nstd34 - Hinds et al 2005 - dbVar Study

nstd34 (Hinds et al. 2005)

Organism:: Human
Study Type:: Control Set
Submitter:: David Hinds
Description:: We examined 100 deletion polymorphisms ranging from 70 bp to 7 kb. See Variant Summary counts for nstd34 in dbVar Variant Summary.
Publication(s):: Hinds et al. 2005

Links

Source: NCBI

Detailed Information: Download 100 Variant Regions, Download 100 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI35 (hg17)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	6	6	Remapped	NC_000001.11
NC_000002.12	Chr2	6	6	Remapped	NC_000002.12
NC_000003.12	Chr3	3	3	Remapped	NC_000003.12
NC_000004.12	Chr4	19	19	Remapped	NC_000004.12
NC_000005.10	Chr5	16	16	Remapped	NC_000005.10
NC_000008.11	Chr8	20	20	Remapped	NC_000008.11
NC_000010.11	Chr10	5	5	Remapped	NC_000010.11
NC_000011.10	Chr11	12	12	Remapped	NC_000011.10
NC_000013.11	Chr13	1	1	Remapped	NC_000013.11
NC_000016.10	Chr16	4	4	Remapped	NC_000016.10
NC_000017.11	Chr17	1	1	Remapped	NC_000017.11
NC_000018.10	Chr18	5	5	Remapped	NC_000018.10
NC_000019.10	Chr19	1	1	Remapped	NC_000019.10
NC_000021.9	Chr21	1	1	Remapped	NC_000021.9
NW_014040927.1	Chr1\|NW_014040927.1	1	1	Remapped	NW_014040927.1
NW_018654717.1	Chr8\|NW_018654717.1	2	2	Remapped	NW_018654717.1
NW_013171806.1	Chr10\|NW_013171806.1	1	1	Remapped	NW_013171806.1
NW_013171814.1	Chr18\|NW_013171814.1	1	1	Remapped	NW_013171814.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	6	6	Remapped	NC_000001.10
NC_000002.11	Chr2	6	6	Remapped	NC_000002.11
NC_000003.11	Chr3	3	3	Remapped	NC_000003.11
NC_000004.11	Chr4	19	19	Remapped	NC_000004.11
NC_000005.9	Chr5	16	16	Remapped	NC_000005.9
NC_000008.10	Chr8	20	20	Remapped	NC_000008.10
NC_000010.10	Chr10	5	5	Remapped	NC_000010.10
NC_000011.9	Chr11	12	12	Remapped	NC_000011.9
NC_000013.10	Chr13	1	1	Remapped	NC_000013.10
NC_000016.9	Chr16	4	4	Remapped	NC_000016.9
NC_000017.10	Chr17	1	1	Remapped	NC_000017.10
NC_000018.9	Chr18	5	5	Remapped	NC_000018.9
NC_000019.9	Chr19	1	1	Remapped	NC_000019.9
NC_000021.8	Chr21	1	1	Remapped	NC_000021.8

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.8	Chr1	6	6	Submitted	NC_000001.8
NC_000002.9	Chr2	6	6	Submitted	NC_000002.9
NC_000003.9	Chr3	3	3	Submitted	NC_000003.9
NC_000004.9	Chr4	19	19	Submitted	NC_000004.9
NC_000005.8	Chr5	16	16	Submitted	NC_000005.8
NC_000008.9	Chr8	20	20	Submitted	NC_000008.9
NC_000010.8	Chr10	5	5	Submitted	NC_000010.8
NC_000011.8	Chr11	12	12	Submitted	NC_000011.8
NC_000013.9	Chr13	1	1	Submitted	NC_000013.9
NC_000016.8	Chr16	4	4	Submitted	NC_000016.8
NC_000017.9	Chr17	1	1	Submitted	NC_000017.9
NC_000018.8	Chr18	5	5	Submitted	NC_000018.8
NC_000019.8	Chr19	1	1	Submitted	NC_000019.8
NC_000021.7	Chr21	1	1	Submitted	NC_000021.7

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_000001.8	Chr1	6	6	0	0	0	0	6	6	0	0	0	0
NC_000002.9	Chr2	6	6	0	0	0	0	6	6	0	0	0	0
NC_000003.9	Chr3	3	3	0	0	0	0	3	3	0	0	0	0
NC_000004.9	Chr4	19	19	0	0	0	0	19	19	0	0	0	0
NC_000005.8	Chr5	16	16	0	0	0	0	16	16	0	0	0	0
NC_000008.9	Chr8	20	20	0	0	0	0	20	20	0	0	0	0
NC_000010.8	Chr10	5	5	0	0	0	0	5	5	0	0	0	0
NC_000011.8	Chr11	12	12	0	0	0	0	12	12	0	0	0	0
NC_000013.9	Chr13	1	1	0	0	0	0	1	1	0	0	0	0
NC_000016.8	Chr16	4	4	0	0	0	0	4	4	0	0	0	0
NC_000017.9	Chr17	1	1	0	0	0	0	1	1	0	0	0	0
NC_000018.8	Chr18	5	5	0	0	0	0	5	5	0	0	0	0
NC_000019.8	Chr19	1	1	0	0	0	0	1	1	0	0	0	0
NC_000021.7	Chr21	1	1	0	0	0	0	1	1	0	0	0	0

			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_000001.8	Chr1	6	5	0	0	0	1	6	5	0	0	0	1
NC_000002.9	Chr2	6	6	0	0	0	0	6	6	0	0	0	0
NC_000003.9	Chr3	3	3	0	0	0	0	3	3	0	0	0	0
NC_000004.9	Chr4	19	19	0	0	0	0	19	19	0	0	0	0
NC_000005.8	Chr5	16	16	0	0	0	0	16	16	0	0	0	0
NC_000008.9	Chr8	20	18	0	0	0	2	20	18	0	0	0	2
NC_000010.8	Chr10	5	4	0	0	0	1	5	4	0	0	0	1
NC_000011.8	Chr11	12	12	0	0	0	0	12	12	0	0	0	0
NC_000013.9	Chr13	1	1	0	0	0	0	1	1	0	0	0	0
NC_000016.8	Chr16	4	4	0	0	0	0	4	4	0	0	0	0
NC_000017.9	Chr17	1	1	0	0	0	0	1	1	0	0	0	0
NC_000018.8	Chr18	5	4	0	0	0	1	5	4	0	0	0	1
NC_000019.8	Chr19	1	1	0	0	0	0	1	1	0	0	0	0
NC_000021.7	Chr21	1	1	0	0	0	0	1	1	0	0	0	0

Samplesets

Number of Samplesets: 4

Sampleset ID:: 1
Name:: Discovery Panel
Description:: 24 unrelated individuals obtained from the Polymorphism Discovery Resource
Size:: 24
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
CPD0016		NA15072		UNKNOWN	Not reported
CPD0023		NA15386		UNKNOWN	Not reported
CPD0005		NA15245		UNKNOWN	Not reported
CPD0013		NA15590		UNKNOWN	Not reported
CPD0009		NA15213		UNKNOWN	Not reported
CPD0012		NA15385		UNKNOWN	Not reported
CPD0010		NA15221		UNKNOWN	Not reported
CPD0015		NA15056		UNKNOWN	Not reported
CPD0007		NA15236		UNKNOWN	Not reported
CPD0020		NA15242		UNKNOWN	Not reported
CPD0003		NA15215		UNKNOWN	Not reported
CPD0002		NA15036		UNKNOWN	Not reported
CPD0014		NA15038		UNKNOWN	Not reported
CPD0022		NA15324		UNKNOWN	Not reported
CPD0021		NA15268		UNKNOWN	Not reported
CPD0017		NA15144		UNKNOWN	Not reported
CPD0008	B-Lymphocyte	NA15510	Female	UNKNOWN	Not reported
CPD0011		NA15227		UNKNOWN	Not reported
CPD0001		NA15029		UNKNOWN	Not reported
CPD0019		NA15226		UNKNOWN	Not reported
CPD0024		NA15594		UNKNOWN	Not reported
CPD0006		NA15224		UNKNOWN	Not reported
CPD0004		NA15223		UNKNOWN	Not reported
CPD0018		NA15216		UNKNOWN	Not reported

Sampleset ID:: 2
Name:: Diversity Panel - African American
Size:: 23
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 2
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
NA17138	NA17138	Female	African American	Not reported
NA17109	NA17109	Male	African American	Not reported
NA17139	NA17139	Female	African American	Not reported
NA17110	NA17110	Female	African American	Not reported
NA17102	NA17102	Male	African American	Not reported
NA17107	NA17107	Male	African American	Not reported
NA17137	NA17137	Female	African American	Not reported
NA17106	NA17106	Male	African American	Not reported
NA17116	NA17116	Female	African American	Not reported
NA17111	NA17111	Male	African American	Not reported
NA17104	NA17104	Male	African American	Not reported
NA17105	NA17105	Male	African American	Not reported
NA17135	NA17135	Female	African American	Not reported
NA17134	NA17134	Female	African American	Not reported
NA17115	NA17115	Male	African American	Not reported
NA17112	NA17112	Female	African American	Not reported
NA17108	NA17108	Male	African American	Not reported
NA17140	NA17140	Female	African American	Not reported
NA17113	NA17113	Female	African American	Not reported
NA17103	NA17103	Male	African American	Not reported
NA17133	NA17133	Female	African American	Not reported
NA17136	NA17136	Female	African American	Not reported
NA17114	NA17114	Male	African American	Not reported

Sampleset ID:: 3
Name:: Diversity Panel - European Americans
Size:: 24
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 3
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
NA10860	NA10860	Male	European American	Not reported
NA10853	NA10853	Male	European American	Not reported
NA06990	NA06990	Female	European American	Not reported
NA10852	NA10852	Female	European American	Not reported
NA07348	NA07348	Female	European American	Not reported
NA10851	NA10851	Male	European American	Not reported
NA12548	NA12548	Female	European American	Not reported
NA10843	NA10843	Female	European American	Not reported
NA10854	NA10854	Female	European American	Not reported
NA07349	NA07349	Male	European American	Not reported
NA07019	NA07019	Female	European American	Not reported
NA10844	NA10844	Female	European American	Not reported
NA12560	NA12560	Male	European American	Not reported
NA10857	NA10857	Male	European American	Not reported
NA17201	NA17201	Male	European American	Not reported
NA10858	NA10858	Male	European American	Not reported
NA10831	NA10831	Female	European American	Not reported
NA10830	NA10830	Male	European American	Not reported
NA10861	NA10861	Female	European American	Not reported
NA10848	NA10848	Male	European American	Not reported
NA10842	NA10842	Male	European American	Not reported
NA12547	NA12547	Male	European American	Not reported
NA10850	NA10850	Female	European American	Not reported
NA10845	NA10845	Male	European American	Not reported

Sampleset ID:: 4
Name:: Diversity Panel - Han Chinese
Size:: 24
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 4
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
NA17756	NA17756	Female	Han Chinese	Not reported
NA17735	NA17735	Female	Han Chinese	Not reported
NA17746	NA17746	Female	Han Chinese	Not reported
NA17759	NA17759	Male	Han Chinese	Not reported
NA17736	NA17736	Male	Han Chinese	Not reported
NA17738	NA17738	Female	Han Chinese	Not reported
NA17740	NA17740	Female	Han Chinese	Not reported
NA17745	NA17745	Female	Han Chinese	Not reported
NA17744	NA17744	Female	Han Chinese	Not reported
NA17743	NA17743	Male	Han Chinese	Not reported
NA17757	NA17757	Female	Han Chinese	Not reported
NA17741	NA17741	Female	Han Chinese	Not reported
NA17742	NA17742	Male	Han Chinese	Not reported
NA17739	NA17739	Female	Han Chinese	Not reported
NA17755	NA17755	Male	Han Chinese	Not reported
NA17737	NA17737	Male	Han Chinese	Not reported
NA17761	NA17761	Male	Han Chinese	Not reported
NA17733	NA17733	Female	Han Chinese	Not reported
NA17752	NA17752	Female	Han Chinese	Not reported
NA17747	NA17747	Female	Han Chinese	Not reported
NA17734	NA17734	Female	Han Chinese	Not reported
NA17753	NA17753	Male	Han Chinese	Not reported
NA17754	NA17754	Female	Han Chinese	Not reported
NA17749	NA17749	Male	Han Chinese	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Oligo aCGH	Probe signal intensity	Custom Perlegen arrays	100
2	Validation	PCR	Manual observation		100

Validations

Experiment ID	Method	Analysis	Number of Variant Calls Validated
2	PCR	Manual observation	100

dbVar

Database of genomic structural variation

nstd34 (Hinds et al. 2005)

Links

Detailed Information: Download 100 Variant Regions, Download 100 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI35 (hg17)

Remapping summary: NCBI35->GRCh37.p13NCBI35->GRCh38.p12

Samplesets

Number of Samplesets: 4

Experimental Details

Validations

Variant Summary for:

Remapping summary: