nstd177 - Louzada et al 2020 - dbVar Study

nstd177 (Louzada et al. 2020)

Organism:: Human
Study Type:: Control Set
Submitter:: Edward Hollox
Description:: We analysed sequences from 6466 genomes from across the world for structural variation at the glycophorin locus, confirming 15 variants in the 1000 Genomes project cohort, discovering 9 new variants, and characterising a selection using fibre-FISH and breakpoint mapping. We identify variants predicted to create novel fusion genes and a common inversion duplication variant at appreciable frequencies in West Africans. See Variant Summary counts for nstd177 in dbVar Variant Summary.
Publication(s):: Louzada et al. 2020

Links

Source: NCBI

Detailed Information: Download 22 Variant Regions, Download 23 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000004.12	Chr4	22	23	Remapped	NC_000004.12

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000004.11	Chr4	22	23	Submitted	NC_000004.11

Remapping summary:

			Variant Region remap status						Variant Call remap status
Sequence ID	Chr	Variant Regions on source	Perfect	Good	Pass	Fail	Mult	Variant Calls on source	Perfect	Good	Pass	Fail	Mult
NC_000004.11	Chr4	22	22	0	0	0	0	23	23	0	0	0	0

Samplesets

Number of Samplesets: 1

Size:: 23
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
SAMN00004490	NA20867	Male	GIH	Not reported
SAMN01096750	HG03837	Male	STU	Not reported
BR981404021	BR981404021			Not reported
BR1183605501	BR1183605501			Not reported
SAMN01761532	HG04039	Male	STU	Not reported
SAMN01091015	HG03729	Male	ITU	Not reported
HGDP01172	HGDP01172			Not reported
BR1296010301	BR1296010301			Not reported
SAMN00801317	NA12249	Female	CEU	Not reported
SAMN00000940	NA18646	Female	CHB	Not reported
BR1099223302	BR1099223302			Not reported
BR54409051	BR54409051			Not reported
SAMN00001127	NA19360	Male	LWK	Not reported
BR1086675791	BR1086675791			Not reported
SAMN00001677	NA19144	Male	YRI	Not reported
SAMN00001617	NA18593	Female	CHB	Not reported
SAMN01096729	HG03686	Male	STU	Not reported
HGDP00543	HGDP00543			Not reported
SAMN00262971	HG01986	Male	ACB	Not reported
BR210800138	BR210800138			Not reported
SAMN01036710	HG02716	Female	GWD	Not reported
SAMN00779982	HG02679	Female	GWD	Not reported
SAMN00000570	NA19223	Male	YRI	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	PCR	Sequence alignment	9
2	Discovery	Sequencing	Read depth	14

dbVar

Database of genomic structural variation

nstd177 (Louzada et al. 2020)

Links

Detailed Information: Download 22 Variant Regions, Download 23 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Submitted: GRCh37 (hg19)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

nstd177 (Louzada et al. 2020)

Links

Detailed Information: Download 22 Variant Regions, Download 23 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37 (hg19)

Remapping summary: GRCh37->GRCh38.p12

Samplesets

Number of Samplesets: 1

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: