/0	10	0	0	10	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0002c0002t0001g0006	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0003c0004t0001g0001	0/0	1	1	0	0	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
a0004c0003t0001g0005	0/0	1	0	0	1	0	0	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG00140	hp1	a0001	c0001	t0001	g0001	EUR	GBR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG00642	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG00738	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01069	hp1	a0001	c0001	t0001	g0002	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01074	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01099	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01109	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01167	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01192	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01243	hp1	a0001	c0001	t0001	g0001	AMR	PUR	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01255	hp1	a0001	c0001	t0001	g0002	AMR	CLM	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01256	hp1	a0001	c0001	t0001	g0002	AMR	CLM	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01258	hp2	a0001	c0001	t0001	g0002	AMR	CLM	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01261	hp1	a0001	c0001	t0001	g0001	AMR	CLM	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01358	hp1	a0001	c0001	t0001	g0001	AMR	CLM	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01433	hp1	a0001	c0001	t0001	g0002	AMR	CLM	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01515	hp1	a0001	c0001	t0001	g0001	EUR	IBS	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01928	hp1	a0001	c0001	t0001	g0001	AMR	PEL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01934	hp1	a0001	c0001	t0001	g0001	AMR	PEL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01943	hp1	a0001	c0001	t0001	g0001	AMR	PEL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG01952	hp1	a0001	c0001	t0001	g0001	AMR	PEL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02015	hp1	a0001	c0001	t0001	g0009	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02027	hp1	a0002	c0002	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02040	hp1	a0001	c0001	t0001	g0008	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02055	hp1	a0001	c0001	t0001	g0001	AFR	ACB	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02056	hp1	a0002	c0002	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02071	hp1	a0002	c0002	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02074	hp1	a0001	c0001	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02083	hp1	a0001	c0001	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02129	hp1	a0002	c0002	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02132	hp1	a0001	c0001	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02135	hp1	a0002	c0002	t0001	g0001	EAS	KHV	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02145	hp1	a0001	c0001	t0001	g0001	AFR	ACB	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02258	hp1	a0001	c0001	t0001	g0001	AFR	ACB	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02572	hp1	a0003	c0004	t0001	g0001	AFR	GWD	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02602	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02647	hp1	a0001	c0001	t0003	g0001	AFR	GWD	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02698	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02717	hp1	a0001	c0001	t0001	g0001	AFR	GWD	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02738	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02895	hp1	a0001	c0001	t0001	g0001	AFR	GWD	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG02965	hp1	a0001	c0001	t0001	g0001	AFR	ESN	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03017	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03130	hp1	a0001	c0001	t0001	g0001	AFR	ESN	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03225	hp1	a0001	c0001	t0001	g0001	AFR	MSL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03490	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03492	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03579	hp1	a0001	c0001	t0001	g0001	AFR	MSL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03654	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03688	hp2	a0001	c0001	t0001	g0001	SAS	STU	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03710	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03942	hp1	a0001	c0001	t0001	g0001	SAS	BEB	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG04115	hp1	a0001	c0001	t0001	g0001	SAS	STU	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG04199	hp1	a0001	c0001	t0001	g0001	SAS	STU	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG04204	hp1	a0001	c0001	t0001	g0001	SAS	STU	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG04228	hp1	a0001	c0001	t0001	g0001	SAS	STU	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18612	hp2	a0001	c0001	t0001	g0004	EAS	CHB	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18747	hp1	a0001	c0001	t0001	g0001	EAS	CHB	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18940	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18943	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18944	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18945	hp1	a0002	c0002	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18948	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18952	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18960	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18961	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18962	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18965	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18966	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18967	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18970	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18971	hp1	a0001	c0001	t0002	g0003	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18977	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18982	hp1	a0002	c0002	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18985	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18986	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18989	hp1	a0001	c0001	t0002	g0003	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18990	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18994	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18995	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19000	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19004	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19005	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19006	hp1	a0001	c0001	t0002	g0003	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19007	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19055	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19056	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19060	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19063	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19066	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19067	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19068	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19070	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19072	hp1	a0002	c0002	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19075	hp1	a0001	c0001	t0001	g0007	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19076	hp1	a0004	c0003	t0001	g0005	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19079	hp1	a0001	c0001	t0001	g0004	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19082	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19083	hp1	a0002	c0002	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19085	hp1	a0002	c0002	t0001	g0006	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19086	hp1	a0002	c0002	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19088	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA19089	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA20752	hp1	a0001	c0001	t0001	g0001	EUR	TSI	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA20805	hp1	a0001	c0001	t0001	g0001	EUR	TSI	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA20905	hp1	a0001	c0001	t0001	g0001	SAS	GIH	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
HG03471	hp1	a0001	c0001	t0001	g0001	AFR	MSL	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018
NA18955	hp1	a0001	c0001	t0001	g0001	EAS	JPT	TSPY2_chrY_6241223_6254018	TSPY2	chrY	6241223	6254018

chr:pos	ref	alt	# # of ahapid:amino-acid(protein) level	ahapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	status	chr	pos
chrY:6246324	C C	T T	1	a0003 a0003	1	HG02572.hp1 HG02572.hp1	missense_variant	MODERATE	c.56C>T c.56C>T	p.Ser19Phe p.Ser19Phe	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/6	102/1166	56/927	19/308		chrY	6246324
chrY:6246352	C C	CT CT	1	a0004 a0004	1	NA19076.hp1 NA19076.hp1	frameshift_variant	HIGH	c.86dupT c.86dupT	p.Leu29fs p.Leu29fs	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/6	133/1166	87/927	29/308	INFO_REALIGN_3_PRIME	chrY	6246352
chrY:6246408	A A	AG AG	1	a0004 a0004	1	NA19076.hp1 NA19076.hp1	frameshift_variant	HIGH	c.145dupG c.145dupG	p.Ala49fs p.Ala49fs	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/6	192/1166	146/927	49/308	INFO_REALIGN_3_PRIME	chrY	6246408
chrY:6246522	A A	G G	2	a0002 a0004 a0002 a0004	12	HG02027.hp1 HG02056.hp1 HG02071.hp1 others(9): Show HG02027.hp1 HG02056.hp1 HG02071.hp1 HG02129.hp1 HG02135.hp1 NA18945.hp1 NA18982.hp1 NA19072.hp1 NA19076.hp1 NA19083.hp1 NA19085.hp1 NA19086.hp1	missense_variant	MODERATE	c.254A>G c.254A>G	p.Glu85Gly p.Glu85Gly	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/6	300/1166	254/927	85/308		chrY	6246522

chr:pos	ref	alt	# # of chapid	chapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos

chr:pos	ref	alt	# # of thapid:transcript level	thapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	transcript_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:6248894	A A	G G	2	a0001c0001t0002 a0001c0001t0003 a0001c0001t0002 a0001c0001t0003	4	HG02647.hp1 NA18971.hp1 NA18989.hp1 others(1): Show HG02647.hp1 NA18971.hp1 NA18989.hp1 NA19006.hp1	3_prime_UTR_variant	MODIFIER	c.69A>G c.69A>G		TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	6/6				69		chrY	6248894
chrY:6248912	C C	CT CT	1	a0001c0001t0002 a0001c0001t0002	3	NA18971.hp1 NA18989.hp1 NA19006.hp1 NA18971.hp1 NA18989.hp1 NA19006.hp1	3_prime_UTR_variant	MODIFIER	c.89dupT c.89dupT		TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	6/6				90	INFO_REALIGN_3_PRIME	chrY	6248912

chr:pos	ref	alt	# # of ghapid:genebody level	ghapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	genename	geneid	featuretype	featureid	genebody_biotype	rank	status	chr	pos
chrY:6246857	A A	G G	1	a0001c0001t0001g0009 a0001c0001t0001g0009	1	HG02015.hp1 HG02015.hp1	intron_variant	MODIFIER	c.486+103A>G c.486+103A>G	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/5		chrY	6246857
chrY:6246872	C C	T T	1	a0001c0001t0001g0008 a0001c0001t0001g0008	1	HG02040.hp1 HG02040.hp1	intron_variant	MODIFIER	c.486+118C>T c.486+118C>T	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/5		chrY	6246872
chrY:6246921	T T	TC TC	1	a0004c0003t0001g0005 a0004c0003t0001g0005	1	NA19076.hp1 NA19076.hp1	intron_variant	MODIFIER	c.486+169dupC c.486+169dupC	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/5	INFO_REALIGN_3_PRIME	chrY	6246921
chrY:6247222	CG CG	C C	1	a0004c0003t0001g0005 a0004c0003t0001g0005	1	NA19076.hp1 NA19076.hp1	intron_variant	MODIFIER	c.487-130delG c.487-130delG	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	1/5	INFO_REALIGN_3_PRIME	chrY	6247222
chrY:6248307	T T	G G	1	a0002c0002t0001g0006 a0002c0002t0001g0006	1	NA19085.hp1 NA19085.hp1	intron_variant	MODIFIER	c.904+199T>G c.904+199T>G	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5		chrY	6248307
chrY:6248326	C C	CG CG	1	a0001c0001t0001g0007 a0001c0001t0001g0007	1	NA19075.hp1 NA19075.hp1	intron_variant	MODIFIER	c.904+221dupG c.904+221dupG	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	6248326
chrY:6248463	A A	G G	1	a0001c0001t0002g0003 a0001c0001t0002g0003	3	NA18971.hp1 NA18989.hp1 NA19006.hp1 NA18971.hp1 NA18989.hp1 NA19006.hp1	intron_variant	MODIFIER	c.905-340A>G c.905-340A>G	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5		chrY	6248463
chrY:6248541	G G	C C	1	a0001c0001t0001g0002 a0001c0001t0001g0002	5	HG01069.hp1 HG01255.hp1 HG01256.hp1 others(2): Show HG01069.hp1 HG01255.hp1 HG01256.hp1 HG01258.hp2 HG01433.hp1	intron_variant	MODIFIER	c.905-262G>C c.905-262G>C	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5		chrY	6248541
chrY:6248686	G G	A A	1	a0001c0001t0001g0004 a0001c0001t0001g0004	2	NA18612.hp2 NA19079.hp1 NA18612.hp2 NA19079.hp1	intron_variant	MODIFIER	c.905-117G>A c.905-117G>A	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5		chrY	6248686
chrY:6248699	CA CA	C C	1	a0001c0001t0001g0007 a0001c0001t0001g0007	1	NA19075.hp1 NA19075.hp1	intron_variant	MODIFIER	c.905-101delA c.905-101delA	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	6248699
chrY:6248703	TG TG	T T	1	a0004c0003t0001g0005 a0004c0003t0001g0005	1	NA19076.hp1 NA19076.hp1	intron_variant	MODIFIER	c.905-96delG c.905-96delG	TSPY2	ENSG00000168757.13	transcript	ENST00000320701.9	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	6248703

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🧬 JoGo Online Haplotype Explorer TSPY2_chrY_6241223_6254018

JoGo Local Haplotype Explorer (on iGV) TSPY2_chrY_6241223_6254018

Translation Multiple Alignment View

🧬 Gene Summary

AAmino acid(protein) Level Haplotype Info (Total: 4)

CCoding Level Haplotype Info (Total: 4)

TTranscript Level Haplotype Info (Total: 3)

GGenebody Level Haplotype Info (Total: 9)

A C AC Level (Amino Acid + Coding) Haplotype Info (Total: 4)

A C T ACT Level (Amino Acid + Coding + Transcript) Haplotype Info (Total: 6)

A C T G ACTG Level (Amino Acid + Coding + Transcript + Genebody) Haplotype Info (Total: 12)

Haplotype Details by Sample (Haploid Level) (Total: 108)

AAmino acid(protein) Level Haplotype Related Variants (Effect to Protein Coding Variants) (Total: 4)

CCoding Level Variants (Synonymous Mutations) (Total: 0)

TTranscript Level Haplotype Variants (5'UTR+3'UTR) (Total: 2)

GGenebody Level Haplotype Variants (Intron) (Total: 11)

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Annotation (Repeats)

Annotation (SNP Array)