nstd109 - Wildschutte et al 2015 - dbVar Study

nstd109 (Wildschutte et al. 2015)

Organism:: Human
Study Type:: Collection
Submitter:: Jeffrey Kidd
Description:: Discovery and assembly of polymorphic Alu insertions from 53 human genomes. See Variant Summary counts for nstd109 in dbVar Variant Summary.
Project:: PRJNA236787
Publication(s):: Wildschutte et al. 2015

Links

Source: NCBI

Detailed Information: Download 1614 Variant Regions, Download 1614 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	84	84	Remapped	NC_000001.11
NC_000002.12	Chr2	141	141	Remapped	NC_000002.12
NC_000003.12	Chr3	120	120	Remapped	NC_000003.12
NC_000004.12	Chr4	123	123	Remapped	NC_000004.12
NC_000005.10	Chr5	114	114	Remapped	NC_000005.10
NC_000006.12	Chr6	135	135	Remapped	NC_000006.12
NC_000007.14	Chr7	76	76	Remapped	NC_000007.14
NC_000008.11	Chr8	104	104	Remapped	NC_000008.11
NC_000009.12	Chr9	60	60	Remapped	NC_000009.12
NC_000010.11	Chr10	79	79	Remapped	NC_000010.11
NC_000011.10	Chr11	76	76	Remapped	NC_000011.10
NC_000012.12	Chr12	90	90	Remapped	NC_000012.12
NC_000013.11	Chr13	92	92	Remapped	NC_000013.11
NC_000014.9	Chr14	64	64	Remapped	NC_000014.9
NC_000015.10	Chr15	58	58	Remapped	NC_000015.10
NC_000016.10	Chr16	19	19	Remapped	NC_000016.10
NC_000017.11	Chr17	28	28	Remapped	NC_000017.11
NC_000018.10	Chr18	47	47	Remapped	NC_000018.10
NC_000019.10	Chr19	5	5	Remapped	NC_000019.10
NC_000020.11	Chr20	26	26	Remapped	NC_000020.11
NC_000021.9	Chr21	28	28	Remapped	NC_000021.9
NC_000022.11	Chr22	4	4	Remapped	NC_000022.11
NC_000023.11	ChrX	38	38	Remapped	NC_000023.11
NC_000024.10	ChrY	1	1	Remapped	NC_000024.10
NT_113901.1	Unplaced\|NT_113901.1	1	1	Remapped	NT_113901.1
NW_003315907.2	Chr1\|NW_003315907.2	1	1	Remapped	NW_003315907.2
NW_009646196.1	Chr1\|NW_009646196.1	1	1	Remapped	NW_009646196.1
NW_014040925.1	Chr1\|NW_014040925.1	1	1	Remapped	NW_014040925.1
NT_187529.1	Chr2\|NT_187529.1	1	1	Remapped	NT_187529.1
NW_003315908.1	Chr2\|NW_003315908.1	1	1	Remapped	NW_003315908.1
NT_187540.1	Chr4\|NT_187540.1	1	1	Remapped	NT_187540.1
NW_003315921.1	Chr6\|NW_003315921.1	1	1	Remapped	NW_003315921.1
NW_009646200.1	Chr6\|NW_009646200.1	3	3	Remapped	NW_009646200.1
NT_187564.1	Chr7\|NT_187564.1	1	1	Remapped	NT_187564.1
NT_187567.1	Chr8\|NT_187567.1	1	1	Remapped	NT_187567.1
NT_187576.1	Chr8\|NT_187576.1	1	1	Remapped	NT_187576.1
NT_187577.1	Chr8\|NT_187577.1	1	1	Remapped	NT_187577.1
NW_018654717.1	Chr8\|NW_018654717.1	3	3	Remapped	NW_018654717.1
NW_013171806.1	Chr10\|NW_013171806.1	1	1	Remapped	NW_013171806.1
NT_187581.1	Chr11\|NT_187581.1	1	1	Remapped	NT_187581.1
NW_019805495.1	Chr11\|NW_019805495.1	1	1	Remapped	NW_019805495.1
NT_187587.1	Chr12\|NT_187587.1	1	1	Remapped	NT_187587.1
NW_003315938.1	Chr12\|NW_003315938.1	1	1	Remapped	NW_003315938.1
NW_003315939.2	Chr12\|NW_003315939.2	1	1	Remapped	NW_003315939.2
NW_003315941.1	Chr12\|NW_003315941.1	1	1	Remapped	NW_003315941.1
NW_018654718.1	Chr12\|NW_018654718.1	2	2	Remapped	NW_018654718.1
NT_187595.1	Chr13\|NT_187595.1	1	1	Remapped	NT_187595.1
NW_011332698.1	Chr13\|NW_011332698.1	1	1	Remapped	NW_011332698.1
NW_011332699.1	Chr13\|NW_011332699.1	1	1	Remapped	NW_011332699.1
NW_011332700.1	Chr13\|NW_011332700.1	1	1	Remapped	NW_011332700.1
NT_187598.1	Chr14\|NT_187598.1	1	1	Remapped	NT_187598.1
NT_187659.1	Chr15\|NT_187659.1	1	1	Remapped	NT_187659.1
NT_187660.1	Chr15\|NT_187660.1	1	1	Remapped	NT_187660.1
NW_011332701.1	Chr15\|NW_011332701.1	1	1	Remapped	NW_011332701.1
NT_187614.1	Chr17\|NT_187614.1	2	2	Remapped	NT_187614.1
NW_003315954.1	Chr17\|NW_003315954.1	2	2	Remapped	NW_003315954.1
NW_003871091.1	Chr17\|NW_003871091.1	1	1	Remapped	NW_003871091.1
NW_018654724.1	Chr18\|NW_018654724.1	1	1	Remapped	NW_018654724.1
NW_019805503.1	Chr18\|NW_019805503.1	1	1	Remapped	NW_019805503.1
NW_003315968.2	Chr21\|NW_003315968.2	1	1	Remapped	NW_003315968.2

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	84	84	Submitted	NC_000001.10
NC_000002.11	Chr2	141	141	Submitted	NC_000002.11
NC_000003.11	Chr3	120	120	Submitted	NC_000003.11
NC_000004.11	Chr4	123	123	Submitted	NC_000004.11
NC_000005.9	Chr5	114	114	Submitted	NC_000005.9
NC_000006.11	Chr6	135	135	Submitted	NC_000006.11
NC_000007.13	Chr7	76	76	Submitted	NC_000007.13
NC_000008.10	Chr8	105	105	Submitted	NC_000008.10
NC_000009.11	Chr9	60	60	Submitted	NC_000009.11
NC_000010.10	Chr10	79	79	Submitted	NC_000010.10
NC_000011.9	Chr11	76	76	Submitted	NC_000011.9
NC_000012.11	Chr12	90	90	Submitted	NC_000012.11
NC_000013.10	Chr13	91	91	Submitted	NC_000013.10
NC_000014.8	Chr14	64	64	Submitted	NC_000014.8
NC_000015.9	Chr15	58	58	Submitted	NC_000015.9
NC_000016.9	Chr16	19	19	Submitted	NC_000016.9
NC_000017.10	Chr17	28	28	Submitted	NC_000017.10
NC_000018.9	Chr18	47	47	Submitted	NC_000018.9
NC_000019.9	Chr19	5	5	Submitted	NC_000019.9
NC_000020.10	Chr20	26	26	Submitted	NC_000020.10
NC_000021.8	Chr21	28	28	Submitted	NC_000021.8
NC_000022.10	Chr22	4	4	Submitted	NC_000022.10
NC_000023.10	ChrX	38	38	Submitted	NC_000023.10
NC_000024.9	ChrY	1	1	Submitted	NC_000024.9
NT_113923.1	Unplaced\|NT_113923.1	1	1	Submitted	NT_113923.1
NT_113901.1	Chr7\|NT_113901.1	1	1	Submitted	NT_113901.1

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	84	81	0	0	0	3	84	81	0	0	0	3
NC_000002.11	Chr2	141	139	0	0	0	2	141	139	0	0	0	2
NC_000003.11	Chr3	120	120	0	0	0	0	120	120	0	0	0	0
NC_000004.11	Chr4	123	122	0	0	0	1	123	122	0	0	0	1
NC_000005.9	Chr5	114	114	0	0	0	0	114	114	0	0	0	0
NC_000006.11	Chr6	135	131	0	0	0	4	135	131	0	0	0	4
NC_000007.13	Chr7	76	75	0	0	0	1	76	75	0	0	0	1
NC_000008.10	Chr8	105	100	0	0	0	5	105	100	0	0	0	5
NC_000009.11	Chr9	60	60	0	0	0	0	60	60	0	0	0	0
NC_000010.10	Chr10	79	78	0	0	0	1	79	78	0	0	0	1
NC_000011.9	Chr11	76	74	0	0	0	2	76	74	0	0	0	2
NC_000012.11	Chr12	90	84	0	0	0	6	90	84	0	0	0	6
NC_000013.10	Chr13	91	88	0	0	0	3	91	88	0	0	0	3
NC_000014.8	Chr14	64	63	0	0	0	1	64	63	0	0	0	1
NC_000015.9	Chr15	58	56	0	0	0	2	58	56	0	0	0	2
NC_000016.9	Chr16	19	19	0	0	0	0	19	19	0	0	0	0
NC_000017.10	Chr17	28	23	0	0	0	5	28	23	0	0	0	5
NC_000018.9	Chr18	47	45	0	0	0	2	47	45	0	0	0	2
NC_000019.9	Chr19	5	5	0	0	0	0	5	5	0	0	0	0
NC_000020.10	Chr20	26	26	0	0	0	0	26	26	0	0	0	0
NC_000021.8	Chr21	28	27	0	0	0	1	28	27	0	0	0	1
NC_000022.10	Chr22	4	4	0	0	0	0	4	4	0	0	0	0
NC_000023.10	ChrX	38	38	0	0	0	0	38	38	0	0	0	0
NC_000024.9	ChrY	1	1	0	0	0	0	1	1	0	0	0	0
NT_113901.1	Chr7\|NT_113901.1	1	1	0	0	0	0	1	1	0	0	0	0
NT_113923.1	Unplaced\|NT_113923.1	1	0	0	0	0	1	1	0	0	0	0	1

Samplesets

Number of Samplesets: 1

Name:: HGDP-53
Description:: 53 samples from 7 populations from HGDP panel
Size:: 53
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
SAMN02603818	HGDP00991	Male	San	Not reported
SAMN02603828	HGDP01267	Female	Mozabite	Not reported
SAMN02603822	HGDP01036	Male	San	Not reported
SAMN02603808	HGDP00877	Male	Maya	Not reported
SAMN02603827	HGDP01264	Male	Mozabite	Not reported
SAMN02603809	HGDP00948	Male	Yakut	Not reported
SAMN02603790	HGDP00471	Female	Mbuti_Pygmy	Not reported
SAMN02603824	HGDP01258	Male	Mozabite	Not reported
SAMN02603782	HGDP00239	Female	Pathan	Not reported
SAMN02603815	HGDP00964	Male	Yakut	Not reported
SAMN02603821	HGDP01032	Male	San	Not reported
SAMN02603829	HGDP01274	Female	Mozabite	Not reported
SAMN02603788	HGDP00462	Male	Mbuti_Pygmy	Not reported
SAMN02603816	HGDP00967	Female	Yakut	Not reported
SAMN02603795	HGDP00713	Female	Cambodian	Not reported
SAMN02603797	HGDP00716	Male	Cambodian	Not reported
SAMN02603817	HGDP00987	Male	San	Not reported
SAMN02603796	HGDP00715	Male	Cambodian	Not reported
SAMN02603785	HGDP00258	Male	Pathan	Not reported
SAMN02603831	HGDP01277	Female	Mozabite	Not reported
SAMN02603803	HGDP00856	Male	Maya	Not reported
SAMN02603802	HGDP00855	Female	Maya	Not reported
SAMN02603798	HGDP00719	Female	Cambodian	Not reported
SAMN02603800	HGDP00721	Female	Cambodian	Not reported
SAMN02603819	HGDP00992	Male	San	Not reported
SAMN02603787	HGDP00456	Male	Mbuti_Pygmy	Not reported
SAMN02603813	HGDP00960	Male	Yakut	Not reported
SAMN02603823	HGDP01081	Male	Mbuti_Pygmy	Not reported
SAMN02603780	HGDP00232	Female	Pathan	Not reported
SAMN02603812	HGDP00959	Female	Yakut	Not reported
SAMN02603830	HGDP01275	Female	Mozabite	Not reported
SAMN02603783	HGDP00243	Male	Pathan	Not reported
SAMN02603799	HGDP00720	Male	Cambodian	Not reported
SAMN02603806	HGDP00860	Female	Maya	Not reported
SAMN02603793	HGDP00711	Male	Cambodian	Not reported
SAMN02603794	HGDP00712	Female	Cambodian	Not reported
SAMN02603784	HGDP00247	Female	Pathan	Not reported
SAMN02603804	HGDP00857	Female	Maya	Not reported
SAMN02603805	HGDP00858	Female	Maya	Not reported
SAMN02603791	HGDP00474	Male	Mbuti_Pygmy	Not reported
SAMN02603820	HGDP01029	Male	San	Not reported
SAMN02603810	HGDP00950	Male	Yakut	Not reported
SAMN02603786	HGDP00449	Male	Mbuti_Pygmy	Not reported
SAMN02603826	HGDP01262	Male	Mozabite	Not reported
SAMN02603781	HGDP00237	Female	Pathan	Not reported
SAMN02603801	HGDP00854	Female	Maya	Not reported
SAMN02603779	HGDP00222	Male	Pathan	Not reported
SAMN02603807	HGDP00868	Female	Maya	Not reported
SAMN02603814	HGDP00963	Female	Yakut	Not reported
SAMN02603792	HGDP00476	Female	Mbuti_Pygmy	Not reported
SAMN02603778	HGDP00213	Male	Pathan	Not reported
SAMN02603811	HGDP00955	Female	Yakut	Not reported
SAMN02603825	HGDP01259	Male	Mozabite	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	de novo and local sequence assembly	Illumina HiSeq 2000	1,614

dbVar

Database of genomic structural variation

nstd109 (Wildschutte et al. 2015)

Links

Detailed Information: Download 1614 Variant Regions, Download 1614 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

nstd109 (Wildschutte et al. 2015)

Links

Detailed Information: Download 1614 Variant Regions, Download 1614 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: