Joint Open Genome and Omics Platform (JoGo)

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geneid	728042
ensemblid	ENSG00000226600.3
hgncid	33290
symbol	CT47A9
name	cancer/testis antigen family 47 member A9
refseq_nuc	NM_001080138.2
refseq_prot	NP_001073607.1
ensembl_nuc	ENST00000417256.3
ensembl_prot	ENSP00000408204.2
mane_status	MANE Select
chr	chrX
start	120943561
end	120946883
strand	-
ver	v1.2
region	chrX:120943561-120946883
region5000	chrX:120938561-120951883
regionname0	CT47A9_chrX_120943561_120946883
regionname5000	CT47A9_chrX_120938561_120951883

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	288	6	0	0	6	0	0	6	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
a0002	0/0	288	1	0	0	1	0	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
a0003	0/0	31	1	0	0	1	0	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883

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	867	6	0	0	6	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
c0002	0/0	867	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
c0003	0/0	868	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883

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	432	8	0	0	8	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883

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	6	0	0	6	0	0	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
g0002	0/0	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
g0003	0/0	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883

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	867	6	0	0	6	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
a0002c0002	0/0	867	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
a0003c0003	0/0	868	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883

acthapid	grch38 chm13v2	tlen	total	AFR	AMR	EAS	EUR	SAS	regionname	genename	tseq	chr	start	end
a0001c0001t0001	0/0	1298	6	0	0	6	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
a0002c0002t0001	0/0	1298	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883
a0003c0003t0001	0/0	1299	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	copy fasta	chrX	120938561	120951883

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	6	0	0	6	0	0	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
a0002c0002t0001g0002	0/0	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
a0003c0003t0001g0003	0/0	1	0	0	1	0	0	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883

sampleid	ID haplotypeid	ahapid	chapid	thapid	ghapid	gpopname	popname	regionname	genename	chr	start	end
HG00597	hp1	a0003	c0003	t0001	g0003	EAS	CHS	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
HG00597	hp2	a0002	c0002	t0001	g0002	EAS	CHS	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
NA18967	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
NA19004	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
NA19005	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
NA19066	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
NA19086	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883
NA19088	hp1	a0001	c0001	t0001	g0001	EAS	JPT	CT47A9_chrX_120938561_120951883	CT47A9	chrX	120938561	120951883

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
chrX:120946462	C C	T T	1	a0002 a0002	1	HG00597.hp2 HG00597.hp2	missense_variant	MODERATE	c.163G>A c.163G>A	p.Ala55Thr p.Ala55Thr	CT47A9	ENSG00000226600.3	transcript	ENST00000417256.3	protein_coding	1/3	422/1298	163/867	55/288			chrX	120946462
chrX:120946608	T T	TC TC	1	a0003 a0003	1	HG00597.hp1 HG00597.hp1	frameshift_variant	HIGH	c.16dupG c.16dupG	p.Asp6fs p.Asp6fs	CT47A9	ENSG00000226600.3	transcript	ENST00000417256.3	protein_coding	1/3	275/1298	16/867	6/288			chrX	120946608

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