nstd194 - Lee et al 2020 - dbVar Study

nstd194 (Lee et al. 2020)

Organism:: Human
Study Type:: Collection
Submitter:: Jin-young Lee
Description:: To systematically identify non-reference insertion structural variants among human populations, we developed an insertion detection pipeline, InserTag, which generates unmapped contigs by local de-novo assembly and then infers the full-sequence of insertion variants by tracing the contigs from non-human primates and other human assemblies. By application of the pipeline to 1000 Genomes Project database, we could identify 1,696 non-reference insertion variants in 2,535 individuals and re-classify the variants as retention of ancestral sequences or novel sequence insertions based on the ancestral state. Here, we report 1114 variants which are larger than 100 bp and have genotypes. See Variant Summary counts for nstd194 in dbVar Variant Summary.
Publication(s):: Lee et al. 2020

Links

Source: NCBI

Detailed Information: Download 1114 Variant Regions, Download 1114 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p13 (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	90	90	Remapped	NC_000001.11
NC_000002.12	Chr2	81	81	Remapped	NC_000002.12
NC_000003.12	Chr3	75	75	Remapped	NC_000003.12
NC_000004.12	Chr4	90	90	Remapped	NC_000004.12
NC_000005.10	Chr5	69	69	Remapped	NC_000005.10
NC_000006.12	Chr6	54	54	Remapped	NC_000006.12
NC_000007.14	Chr7	64	64	Remapped	NC_000007.14
NC_000008.11	Chr8	58	58	Remapped	NC_000008.11
NC_000009.12	Chr9	42	42	Remapped	NC_000009.12
NC_000010.11	Chr10	63	63	Remapped	NC_000010.11
NC_000011.10	Chr11	62	62	Remapped	NC_000011.10
NC_000012.12	Chr12	60	60	Remapped	NC_000012.12
NC_000013.11	Chr13	38	38	Remapped	NC_000013.11
NC_000014.9	Chr14	37	37	Remapped	NC_000014.9
NC_000015.10	Chr15	41	41	Remapped	NC_000015.10
NC_000016.10	Chr16	21	21	Remapped	NC_000016.10
NC_000017.11	Chr17	46	46	Remapped	NC_000017.11
NC_000018.10	Chr18	42	42	Remapped	NC_000018.10
NC_000019.10	Chr19	23	23	Remapped	NC_000019.10
NC_000020.11	Chr20	27	27	Remapped	NC_000020.11
NC_000021.9	Chr21	18	18	Remapped	NC_000021.9
NC_000022.11	Chr22	12	12	Remapped	NC_000022.11
NT_187514.1	Chr1\|NT_187514.1	1	1	Remapped	NT_187514.1
NT_187516.1	Chr1\|NT_187516.1	1	1	Remapped	NT_187516.1
NW_003315907.2	Chr1\|NW_003315907.2	1	1	Remapped	NW_003315907.2
NW_009646194.1	Chr1\|NW_009646194.1	1	1	Remapped	NW_009646194.1
NW_014040925.1	Chr1\|NW_014040925.1	1	1	Remapped	NW_014040925.1
NW_018654706.1	Chr1\|NW_018654706.1	1	1	Remapped	NW_018654706.1
NT_187525.1	Chr2\|NT_187525.1	1	1	Remapped	NT_187525.1
NT_187527.1	Chr2\|NT_187527.1	1	1	Remapped	NT_187527.1
NT_187531.1	Chr2\|NT_187531.1	1	1	Remapped	NT_187531.1
NW_015495299.1	Chr2\|NW_015495299.1	1	1	Remapped	NW_015495299.1
NW_018654709.1	Chr2\|NW_018654709.1	1	1	Remapped	NW_018654709.1
NT_187533.1	Chr3\|NT_187533.1	1	1	Remapped	NT_187533.1
NT_187536.1	Chr3\|NT_187536.1	1	1	Remapped	NT_187536.1
NT_187538.1	Chr3\|NT_187538.1	1	1	Remapped	NT_187538.1
NW_003871060.2	Chr3\|NW_003871060.2	1	1	Remapped	NW_003871060.2
NW_012132916.1	Chr3\|NW_012132916.1	1	1	Remapped	NW_012132916.1
NW_019805488.1	Chr3\|NW_019805488.1	1	1	Remapped	NW_019805488.1
NW_019805489.1	Chr3\|NW_019805489.1	1	1	Remapped	NW_019805489.1
NT_187541.1	Chr4\|NT_187541.1	1	1	Remapped	NT_187541.1
NT_187544.1	Chr4\|NT_187544.1	1	1	Remapped	NT_187544.1
NW_003315914.1	Chr4\|NW_003315914.1	1	1	Remapped	NW_003315914.1
NW_013171801.1	Chr4\|NW_013171801.1	1	1	Remapped	NW_013171801.1
NW_017363814.1	Chr4\|NW_017363814.1	1	1	Remapped	NW_017363814.1
NT_187551.1	Chr5\|NT_187551.1	1	1	Remapped	NT_187551.1
NW_003315917.2	Chr5\|NW_003315917.2	1	1	Remapped	NW_003315917.2
NW_003315920.1	Chr5\|NW_003315920.1	1	1	Remapped	NW_003315920.1
NW_018654712.1	Chr5\|NW_018654712.1	1	1	Remapped	NW_018654712.1
NT_187556.1	Chr6\|NT_187556.1	1	1	Remapped	NT_187556.1
NW_009646200.1	Chr6\|NW_009646200.1	1	1	Remapped	NW_009646200.1
NW_013171803.1	Chr6\|NW_013171803.1	1	1	Remapped	NW_013171803.1
NW_017363815.1	Chr6\|NW_017363815.1	1	1	Remapped	NW_017363815.1
NT_187564.1	Chr7\|NT_187564.1	1	1	Remapped	NT_187564.1
NW_003315922.2	Chr7\|NW_003315922.2	1	1	Remapped	NW_003315922.2
NW_017852929.1	Chr7\|NW_017852929.1	1	1	Remapped	NW_017852929.1
NW_019805493.1	Chr7\|NW_019805493.1	1	1	Remapped	NW_019805493.1
NT_187565.1	Chr8\|NT_187565.1	1	1	Remapped	NT_187565.1
NT_187567.1	Chr8\|NT_187567.1	1	1	Remapped	NT_187567.1
NT_187569.1	Chr8\|NT_187569.1	1	1	Remapped	NT_187569.1
NW_017852931.1	Chr8\|NW_017852931.1	1	1	Remapped	NW_017852931.1
NW_018654717.1	Chr8\|NW_018654717.1	1	1	Remapped	NW_018654717.1
NW_019805494.1	Chr8\|NW_019805494.1	1	1	Remapped	NW_019805494.1
NW_013171804.1	Chr9\|NW_013171804.1	1	1	Remapped	NW_013171804.1
NW_013171805.1	Chr9\|NW_013171805.1	1	1	Remapped	NW_013171805.1
NW_003315934.1	Chr10\|NW_003315934.1	1	1	Remapped	NW_003315934.1
NW_009646202.1	Chr10\|NW_009646202.1	1	1	Remapped	NW_009646202.1
NT_187657.1	Chr11\|NT_187657.1	1	1	Remapped	NT_187657.1
NT_187583.1	Chr11\|NT_187583.1	1	1	Remapped	NT_187583.1
NT_187584.1	Chr11\|NT_187584.1	1	1	Remapped	NT_187584.1
NW_003315936.1	Chr11\|NW_003315936.1	1	1	Remapped	NW_003315936.1
NW_011332695.1	Chr11\|NW_011332695.1	1	1	Remapped	NW_011332695.1
NW_013171808.1	Chr11\|NW_013171808.1	1	1	Remapped	NW_013171808.1
NW_017363816.1	Chr11\|NW_017363816.1	1	1	Remapped	NW_017363816.1
NW_019805497.1	Chr11\|NW_019805497.1	2	2	Remapped	NW_019805497.1
NT_187658.1	Chr12\|NT_187658.1	1	1	Remapped	NT_187658.1
NW_003571050.1	Chr12\|NW_003571050.1	1	1	Remapped	NW_003571050.1
NW_018654718.1	Chr12\|NW_018654718.1	1	1	Remapped	NW_018654718.1
NT_187595.1	Chr13\|NT_187595.1	2	2	Remapped	NT_187595.1
NT_187597.1	Chr13\|NT_187597.1	1	1	Remapped	NT_187597.1
NW_013171810.1	Chr13\|NW_013171810.1	1	1	Remapped	NW_013171810.1
NW_013171811.1	Chr13\|NW_013171811.1	1	1	Remapped	NW_013171811.1
NT_187601.1	Chr14\|NT_187601.1	1	1	Remapped	NT_187601.1
NW_018654722.1	Chr14\|NW_018654722.1	1	1	Remapped	NW_018654722.1
NT_187660.1	Chr15\|NT_187660.1	1	1	Remapped	NT_187660.1
NT_187605.1	Chr15\|NT_187605.1	1	1	Remapped	NT_187605.1
NW_003315944.2	Chr15\|NW_003315944.2	2	2	Remapped	NW_003315944.2
NT_187615.1	Chr17\|NT_187615.1	1	1	Remapped	NT_187615.1
NW_003871091.1	Chr17\|NW_003871091.1	1	1	Remapped	NW_003871091.1
NW_017363818.1	Chr17\|NW_017363818.1	1	1	Remapped	NW_017363818.1
NW_003315960.1	Chr18\|NW_003315960.1	1	1	Remapped	NW_003315960.1
NW_013171814.1	Chr18\|NW_013171814.1	1	1	Remapped	NW_013171814.1
NW_014040928.1	Chr18\|NW_014040928.1	2	2	Remapped	NW_014040928.1
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_003315963.1	Chr19\|NW_003315963.1	1	1	Remapped	NW_003315963.1
NT_187625.1	Chr20\|NT_187625.1	1	1	Remapped	NT_187625.1
NT_187628.1	Chr21\|NT_187628.1	1	1	Remapped	NT_187628.1
NT_187631.1	Chr22\|NT_187631.1	1	1	Remapped	NT_187631.1
NT_187562.1	Chr7\|NT_187562.1	1	1	Remapped	NT_187562.1
NT_187576.1	Chr8\|NT_187576.1	1	1	Remapped	NT_187576.1
NT_187593.1	Chr13\|NT_187593.1	1	1	Remapped	NT_187593.1
NT_187600.1	Chr14\|NT_187600.1	2	2	Remapped	NT_187600.1
NW_011332701.1	Chr15\|NW_011332701.1	1	1	Remapped	NW_011332701.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	90	90	Submitted	NC_000001.10
NC_000002.11	Chr2	81	81	Submitted	NC_000002.11
NC_000003.11	Chr3	75	75	Submitted	NC_000003.11
NC_000004.11	Chr4	90	90	Submitted	NC_000004.11
NC_000005.9	Chr5	69	69	Submitted	NC_000005.9
NC_000006.11	Chr6	55	55	Submitted	NC_000006.11
NC_000007.13	Chr7	64	64	Submitted	NC_000007.13
NC_000008.10	Chr8	58	58	Submitted	NC_000008.10
NC_000009.11	Chr9	42	42	Submitted	NC_000009.11
NC_000010.10	Chr10	63	63	Submitted	NC_000010.10
NC_000011.9	Chr11	62	62	Submitted	NC_000011.9
NC_000012.11	Chr12	60	60	Submitted	NC_000012.11
NC_000013.10	Chr13	38	38	Submitted	NC_000013.10
NC_000014.8	Chr14	37	37	Submitted	NC_000014.8
NC_000015.9	Chr15	41	41	Submitted	NC_000015.9
NC_000016.9	Chr16	21	21	Submitted	NC_000016.9
NC_000017.10	Chr17	46	46	Submitted	NC_000017.10
NC_000018.9	Chr18	42	42	Submitted	NC_000018.9
NC_000019.9	Chr19	23	23	Submitted	NC_000019.9
NC_000020.10	Chr20	27	27	Submitted	NC_000020.10
NC_000021.8	Chr21	18	18	Submitted	NC_000021.8
NC_000022.10	Chr22	12	12	Submitted	NC_000022.10

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	90	84	0	0	0	6	90	84	0	0	0	6
NC_000002.11	Chr2	81	76	0	0	0	5	81	76	0	0	0	5
NC_000003.11	Chr3	75	68	0	0	0	7	75	68	0	0	0	7
NC_000004.11	Chr4	90	85	0	0	0	5	90	85	0	0	0	5
NC_000005.9	Chr5	69	65	0	0	0	4	69	65	0	0	0	4
NC_000006.11	Chr6	55	50	0	0	1	4	55	50	0	0	1	4
NC_000007.13	Chr7	64	59	0	0	0	5	64	59	0	0	0	5
NC_000008.10	Chr8	58	51	0	0	0	7	58	51	0	0	0	7
NC_000009.11	Chr9	42	40	0	0	0	2	42	40	0	0	0	2
NC_000010.10	Chr10	63	61	0	0	0	2	63	61	0	0	0	2
NC_000011.9	Chr11	62	55	0	0	0	7	62	55	0	0	0	7
NC_000012.11	Chr12	60	58	0	0	0	2	60	58	0	0	0	2
NC_000013.10	Chr13	38	32	0	0	0	6	38	32	0	0	0	6
NC_000014.8	Chr14	37	33	0	0	0	4	37	33	0	0	0	4
NC_000015.9	Chr15	41	37	0	0	0	4	41	37	0	0	0	4
NC_000016.9	Chr16	21	21	0	0	0	0	21	21	0	0	0	0
NC_000017.10	Chr17	46	43	0	0	0	3	46	43	0	0	0	3
NC_000018.9	Chr18	42	36	0	0	0	6	42	36	0	0	0	6
NC_000019.9	Chr19	23	22	0	0	0	1	23	22	0	0	0	1
NC_000020.10	Chr20	27	26	0	0	0	1	27	26	0	0	0	1
NC_000021.8	Chr21	18	17	0	0	0	1	18	17	0	0	0	1
NC_000022.10	Chr22	12	11	0	0	0	1	12	11	0	0	0	1

Samplesets

Number of Samplesets: 1

Name:: 1KGP
Description:: Individuals of 1KGP final phase
Size:: 2,535
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 1 (displaying 100 of the 2535 samples)
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
SAMN00016971	HG00179	Female	FIN	Not reported
SAMN00016969	HG00177	Female	FIN	Not reported
SAMN00006344	HG00126	Male	GBR	Not reported
SAMN00004677	HG00233	Female	GBR	Not reported
SAMN00004646	HG00128	Female	GBR	Not reported
SAMN00006354	HG00245	Female	GBR	Not reported
SAMN00004657	HG00139	Male	GBR	Not reported
SAMN00016977	HG00186	Male	FIN	Not reported
SAMN00004642	HG00116	Male	GBR	Not reported
SAMN00004651	HG00133	Female	GBR	Not reported
SAMN00004629	HG00103	Male	GBR	Not reported
SAMN00004668	HG00150	Female	GBR	Not reported
SAMN00004628	HG00102	Female	GBR	Not reported
SAMN00004639	HG00113	Male	GBR	Not reported
SAMN00006358	HG00253	Female	GBR	Not reported
SAMN00006365	HG00261	Female	GBR	Not reported
SAMN00006343	HG00125	Female	GBR	Not reported
SAMN00004672	HG00155	Male	GBR	Not reported
SAMN00004633	HG00107	Male	GBR	Not reported
SAMN00004664	HG00146	Female	GBR	Not reported
SAMN00016968	HG00176	Female	FIN	Not reported
SAMN00006351	HG00242	Male	GBR	Not reported
SAMN00004643	HG00117	Male	GBR	Not reported
SAMN00004680	HG00238	Female	GBR	Not reported
SAMN00004667	HG00149	Male	GBR	Not reported
SAMN00004660	HG00142	Male	GBR	Not reported
SAMN00004647	HG00129	Male	GBR	Not reported
SAMN00004656	HG00138	Male	GBR	Not reported
SAMN00006341	HG00123	Female	GBR	Not reported
SAMN00004666	HG00148	Male	GBR	Not reported
SAMN00006353	HG00244	Male	GBR	Not reported
SAMN00016980	HG00189	Male	FIN	Not reported
SAMN00016973	HG00181	Male	FIN	Not reported
SAMN00004627	HG00101	Male	GBR	Not reported
SAMN00009091	HG00250	Female	GBR	Not reported
SAMN00004661	HG00143	Male	GBR	Not reported
SAMN00006342	HG00124	Female	GBR	Not reported
SAMN00004676	HG00160	Male	GBR	Not reported
SAMN00006352	HG00243	Male	GBR	Not reported
SAMN00016965	HG00171	Female	FIN	Not reported
SAMN00004679	HG00235	Female	GBR	Not reported
SAMN00004682	HG00255	Female	GBR	Not reported
SAMN00004631	HG00105	Male	GBR	Not reported
SAMN00004655	HG00137	Female	GBR	Not reported
SAMN00004650	HG00132	Female	GBR	Not reported
SAMN00009092	HG00251	Male	GBR	Not reported
SAMN00006350	HG00239	Female	GBR	Not reported
SAMN00004635	HG00109	Male	GBR	Not reported
SAMN00006340	HG00122	Female	GBR	Not reported
SAMN00009088	HG00154	Female	GBR	Not reported
SAMN00006364	HG00260	Male	GBR	Not reported
SAMN00006338	HG00119	Male	GBR	Not reported
SAMN00016975	HG00183	Male	FIN	Not reported
SAMN00004634	HG00108	Male	GBR	Not reported
SAMN00016974	HG00182	Male	FIN	Not reported
SAMN00004681	HG00240	Female	GBR	Not reported
SAMN00006337	HG00118	Female	GBR	Not reported
SAMN00006357	HG00252	Male	GBR	Not reported
SAMN00016981	HG00190	Male	FIN	Not reported
SAMN00004674	HG00157	Male	GBR	Not reported
SAMN00016967	HG00174	Female	FIN	Not reported
SAMN00004654	HG00136	Male	GBR	Not reported
SAMN00004636	HG00110	Female	GBR	Not reported
SAMN00006359	HG00254	Female	GBR	Not reported
SAMN00016978	HG00187	Male	FIN	Not reported
SAMN00016979	HG00188	Male	FIN	Not reported
SAMN00004626	HG00100	Female	GBR	Not reported
SAMN00009089	HG00246	Male	GBR	Not reported
SAMN00004648	HG00130	Female	GBR	Not reported
SAMN00004638	HG00112	Male	GBR	Not reported
SAMN00004622	HG00096	Male	GBR	Not reported
SAMN00006339	HG00121	Female	GBR	Not reported
SAMN00004658	HG00140	Male	GBR	Not reported
SAMN00006360	HG00256	Male	GBR	Not reported
SAMN00004625	HG00099	Female	GBR	Not reported
SAMN00004637	HG00111	Female	GBR	Not reported
SAMN00004675	HG00158	Female	GBR	Not reported
SAMN00016976	HG00185	Male	FIN	Not reported
SAMN00006349	HG00237	Female	GBR	Not reported
SAMN00004641	HG00115	Male	GBR	Not reported
SAMN00004640	HG00114	Male	GBR	Not reported
SAMN00016972	HG00180	Female	FIN	Not reported
SAMN00004649	HG00131	Male	GBR	Not reported
SAMN00006362	HG00258	Female	GBR	Not reported
SAMN00004632	HG00106	Female	GBR	Not reported
SAMN00004678	HG00234	Male	GBR	Not reported
SAMN00006363	HG00259	Female	GBR	Not reported
SAMN00016966	HG00173	Female	FIN	Not reported
SAMN00004645	HG00127	Female	GBR	Not reported
SAMN00004644	HG00120	Female	GBR	Not reported
SAMN00004659	HG00141	Male	GBR	Not reported
SAMN00004669	HG00151	Male	GBR	Not reported
SAMN00004623	HG00097	Female	GBR	Not reported
SAMN00004663	HG00145	Male	GBR	Not reported
SAMN00006345	HG00159	Male	GBR	Not reported
SAMN00006347	HG00232	Female	GBR	Not reported
SAMN00006361	HG00257	Female	GBR	Not reported
SAMN00006348	HG00236	Female	GBR	Not reported
SAMN00006346	HG00231	Female	GBR	Not reported
SAMN00016970	HG00178	Female	FIN	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Number of Variant Calls
1	Discovery	Sequencing	de novo and local sequence assembly	1,114

dbVar

Database of genomic structural variation

nstd194 (Lee et al. 2020)

Links

Detailed Information: Download 1114 Variant Regions, Download 1114 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p13 (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

nstd194 (Lee et al. 2020)

Links

Detailed Information: Download 1114 Variant Regions, Download 1114 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p13 (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: