nstd78 - Schrider et al 2013 - dbVar Study

nstd78 (Schrider et al. 2013)

Organism:: Human
Study Type:: Control Set
Submitter:: Fábio Navarro
Description:: An important class of gene copy-number polymorphism is gene duplications caused by retrotransposition, which result in a new intron-less copy of the parental gene (retroCNV) being inserted into a random location in the genome. Here we report the first genome-wide analysis of these variants in humans. We find that retroCNVs account for a substantial fraction of gene copy-number differences between any two individuals. Moreover, we show that these variants may often result in expressed chimeric transcripts, underscoring their potential influence in the evolution of novel gene functions. See Variant Summary counts for nstd78 in dbVar Variant Summary.
Publication(s):: Schrider et al. 2013

Links

Source: NCBI

Detailed Information: Download 38 Variant Regions, Download 38 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_000001.11	Chr1	4	4	Remapped	NC_000001.11
NC_000002.12	Chr2	2	2	Remapped	NC_000002.12
NC_000003.12	Chr3	2	2	Remapped	NC_000003.12
NC_000004.12	Chr4	1	1	Remapped	NC_000004.12
NC_000005.10	Chr5	3	3	Remapped	NC_000005.10
NC_000006.12	Chr6	5	5	Remapped	NC_000006.12
NC_000010.11	Chr10	3	3	Remapped	NC_000010.11
NC_000011.10	Chr11	3	3	Remapped	NC_000011.10
NC_000012.12	Chr12	2	2	Remapped	NC_000012.12
NC_000013.11	Chr13	2	2	Remapped	NC_000013.11
NC_000014.9	Chr14	1	1	Remapped	NC_000014.9
NC_000015.10	Chr15	2	2	Remapped	NC_000015.10
NC_000016.10	Chr16	2	2	Remapped	NC_000016.10
NC_000017.11	Chr17	2	2	Remapped	NC_000017.11
NC_000018.10	Chr18	1	1	Remapped	NC_000018.10
NC_000019.10	Chr19	1	1	Remapped	NC_000019.10
NC_000023.11	ChrX	1	1	Remapped	NC_000023.11
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	5	5	Submitted	NC_000001.10
NC_000002.11	Chr2	2	2	Submitted	NC_000002.11
NC_000003.11	Chr3	2	2	Submitted	NC_000003.11
NC_000004.11	Chr4	1	1	Submitted	NC_000004.11
NC_000005.9	Chr5	3	3	Submitted	NC_000005.9
NC_000006.11	Chr6	5	5	Submitted	NC_000006.11
NC_000010.10	Chr10	3	3	Submitted	NC_000010.10
NC_000011.9	Chr11	3	3	Submitted	NC_000011.9
NC_000012.11	Chr12	2	2	Submitted	NC_000012.11
NC_000013.10	Chr13	2	2	Submitted	NC_000013.10
NC_000014.8	Chr14	1	1	Submitted	NC_000014.8
NC_000015.9	Chr15	2	2	Submitted	NC_000015.9
NC_000016.9	Chr16	2	2	Submitted	NC_000016.9
NC_000017.10	Chr17	2	2	Submitted	NC_000017.10
NC_000018.9	Chr18	1	1	Submitted	NC_000018.9
NC_000019.9	Chr19	1	1	Submitted	NC_000019.9
NC_000023.10	ChrX	1	1	Submitted	NC_000023.10

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_000001.10	Chr1	5	4	0	0	1	0	5	4	0	0	1	0
NC_000002.11	Chr2	2	2	0	0	0	0	2	2	0	0	0	0
NC_000003.11	Chr3	2	2	0	0	0	0	2	2	0	0	0	0
NC_000004.11	Chr4	1	1	0	0	0	0	1	1	0	0	0	0
NC_000005.9	Chr5	3	3	0	0	0	0	3	3	0	0	0	0
NC_000006.11	Chr6	5	5	0	0	0	0	5	5	0	0	0	0
NC_000010.10	Chr10	3	3	0	0	0	0	3	3	0	0	0	0
NC_000011.9	Chr11	3	3	0	0	0	0	3	3	0	0	0	0
NC_000012.11	Chr12	2	2	0	0	0	0	2	2	0	0	0	0
NC_000013.10	Chr13	2	2	0	0	0	0	2	2	0	0	0	0
NC_000014.8	Chr14	1	1	0	0	0	0	1	1	0	0	0	0
NC_000015.9	Chr15	2	2	0	0	0	0	2	2	0	0	0	0
NC_000016.9	Chr16	2	2	0	0	0	0	2	2	0	0	0	0
NC_000017.10	Chr17	2	1	0	0	0	1	2	1	0	0	0	1
NC_000018.9	Chr18	1	1	0	0	0	0	1	1	0	0	0	0
NC_000019.9	Chr19	1	1	0	0	0	0	1	1	0	0	0	0
NC_000023.10	ChrX	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 1

Description:: 1000 Genomes Individuals
Size:: 946
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1 (displaying 100 of the 946 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
HG00179	HG00179	Female	FIN	Not reported
HG00268	HG00268	Female	FIN	Not reported
HG00152	HG00152	Male	GBR	Not reported
HG00278	HG00278	Male	FIN	Not reported
HG00236	HG00236	Female	GBR	Not reported
HG00096	HG00096	Male	GBR	Not reported
HG00148	HG00148	Male	GBR	Not reported
HG00257	HG00257	Female	GBR	Not reported
HG00188	HG00188	Male	FIN	Not reported
HG00185	HG00185	Male	FIN	Not reported
HG00280	HG00280	Male	FIN	Not reported
HG00262	HG00262	Female	GBR	Not reported
HG00133	HG00133	Female	GBR	Not reported
HG00259	HG00259	Female	GBR	Not reported
HG00177	HG00177	Female	FIN	Not reported
HG00277	HG00277	Male	FIN	Not reported
HG00231	HG00231	Female	GBR	Not reported
HG00281	HG00281	Female	FIN	Not reported
HG00158	HG00158	Female	GBR	Not reported
HG00127	HG00127	Female	GBR	Not reported
HG00176	HG00176	Female	FIN	Not reported
HG00112	HG00112	Male	GBR	Not reported
HG00269	HG00269	Female	FIN	Not reported
HG00258	HG00258	Female	GBR	Not reported
HG00276	HG00276	Female	FIN	Not reported
HG00247	HG00247	Female	GBR	Not reported
HG00186	HG00186	Male	FIN	Not reported
HG00275	HG00275	Female	FIN	Not reported
HG00267	HG00267	Male	FIN	Not reported
HG00124	HG00124	Female	GBR	Not reported
HG00253	HG00253	Female	GBR	Not reported
HG00270	HG00270	Female	FIN	Not reported
HG00142	HG00142	Male	GBR	Not reported
HG00254	HG00254	Female	GBR	Not reported
HG00250	HG00250	Female	GBR	Not reported
HG00249	HG00249	Female	GBR	Not reported
HG00120	HG00120	Female	GBR	Not reported
HG00138	HG00138	Male	GBR	Not reported
HG00103	HG00103	Male	GBR	Not reported
HG00141	HG00141	Male	GBR	Not reported
HG00143	HG00143	Male	GBR	Not reported
HG00187	HG00187	Male	FIN	Not reported
HG00137	HG00137	Female	GBR	Not reported
HG00118	HG00118	Female	GBR	Not reported
HG00178	HG00178	Female	FIN	Not reported
HG00260	HG00260	Male	GBR	Not reported
HG00116	HG00116	Male	GBR	Not reported
HG00243	HG00243	Male	GBR	Not reported
HG00273	HG00273	Male	FIN	Not reported
HG00261	HG00261	Female	GBR	Not reported
HG00245	HG00245	Female	GBR	Not reported
HG00140	HG00140	Male	GBR	Not reported
HG00264	HG00264	Male	GBR	Not reported
HG00190	HG00190	Male	FIN	Not reported
HG00242	HG00242	Male	GBR	Not reported
HG00117	HG00117	Male	GBR	Not reported
HG00156	HG00156	Male	GBR	Not reported
HG00266	HG00266	Female	FIN	Not reported
HG00263	HG00263	Female	GBR	Not reported
HG00180	HG00180	Female	FIN	Not reported
HG00237	HG00237	Female	GBR	Not reported
HG00123	HG00123	Female	GBR	Not reported
HG00246	HG00246	Male	GBR	Not reported
HG00139	HG00139	Male	GBR	Not reported
HG00160	HG00160	Male	GBR	Not reported
HG00183	HG00183	Male	FIN	Not reported
HG00159	HG00159	Male	GBR	Not reported
HG00149	HG00149	Male	GBR	Not reported
HG00125	HG00125	Female	GBR	Not reported
HG00171	HG00171	Female	FIN	Not reported
HG00232	HG00232	Female	GBR	Not reported
HG00271	HG00271	Male	FIN	Not reported
HG00174	HG00174	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
HG00272	HG00272	Female	FIN	Not reported
HG00136	HG00136	Male	GBR	Not reported
HG00251	HG00251	Male	GBR	Not reported
HG00155	HG00155	Male	GBR	Not reported
HG00274	HG00274	Female	FIN	Not reported
HG00111	HG00111	Female	GBR	Not reported
HG00106	HG00106	Female	GBR	Not reported
HG00189	HG00189	Male	FIN	Not reported
HG00233	HG00233	Female	GBR	Not reported
HG00252	HG00252	Male	GBR	Not reported
HG00131	HG00131	Male	GBR	Not reported
HG00108	HG00108	Male	GBR	Not reported
HG00119	HG00119	Male	GBR	Not reported
HG00146	HG00146	Female	GBR	Not reported
HG00239	HG00239	Female	GBR	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	Paired-end mapping	38
2	Validation	PCR	Manual observation	27

Validations

Experiment ID	Method	Analysis	Number of Variant Calls Validated
2	PCR	Manual observation	27

dbVar

Database of genomic structural variation

nstd78 (Schrider et al. 2013)

Links

Detailed Information: Download 38 Variant Regions, Download 38 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

Variant Summary for:

Remapping summary: