Joint Open Genome and Omics Platform (JoGo)

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geneid	442867
ensemblid	ENSG00000183795.8
hgncid	25449
symbol	BPY2B
name	basic charge Y-linked 2B
refseq_nuc	NM_001002760.1
refseq_prot	NP_001002760.1
ensembl_nuc	ENST00000382392.5
ensembl_prot	ENSP00000371829.1
mane_status	MANE Select
chr	chrY
start	24618004
end	24639207
strand	+
ver	v1.2
region	chrY:24618004-24639207
region5000	chrY:24613004-24644207
regionname0	BPY2B_chrY_24618004_24639207
regionname5000	BPY2B_chrY_24613004_24644207

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	106	2	0	0	2	0	0	2	BPY2B_chrY_24613004_24644207	BPY2B	copy fasta	chrY	24613004	24644207

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	321	2	0	0	2	0	0	BPY2B_chrY_24613004_24644207	BPY2B	copy fasta	chrY	24613004	24644207

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	886	2	0	0	2	0	0	BPY2B_chrY_24613004_24644207	BPY2B	copy fasta	chrY	24613004	24644207

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	1	0	0	1	0	0	BPY2B_chrY_24613004_24644207	BPY2B	chrY	24613004	24644207
g0002	0/0	1	0	0	1	0	0	BPY2B_chrY_24613004_24644207	BPY2B	chrY	24613004	24644207

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	321	2	0	0	2	0	0	BPY2B_chrY_24613004_24644207	BPY2B	copy fasta	chrY	24613004	24644207

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1206	2	0	0	2	0	0	BPY2B_chrY_24613004_24644207	BPY2B	copy fasta	chrY	24613004	24644207

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	1	0	0	1	0	0	BPY2B_chrY_24613004_24644207	BPY2B	chrY	24613004	24644207
a0001c0001t0001g0002	0/0	1	0	0	1	0	0	BPY2B_chrY_24613004_24644207	BPY2B	chrY	24613004	24644207

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
NA18974	hp1	a0001	c0001	t0001	g0002	EAS	JPT	BPY2B_chrY_24613004_24644207	BPY2B	chrY	24613004	24644207
NA18985	hp1	a0001	c0001	t0001	g0001	EAS	JPT	BPY2B_chrY_24613004_24644207	BPY2B	chrY	24613004	24644207

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	distance	status	chr	pos

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

chr:pos	ref	alt	# # of ghapid:genebody level	ghapids	# # of haplotypeids	haplotypeids	annotation	impact	hgvs_c	hgvs_p	genename	geneid	featuretype	featureid	genebody_biotype	rank	cdna cdna pos length	cds cds pos length	aa aa pos length	distance	status	chr	pos
chrY:24618537	A A	C C	1	a0001c0001t0001g0002 a0001c0001t0001g0002	1	NA18974.hp1 NA18974.hp1	intron_variant	MODIFIER	c.-179+105A>C c.-179+105A>C		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	2/8						chrY	24618537
chrY:24629912	G G	GT GT	1	a0001c0001t0001g0002 a0001c0001t0001g0002	1	NA18974.hp1 NA18974.hp1	intron_variant	MODIFIER	c.197-1263dupT c.197-1263dupT		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	5/8					INFO_REALIGN_3_PRIME	chrY	24629912
chrY:24631011	T T	C C	2	a0001c0001t0001g0001 a0001c0001t0001g0002 a0001c0001t0001g0001 a0001c0001t0001g0002	2	NA18974.hp1 NA18985.hp1 NA18974.hp1 NA18985.hp1	intron_variant	MODIFIER	c.197-183T>C c.197-183T>C		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	5/8						chrY	24631011
chrY:24631482	C C	T T	1	a0001c0001t0001g0002 a0001c0001t0001g0002	1	NA18974.hp1 NA18974.hp1	intron_variant	MODIFIER	c.302+183C>T c.302+183C>T		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	6/8						chrY	24631482
chrY:24634876	C C	CA CA	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.106+2766dupA c.106+2766dupA		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24634876
chrY:24635083	T T	TG TG	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.106+2970dupG c.106+2970dupG		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24635083
chrY:24635348	TG TG	T T	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.106+3236delG c.106+3236delG		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24635348
chrY:24635503	TG TG	T T	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.107-3162delG c.107-3162delG		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24635503
chrY:24635530	AT AT	A A	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.107-3134delT c.107-3134delT		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24635530
chrY:24636119	AG AG	A A	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.107-2546delG c.107-2546delG		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24636119
chrY:24636466	G G	GC GC	1	a0001c0001t0001g0001 a0001c0001t0001g0001	1	NA18985.hp1 NA18985.hp1	intron_variant	MODIFIER	c.107-2200dupC c.107-2200dupC		BPY2B	ENSG00000183795.8	transcript	ENST00000382392.5	protein_coding	7/8					INFO_REALIGN_3_PRIME	chrY	24636466