nstd116 - Forni et al 2015 - dbVar Study

nstd116 (Forni et al. 2015)

Organism:: Human
Study Type:: Control Set
Submitter:: Edward Hollox
Description:: In this study we use high-coverage phase 3 exome sequences of the 1000 Genomes project to infer diploid copy number of the beta-defensin genomic region, a well-studied CNV that carries several beta-defensin genes involved in the antimicrobial response, signalling, and fertility. We also use these data to call sequence variants, a particular challenge given the multicopy nature of the region. We confidently call copy number and sequence variation of the beta-defensin genes on 1285 samples from 26 global populations. See Variant Summary counts for nstd116 in dbVar Variant Summary.
Publication(s):: Forni et al. 2015

Links

Source: NCBI

Detailed Information: Download 1 Variant Region, Download 1285 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_000008.11	Chr8	1	1,285	Remapped	NC_000008.11
NT_187570.1	Chr8\|NT_187570.1	1	1,285	Remapped	NT_187570.1
NW_018654717.1	Chr8\|NW_018654717.1	1	1,285	Remapped	NW_018654717.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000008.10	Chr8	1	1,285	Submitted	NC_000008.10

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_000008.10	Chr8	1	0	0	0	0	4	1,285	0	0	0	0	5,140

Samplesets

Number of Samplesets: 1

Size:: 1,285
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1 (displaying 100 of the 1285 samples)
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
HG00126	HG00126	Male	GBR	Not reported
HG00100	HG00100	Female	GBR	Not reported
HG00244	HG00244	Male	GBR	Not reported
HG00114	HG00114	Male	GBR	Not reported
HG00265	HG00265	Male	GBR	Not reported
HG00173	HG00173	Female	FIN	Not reported
HG00150	HG00150	Female	GBR	Not reported
HG00256	HG00256	Male	GBR	Not reported
HG00268	HG00268	Female	FIN	Not reported
HG00285	HG00285	Female	FIN	Not reported
HG00327	HG00327	Female	FIN	Not reported
HG00255	HG00255	Female	GBR	Not reported
HG00115	HG00115	Male	GBR	Not reported
HG00310	HG00310	Male	FIN	Not reported
HG00278	HG00278	Male	FIN	Not reported
HG00236	HG00236	Female	GBR	Not reported
HG00318	HG00318	Female	FIN	Not reported
HG00096	HG00096	Male	GBR	Not reported
HG00148	HG00148	Male	GBR	Not reported
HG00257	HG00257	Female	GBR	Not reported
HG00113	HG00113	Male	GBR	Not reported
HG00280	HG00280	Male	FIN	Not reported
HG00262	HG00262	Female	GBR	Not reported
HG00133	HG00133	Female	GBR	Not reported
HG00099	HG00099	Female	GBR	Not reported
HG00177	HG00177	Female	FIN	Not reported
HG00231	HG00231	Female	GBR	Not reported
HG00281	HG00281	Female	FIN	Not reported
HG00158	HG00158	Female	GBR	Not reported
HG00112	HG00112	Male	GBR	Not reported
HG00269	HG00269	Female	FIN	Not reported
HG00290	HG00290	Male	FIN	Not reported
HG00276	HG00276	Female	FIN	Not reported
HG00097	HG00097	Female	GBR	Not reported
HG00275	HG00275	Female	FIN	Not reported
HG00267	HG00267	Male	FIN	Not reported
HG00181	HG00181	Male	FIN	Not reported
HG00325	HG00325	Male	FIN	Not reported
HG00326	HG00326	Female	FIN	Not reported
HG00253	HG00253	Female	GBR	Not reported
HG00142	HG00142	Male	GBR	Not reported
HG00320	HG00320	Female	FIN	Not reported
HG00254	HG00254	Female	GBR	Not reported
HG00309	HG00309	Female	FIN	Not reported
HG00105	HG00105	Male	GBR	Not reported
HG00315	HG00315	Female	FIN	Not reported
HG00250	HG00250	Female	GBR	Not reported
HG00120	HG00120	Female	GBR	Not reported
HG00138	HG00138	Male	GBR	Not reported
HG00103	HG00103	Male	GBR	Not reported
HG00328	HG00328	Female	FIN	Not reported
HG00240	HG00240	Female	GBR	Not reported
HG00143	HG00143	Male	GBR	Not reported
HG00187	HG00187	Male	FIN	Not reported
HG00145	HG00145	Male	GBR	Not reported
HG00118	HG00118	Female	GBR	Not reported
HG00178	HG00178	Female	FIN	Not reported
HG00260	HG00260	Male	GBR	Not reported
HG00288	HG00288	Female	FIN	Not reported
HG00273	HG00273	Male	FIN	Not reported
HG00102	HG00102	Female	GBR	Not reported
HG00284	HG00284	Male	FIN	Not reported
HG00140	HG00140	Male	GBR	Not reported
HG00264	HG00264	Male	GBR	Not reported
HG00190	HG00190	Male	FIN	Not reported
HG00313	HG00313	Female	FIN	Not reported
HG00238	HG00238	Female	GBR	Not reported
HG00117	HG00117	Male	GBR	Not reported
HG00266	HG00266	Female	FIN	Not reported
HG00263	HG00263	Female	GBR	Not reported
HG00180	HG00180	Female	FIN	Not reported
HG00282	HG00282	Female	FIN	Not reported
HG00237	HG00237	Female	GBR	Not reported
HG00123	HG00123	Female	GBR	Not reported
HG00139	HG00139	Male	GBR	Not reported
HG00183	HG00183	Male	FIN	Not reported
HG00109	HG00109	Male	GBR	Not reported
HG00159	HG00159	Male	GBR	Not reported
HG00321	HG00321	Male	FIN	Not reported
HG00149	HG00149	Male	GBR	Not reported
HG00304	HG00304	Female	FIN	Not reported
HG00125	HG00125	Female	GBR	Not reported
HG00171	HG00171	Female	FIN	Not reported
HG00232	HG00232	Female	GBR	Not reported
HG00174	HG00174	Female	FIN	Not reported
HG00324	HG00324	Female	FIN	Not reported
HG00122	HG00122	Female	GBR	Not reported
HG00182	HG00182	Male	FIN	Not reported
HG00151	HG00151	Male	GBR	Not reported
HG00154	HG00154	Female	GBR	Not reported
HG00136	HG00136	Male	GBR	Not reported
HG00251	HG00251	Male	GBR	Not reported
HG00274	HG00274	Female	FIN	Not reported
HG00111	HG00111	Female	GBR	Not reported
HG00106	HG00106	Female	GBR	Not reported
HG00233	HG00233	Female	GBR	Not reported
HG00252	HG00252	Male	GBR	Not reported
HG00119	HG00119	Male	GBR	Not reported
HG00323	HG00323	Female	FIN	Not reported
HG00239	HG00239	Female	GBR	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Read depth	1,285

dbVar

Database of genomic structural variation

nstd116 (Forni et al. 2015)

Links

Detailed Information: Download 1 Variant Region, Download 1285 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

nstd116 (Forni et al. 2015)

Links

Detailed Information: Download 1 Variant Region, Download 1285 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: