Joint Open Genome and Omics Platform (JoGo)

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geneid	7258
ensemblid	ENSG00000258992.7
hgncid	12381
symbol	TSPY1
name	testis specific protein Y-linked 1
refseq_nuc	NM_003308.4
refseq_prot	NP_003299.2
ensembl_nuc	ENST00000451548.6
ensembl_prot	ENSP00000403304.1
mane_status	MANE Select
chr	chrY
start	9466955
end	9469749
strand	+
ver	v1.2
region	chrY:9466955-9469749
region5000	chrY:9461955-9474749
regionname0	TSPY1_chrY_9466955_9469749
regionname5000	TSPY1_chrY_9461955_9474749

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	10	2	1	3	0	4	2	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0002	0/0	88	4	0	1	0	2	1	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0003	0/0	308	4	0	1	1	1	1	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0004	0/0	290	1	0	0	1	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0005	0/0	308	1	0	0	1	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0006	0/0	308	1	1	0	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0007	0/0	171	1	0	0	1	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0008	0/0	308	1	0	0	0	0	1	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749

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	7	1	1	1	0	4	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0002	0/0	927	4	0	1	0	2	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0003	0/0	927	3	0	1	0	1	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0004	0/0	927	2	1	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0005	0/0	927	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0006	0/0	925	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0007	0/0	927	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0008	0/0	927	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0009	0/0	926	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0010	0/0	927	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
c0011	0/0	927	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749

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	236	12	1	2	2	1	6	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
t0002	0/0	235	8	1	1	3	2	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
t0003	0/0	235	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
t0004	0/0	237	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
t0005	0/0	235	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749

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	7	1	0	1	0	5	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0002	0/0	4	0	1	0	2	1	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0003	0/0	2	0	1	0	1	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0004	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0005	0/0	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0006	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0007	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0008	0/0	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0009	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0010	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0011	0/0	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0012	0/0	1	0	1	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
g0013	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749

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	7	1	1	1	0	4	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0001c0004	0/0	927	2	1	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0001c0008	0/0	927	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0002c0002	0/0	927	4	0	1	0	2	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0003c0003	0/0	927	3	0	1	0	1	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0003c0011	0/0	927	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0004c0009	0/0	926	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0005c0010	0/0	927	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0006c0007	0/0	927	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0007c0006	0/0	925	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0008c0005	0/0	927	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1162	6	0	1	1	0	4	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0001c0001t0002	0/0	1161	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0001c0004t0002	0/0	1161	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0001c0004t0003	0/0	1161	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0001c0008t0001	0/0	1162	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0002c0002t0002	0/0	1161	4	0	1	0	2	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0003c0003t0001	0/0	1162	3	0	1	0	1	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0003c0011t0002	0/0	1161	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0004c0009t0004	0/0	1162	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0005c0010t0002	0/0	1161	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0006c0007t0001	0/0	1162	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0007c0006t0005	0/0	1159	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749
a0008c0005t0001	0/0	1162	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	copy fasta	chrY	9461955	9474749

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	4	0	0	1	0	3	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0001c0001t0001g0011	0/0	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0001c0001t0001g0012	0/0	1	0	1	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0001c0001t0002g0001	0/0	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0001c0004t0002g0006	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0001c0004t0003g0008	0/0	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0001c0008t0001g0009	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0002c0002t0002g0002	0/0	4	0	1	0	2	1	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0003c0003t0001g0001	0/0	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0003c0003t0001g0003	0/0	2	0	1	0	1	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0003c0011t0002g0007	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0004c0009t0004g0004	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0005c0010t0002g0013	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0006c0007t0001g0005	0/0	1	1	0	0	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0007c0006t0005g0010	0/0	1	0	0	1	0	0	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
a0008c0005t0001g0001	0/0	1	0	0	0	0	1	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG01069	hp2	a0003	c0003	t0001	g0003	AMR	PUR	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG01106	hp2	a0001	c0001	t0001	g0012	AMR	PUR	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG01358	hp2	a0002	c0002	t0002	g0002	AMR	CLM	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG01515	hp1	a0002	c0002	t0002	g0002	EUR	IBS	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG02602	hp1	a0002	c0002	t0002	g0002	SAS	PJL	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG02647	hp2	a0001	c0004	t0003	g0008	AFR	GWD	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG02698	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG02738	hp1	a0001	c0001	t0001	g0001	SAS	PJL	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG02965	hp2	a0006	c0007	t0001	g0005	AFR	ESN	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG03654	hp1	a0003	c0003	t0001	g0001	SAS	PJL	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG03688	hp2	a0008	c0005	t0001	g0001	SAS	STU	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG04115	hp2	a0001	c0001	t0001	g0011	SAS	STU	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG04228	hp1	a0001	c0001	t0001	g0001	SAS	STU	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA18612	hp2	a0001	c0004	t0002	g0006	EAS	CHB	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA18953	hp1	a0004	c0009	t0004	g0004	EAS	JPT	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA18960	hp2	a0001	c0001	t0001	g0001	EAS	JPT	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA18982	hp1	a0007	c0006	t0005	g0010	EAS	JPT	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA19007	hp2	a0003	c0011	t0002	g0007	EAS	JPT	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA19058	hp1	a0005	c0010	t0002	g0013	EAS	JPT	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA20752	hp2	a0002	c0002	t0002	g0002	EUR	TSI	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA20805	hp2	a0003	c0003	t0001	g0003	EUR	TSI	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
HG03471	hp1	a0001	c0001	t0002	g0001	AFR	MSL	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749
NA18955	hp1	a0001	c0008	t0001	g0009	EAS	JPT	TSPY1_chrY_9461955_9474749	TSPY1	chrY	9461955	9474749

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:9467130	G G	A A	1	a0008 a0008	1	HG03688.hp2 HG03688.hp2	missense_variant	MODERATE	c.130G>A c.130G>A	p.Ala44Thr p.Ala44Thr	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/6	176/1161	130/927	44/308		chrY	9467130
chrY:9467215	C C	T T	1	a0008 a0008	1	HG03688.hp2 HG03688.hp2	missense_variant	MODERATE	c.215C>T c.215C>T	p.Ala72Val p.Ala72Val	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/6	261/1161	215/927	72/308		chrY	9467215
chrY:9467265	G G	T T	1	a0002 a0002	4	HG01358.hp2 HG01515.hp1 HG02602.hp1 others(1): Show HG01358.hp2 HG01515.hp1 HG02602.hp1 NA20752.hp2	stop_gained	HIGH	c.265G>T c.265G>T	p.Glu89* p.Glu89*	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/6	311/1161	265/927	89/308		chrY	9467265
chrY:9467326	C C	T T	6	a0001 a0002 a0003 others(3): Show a0001 a0002 a0003 a0004 a0005 a0008	21	HG01069.hp2 HG01106.hp2 HG01358.hp2 others(18): Show HG01069.hp2 HG01106.hp2 HG01358.hp2 HG01515.hp1 HG02602.hp1 HG02647.hp2 HG02698.hp1 HG02738.hp1 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18612.hp2 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA19007.hp2 NA19058.hp1 NA20752.hp2 NA20805.hp2	missense_variant	MODERATE	c.326C>T c.326C>T	p.Pro109Leu p.Pro109Leu	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/6	372/1161	326/927	109/308		chrY	9467326
chrY:9467432	C C	G G	1	a0003 a0003	4	HG01069.hp2 HG03654.hp1 NA19007.hp2 others(1): Show HG01069.hp2 HG03654.hp1 NA19007.hp2 NA20805.hp2	missense_variant	MODERATE	c.432C>G c.432C>G	p.His144Gln p.His144Gln	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/6	478/1161	432/927	144/308		chrY	9467432
chrY:9468104	AC AC	A A	1	a0007 a0007	1	NA18982.hp1 NA18982.hp1	frameshift_variant	HIGH	c.502delC c.502delC	p.Gln168fs p.Gln168fs	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	2/6	548/1161	502/927	168/308	INFO_REALIGN_3_PRIME	chrY	9468104
chrY:9468304	G G	A A	7	a0001 a0002 a0003 others(4): Show a0001 a0002 a0003 a0004 a0006 a0007 a0008	22	HG01069.hp2 HG01106.hp2 HG01358.hp2 others(19): Show HG01069.hp2 HG01106.hp2 HG01358.hp2 HG01515.hp1 HG02602.hp1 HG02647.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18612.hp2 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1 NA19007.hp2 NA20752.hp2 NA20805.hp2	missense_variant	MODERATE	c.569G>A c.569G>A	p.Gly190Glu p.Gly190Glu	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	3/6	615/1161	569/927	190/308		chrY	9468304
chrY:9468552	CG CG	C C	1	a0007 a0007	1	NA18982.hp1 NA18982.hp1	frameshift_variant	HIGH	c.718delG c.718delG	p.Asp240fs p.Asp240fs	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	4/6	764/1161	718/927	240/308	INFO_REALIGN_3_PRIME	chrY	9468552
chrY:9468791	TC TC	T T	1	a0004 a0004	1	NA18953.hp1 NA18953.hp1	frameshift_variant	HIGH	c.853delC c.853delC	p.Leu285fs p.Leu285fs	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/6	899/1161	853/927	285/308	INFO_REALIGN_3_PRIME	chrY	9468791

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
chrY:9467135	G G	A A	7	a0001c0001 a0001c0008 a0003c0003 others(4): Show a0001c0001 a0001c0008 a0003c0003 a0004c0009 a0006c0007 a0007c0006 a0008c0005	15	HG01069.hp2 HG01106.hp2 HG02698.hp1 others(12): Show HG01069.hp2 HG01106.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1 NA20805.hp2	synonymous_variant	LOW	c.135G>A c.135G>A	p.Val45Val p.Val45Val	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/6	181/1161	135/927	45/308			chrY	9467135
chrY:9468842	G G	A A	1	a0001c0008 a0001c0008	1	NA18955.hp1 NA18955.hp1	synonymous_variant	LOW	c.900G>A c.900G>A	p.Thr300Thr p.Thr300Thr	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/6	946/1161	900/927	300/308			chrY	9468842

chr:pos	ref	alt	# # of thapid:transcript level	thapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	genename	geneid	featuretype	featureid	transcript_biotype	rank	distance	status	chr	pos
chrY:9469648	C C	CT CT	7	a0001c0001t0001 a0001c0008t0001 a0003c0003t0001 others(4): Show a0001c0001t0001 a0001c0008t0001 a0003c0003t0001 a0004c0009t0004 a0006c0007t0001 a0007c0006t0005 a0008c0005t0001	14	HG01069.hp2 HG01106.hp2 HG02698.hp1 others(11): Show HG01069.hp2 HG01106.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1 NA20805.hp2	3_prime_UTR_variant	MODIFIER	c.89dupT c.89dupT	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	6/6	90	INFO_REALIGN_3_PRIME	chrY	9469648
chrY:9469674	G G	C C	1	a0001c0004t0003 a0001c0004t0003	1	HG02647.hp2 HG02647.hp2	3_prime_UTR_variant	MODIFIER	c.113G>C c.113G>C	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	6/6	113		chrY	9469674
chrY:9469701	A A	AG AG	1	a0004c0009t0004 a0004c0009t0004	1	NA18953.hp1 NA18953.hp1	3_prime_UTR_variant	MODIFIER	c.145dupG c.145dupG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	6/6	146	INFO_REALIGN_3_PRIME	chrY	9469701
chrY:9469744	CA CA	C C	1	a0007c0006t0005 a0007c0006t0005	1	NA18982.hp1 NA18982.hp1	3_prime_UTR_variant	MODIFIER	c.185delA c.185delA	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	6/6	185	INFO_REALIGN_3_PRIME	chrY	9469744

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:9467492	C C	T T	1	a0005c0010t0002g0013 a0005c0010t0002g0013	1	NA19058.hp1 NA19058.hp1	splice_region_variant&intron_variant	LOW	c.486+6C>T c.486+6C>T	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467492
chrY:9467562	C C	T T	1	a0002c0002t0002g0002 a0002c0002t0002g0002	4	HG01358.hp2 HG01515.hp1 HG02602.hp1 others(1): Show HG01358.hp2 HG01515.hp1 HG02602.hp1 NA20752.hp2	intron_variant	MODIFIER	c.486+76C>T c.486+76C>T	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467562
chrY:9467583	TG TG	T T	2	a0004c0009t0004g0004 a0006c0007t0001g0005 a0004c0009t0004g0004 a0006c0007t0001g0005	2	HG02965.hp2 NA18953.hp1 HG02965.hp2 NA18953.hp1	intron_variant	MODIFIER	c.486+101delG c.486+101delG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5	INFO_REALIGN_3_PRIME	chrY	9467583
chrY:9467613	G G	A A	2	a0001c0004t0002g0006 a0002c0002t0002g0002 a0001c0004t0002g0006 a0002c0002t0002g0002	5	HG01358.hp2 HG01515.hp1 HG02602.hp1 others(2): Show HG01358.hp2 HG01515.hp1 HG02602.hp1 NA18612.hp2 NA20752.hp2	intron_variant	MODIFIER	c.486+127G>A c.486+127G>A	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467613
chrY:9467619	C C	T T	2	a0001c0001t0001g0012 a0006c0007t0001g0005 a0001c0001t0001g0012 a0006c0007t0001g0005	2	HG01106.hp2 HG02965.hp2 HG01106.hp2 HG02965.hp2	intron_variant	MODIFIER	c.486+133C>T c.486+133C>T	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467619
chrY:9467691	A A	C C	2	a0001c0004t0002g0006 a0002c0002t0002g0002 a0001c0004t0002g0006 a0002c0002t0002g0002	5	HG01358.hp2 HG01515.hp1 HG02602.hp1 others(2): Show HG01358.hp2 HG01515.hp1 HG02602.hp1 NA18612.hp2 NA20752.hp2	intron_variant	MODIFIER	c.486+205A>C c.486+205A>C	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467691
chrY:9467878	C C	T T	1	a0005c0010t0002g0013 a0005c0010t0002g0013	1	NA19058.hp1 NA19058.hp1	intron_variant	MODIFIER	c.487-216C>T c.487-216C>T	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467878
chrY:9467954	C C	G G	10	a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 others(7): Show a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 a0001c0001t0002g0001 a0001c0008t0001g0009 a0003c0003t0001g0001 a0004c0009t0004g0004 a0006c0007t0001g0005 a0007c0006t0005g0010 a0008c0005t0001g0001	13	HG01106.hp2 HG02698.hp1 HG02738.hp1 others(10): Show HG01106.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1	intron_variant	MODIFIER	c.487-140C>G c.487-140C>G	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467954
chrY:9467978	A A	G G	10	a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 others(7): Show a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 a0001c0001t0002g0001 a0001c0008t0001g0009 a0003c0003t0001g0001 a0004c0009t0004g0004 a0006c0007t0001g0005 a0007c0006t0005g0010 a0008c0005t0001g0001	13	HG01106.hp2 HG02698.hp1 HG02738.hp1 others(10): Show HG01106.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1	intron_variant	MODIFIER	c.487-116A>G c.487-116A>G	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	1/5		chrY	9467978
chrY:9468180	AG AG	A A	1	a0006c0007t0001g0005 a0006c0007t0001g0005	1	HG02965.hp2 HG02965.hp2	intron_variant	MODIFIER	c.564+11delG c.564+11delG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	2/5	INFO_REALIGN_3_PRIME	chrY	9468180
chrY:9468206	C C	CG CG	1	a0001c0001t0001g0011 a0001c0001t0001g0011	1	HG04115.hp2 HG04115.hp2	intron_variant	MODIFIER	c.564+40dupG c.564+40dupG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	2/5	INFO_REALIGN_3_PRIME	chrY	9468206
chrY:9468442	A A	G G	1	a0001c0004t0003g0008 a0001c0004t0003g0008	1	HG02647.hp2 HG02647.hp2	intron_variant	MODIFIER	c.676+31A>G c.676+31A>G	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	3/5		chrY	9468442
chrY:9468882	G G	C C	14	a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 others(11): Show a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 a0001c0001t0002g0001 a0001c0004t0002g0006 a0001c0004t0003g0008 a0001c0008t0001g0009 a0002c0002t0002g0002 a0003c0003t0001g0001 a0003c0003t0001g0003 a0004c0009t0004g0004 a0006c0007t0001g0005 a0007c0006t0005g0010 a0008c0005t0001g0001	21	HG01069.hp2 HG01106.hp2 HG01358.hp2 others(18): Show HG01069.hp2 HG01106.hp2 HG01358.hp2 HG01515.hp1 HG02602.hp1 HG02647.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18612.hp2 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1 NA20752.hp2 NA20805.hp2	intron_variant	MODIFIER	c.904+36G>C c.904+36G>C	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5		chrY	9468882
chrY:9468946	G G	GA GA	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.904+103dupA c.904+103dupA	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9468946
chrY:9468950	C C	T T	14	a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 others(11): Show a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 a0001c0001t0002g0001 a0001c0004t0002g0006 a0001c0004t0003g0008 a0001c0008t0001g0009 a0002c0002t0002g0002 a0003c0003t0001g0001 a0003c0003t0001g0003 a0004c0009t0004g0004 a0006c0007t0001g0005 a0007c0006t0005g0010 a0008c0005t0001g0001	21	HG01069.hp2 HG01106.hp2 HG01358.hp2 others(18): Show HG01069.hp2 HG01106.hp2 HG01358.hp2 HG01515.hp1 HG02602.hp1 HG02647.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18612.hp2 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1 NA20752.hp2 NA20805.hp2	intron_variant	MODIFIER	c.904+104C>T c.904+104C>T	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5		chrY	9468950
chrY:9468953	A A	AG AG	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.904+109dupG c.904+109dupG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9468953
chrY:9468993	C C	CAG CAG	14	a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 others(11): Show a0001c0001t0001g0001 a0001c0001t0001g0011 a0001c0001t0001g0012 a0001c0001t0002g0001 a0001c0004t0002g0006 a0001c0004t0003g0008 a0001c0008t0001g0009 a0002c0002t0002g0002 a0003c0003t0001g0001 a0003c0003t0001g0003 a0004c0009t0004g0004 a0006c0007t0001g0005 a0007c0006t0005g0010 a0008c0005t0001g0001	21	HG01069.hp2 HG01106.hp2 HG01358.hp2 others(18): Show HG01069.hp2 HG01106.hp2 HG01358.hp2 HG01515.hp1 HG02602.hp1 HG02647.hp2 HG02698.hp1 HG02738.hp1 HG02965.hp2 HG03471.hp1 HG03654.hp1 HG03688.hp2 HG04115.hp2 HG04228.hp1 NA18612.hp2 NA18953.hp1 NA18955.hp1 NA18960.hp2 NA18982.hp1 NA20752.hp2 NA20805.hp2	intron_variant	MODIFIER	c.904+150_904+151dup others(2): Show c.904+150_904+151dupAG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9468993
chrY:9469014	GT GT	G G	1	a0006c0007t0001g0005 a0006c0007t0001g0005	1	HG02965.hp2 HG02965.hp2	intron_variant	MODIFIER	c.904+170delT c.904+170delT	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469014
chrY:9469025	TG TG	T T	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.904+182delG c.904+182delG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469025
chrY:9469125	G G	C C	1	a0001c0008t0001g0009 a0001c0008t0001g0009	1	NA18955.hp1 NA18955.hp1	intron_variant	MODIFIER	c.904+279G>C c.904+279G>C	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5		chrY	9469125
chrY:9469171	G G	A A	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.904+325G>A c.904+325G>A	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5		chrY	9469171
chrY:9469187	G G	A A	1	a0007c0006t0005g0010 a0007c0006t0005g0010	1	NA18982.hp1 NA18982.hp1	intron_variant	MODIFIER	c.904+341G>A c.904+341G>A	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5		chrY	9469187
chrY:9469195	TC TC	T T	1	a0006c0007t0001g0005 a0006c0007t0001g0005	1	HG02965.hp2 HG02965.hp2	intron_variant	MODIFIER	c.905-341delC c.905-341delC	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469195
chrY:9469341	GT GT	G G	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.905-196delT c.905-196delT	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469341
chrY:9469414	AG AG	A A	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.905-123delG c.905-123delG	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469414
chrY:9469467	G G	GCC GCC	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.905-69_905-68dupCC c.905-69_905-68dupCC	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469467
chrY:9469486	T T	G G	1	a0001c0004t0003g0008 a0001c0004t0003g0008	1	HG02647.hp2 HG02647.hp2	intron_variant	MODIFIER	c.905-53T>G c.905-53T>G	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5		chrY	9469486
chrY:9469503	GA GA	G G	1	a0004c0009t0004g0004 a0004c0009t0004g0004	1	NA18953.hp1 NA18953.hp1	intron_variant	MODIFIER	c.905-32delA c.905-32delA	TSPY1	ENSG00000258992.7	transcript	ENST00000451548.6	protein_coding	5/5	INFO_REALIGN_3_PRIME	chrY	9469503

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🧬 JoGo Online Haplotype Explorer TSPY1_chrY_9461955_9474749

JoGo Local Haplotype Explorer (on iGV) TSPY1_chrY_9461955_9474749

Translation Multiple Alignment View

🧬 Gene Summary

AAmino acid(protein) Level Haplotype Info (Total: 8)

CCoding Level Haplotype Info (Total: 11)

TTranscript Level Haplotype Info (Total: 5)

GGenebody Level Haplotype Info (Total: 13)

A C AC Level (Amino Acid + Coding) Haplotype Info (Total: 11)

A C T ACT Level (Amino Acid + Coding + Transcript) Haplotype Info (Total: 13)

A C T G ACTG Level (Amino Acid + Coding + Transcript + Genebody) Haplotype Info (Total: 16)

Haplotype Details by Sample (Haploid Level) (Total: 23)

AAmino acid(protein) Level Haplotype Related Variants (Effect to Protein Coding Variants) (Total: 9)

CCoding Level Variants (Synonymous Mutations) (Total: 2)

TTranscript Level Haplotype Variants (5'UTR+3'UTR) (Total: 4)

GGenebody Level Haplotype Variants (Intron) (Total: 28)

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Annotation (Repeats)

Annotation (SNP Array)