estd59: dbVar Study Page

estd59

Organism:: Human
Study type:: Control Set
Submitter:: Richard Durbin
Description:: This study contains all structural variation data for the first phase of the 1000 Genomes Project (1K Genomes, 1KG). This includes Deletions, Mobile Element Insertions, Tandem Duplications, and Novel Sequences for both Pilot1 and Pilot2 on all chromosomes. Pilot1 structural variations were determined by low coverage re-sequencing of HapMap samples. Pilot2 structural variations were determined by high coverage re-sequencing of two HapMap trios (YRI and CEU).
Project:: 28889
Publication(s):: Durbin et al. 2010

Links

Source: NCBI

Detailed Information: Download 218039 Variant Regions, Download 2150366 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh37 (hg19)
Remapped: GRCh37.p5 GRCh37.p5 contains hg19 and PATCH updates released by the GRC (Click to go to GRC website).
Submitted: NCBI36 (hg18)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	16,301	160,365	Remapped	NC_000001.10
NC_000002.11	Chr2	16,419	164,967	Remapped	NC_000002.11
NC_000003.11	Chr3	12,634	125,038	Remapped	NC_000003.11
NC_000004.11	Chr4	14,485	158,503	Remapped	NC_000004.11
NC_000005.9	Chr5	12,630	132,646	Remapped	NC_000005.9
NC_000006.11	Chr6	13,155	140,335	Remapped	NC_000006.11
NC_000007.13	Chr7	12,753	123,475	Remapped	NC_000007.13
NC_000008.10	Chr8	11,001	114,662	Remapped	NC_000008.10
NC_000009.11	Chr9	11,196	103,738	Remapped	NC_000009.11
NC_000010.10	Chr10	9,583	101,438	Remapped	NC_000010.10
NC_000011.9	Chr11	10,247	102,082	Remapped	NC_000011.9
NC_000012.11	Chr12	9,480	94,718	Remapped	NC_000012.11
NC_000013.10	Chr13	7,426	80,604	Remapped	NC_000013.10
NC_000014.8	Chr14	7,222	82,698	Remapped	NC_000014.8
NC_000015.9	Chr15	5,691	57,939	Remapped	NC_000015.9
NC_000016.9	Chr16	7,174	59,180	Remapped	NC_000016.9
NC_000017.10	Chr17	7,454	69,660	Remapped	NC_000017.10
NC_000018.9	Chr18	6,175	61,700	Remapped	NC_000018.9
NC_000019.9	Chr19	6,771	55,746	Remapped	NC_000019.9
NC_000020.10	Chr20	4,699	44,875	Remapped	NC_000020.10
NC_000021.8	Chr21	3,496	28,939	Remapped	NC_000021.8
NC_000022.10	Chr22	4,502	44,800	Remapped	NC_000022.10
NC_000023.10	ChrX	6,267	34,940	Remapped	NC_000023.10
NC_000024.9	ChrY	830	1,438	Remapped	NC_000024.9

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NT_167250.1	Chr4\|NT_167250.1	40	866	Remapped	NT_167250.1
NT_113891.2	Chr6\|NT_113891.2	4	36	Remapped	NT_113891.2
NW_003571040.1	Chr7\|NW_003571040.1	183	2,125	Remapped	NW_003571040.1
NW_003315923.1	Chr8\|NW_003315923.1	2	2	Remapped	NW_003315923.1
NW_003571046.1	Chr11\|NW_003571046.1	24	180	Remapped	NW_003571046.1
NW_003315943.1	Chr15\|NW_003315943.1	17	163	Remapped	NW_003315943.1
NW_003315947.1	Chr17\|NW_003315947.1	11	21	Remapped	NW_003315947.1
NW_003315949.1	Chr17\|NW_003315949.1	192	3,183	Remapped	NW_003315949.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	16,317	160,487	Submitted	NC_000001.9
NC_000002.10	Chr2	16,426	165,009	Submitted	NC_000002.10
NC_000003.10	Chr3	12,634	125,038	Submitted	NC_000003.10
NC_000004.10	Chr4	14,535	159,596	Submitted	NC_000004.10
NC_000005.8	Chr5	12,644	132,884	Submitted	NC_000005.8
NC_000006.10	Chr6	13,164	140,389	Submitted	NC_000006.10
NC_000007.12	Chr7	12,879	125,101	Submitted	NC_000007.12
NC_000008.9	Chr8	11,021	114,944	Submitted	NC_000008.9
NC_000009.10	Chr9	11,209	103,842	Submitted	NC_000009.10
NC_000010.9	Chr10	9,617	102,003	Submitted	NC_000010.9
NC_000011.8	Chr11	10,249	102,093	Submitted	NC_000011.8
NC_000012.10	Chr12	9,482	94,734	Submitted	NC_000012.10
NC_000013.9	Chr13	7,426	80,604	Submitted	NC_000013.9
NC_000014.7	Chr14	7,225	82,715	Submitted	NC_000014.7
NC_000015.8	Chr15	5,705	58,057	Submitted	NC_000015.8
NC_000016.8	Chr16	7,176	59,196	Submitted	NC_000016.8
NC_000017.9	Chr17	7,545	71,126	Submitted	NC_000017.9
NC_000018.8	Chr18	6,175	61,700	Submitted	NC_000018.8
NC_000019.8	Chr19	6,776	55,758	Submitted	NC_000019.8
NC_000020.9	Chr20	4,700	44,883	Submitted	NC_000020.9
NC_000021.7	Chr21	3,496	28,939	Submitted	NC_000021.7
NC_000022.9	Chr22	4,512	44,843	Submitted	NC_000022.9
NC_000023.9	ChrX	6,275	34,957	Submitted	NC_000023.9
NC_000024.8	ChrY	851	1,468	Submitted	NC_000024.8

Remapping summary:

			SV remap status						SSV remap status
Sequence ID	Chr	SVs on source	Perfect	Good	Pass	Fail	Mult	SSVs on source	Perfect	Good	Pass	Fail	Mult
NC_000001.9	Chr1	16,317	16,187	44	70	16	0	160,487	160,061	62	242	122	0
NC_000002.10	Chr2	16,426	16,282	29	72	7	36	165,009	164,049	118	604	42	196
NC_000003.10	Chr3	12,634	12,589	27	18	0	0	125,038	124,935	54	49	0	0
NC_000004.10	Chr4	14,535	14,366	71	38	35	25	159,596	157,448	508	495	686	459
NC_000005.8	Chr5	12,644	12,572	17	41	14	0	132,884	132,454	20	172	238	0
NC_000006.10	Chr6	13,164	13,092	28	31	9	4	140,389	139,935	120	244	54	36
NC_000007.12	Chr7	12,879	12,548	164	54	28	85	125,101	122,152	1646	176	314	813
NC_000008.9	Chr8	11,021	10,921	44	38	18	0	114,944	114,076	355	233	280	0
NC_000009.10	Chr9	11,209	11,073	55	68	13	0	103,842	103,148	40	550	104	0
NC_000010.9	Chr10	9,617	9,517	52	14	34	0	102,003	100,606	784	48	565	0
NC_000011.8	Chr11	10,249	10,197	4	22	2	24	102,093	101,720	17	165	11	180
NC_000012.10	Chr12	9,482	9,473	4	3	2	0	94,734	94,643	11	64	16	0
NC_000013.9	Chr13	7,426	7,425	1	0	0	0	80,604	80,600	4	0	0	0
NC_000014.7	Chr14	7,225	7,179	34	9	3	0	82,715	82,460	160	78	17	0
NC_000015.8	Chr15	5,705	5,602	46	32	11	14	58,057	57,390	186	220	108	153
NC_000016.8	Chr16	7,176	7,156	9	9	2	0	59,196	59,027	145	8	16	0
NC_000017.9	Chr17	7,545	6,994	249	57	55	190	71,126	63,809	2798	453	832	3234
NC_000018.8	Chr18	6,175	6,163	4	8	0	0	61,700	61,674	19	7	0	0
NC_000019.8	Chr19	6,776	6,738	21	12	5	0	55,758	55,545	161	40	12	0
NC_000020.9	Chr20	4,700	4,679	15	5	1	0	44,883	44,844	26	5	8	0
NC_000021.7	Chr21	3,496	3,488	7	1	0	0	28,939	28,931	7	1	0	0
NC_000022.9	Chr22	4,512	4,476	8	18	10	0	44,843	44,667	22	111	43	0
NC_000023.9	ChrX	6,275	6,176	57	33	8	1	34,957	34,711	81	147	17	1
NC_000024.8	ChrY	851	813	16	1	21	0	1,468	1,416	20	2	30	0

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: HapMap_Samples
Description:: HapMap Samples
Size:: 185
Sampleset Phenotype(s):: None

Samples for sampleset 1 (displaying 100 of the 185 samples)
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
NA18570	B-Lymphocyte	NA18570	Female	HAN CHINESE	None
NA12812	B-Lymphocyte	NA12812	Male	UTAH/MORMON	None
NA18502	B-Lymphocyte	NA18502	Female	YORUBA	None
NA11993	B-Lymphocyte	NA11993	Female	UTAH/MORMON	None
NA18558	B-Lymphocyte	NA18558	Male	HAN CHINESE	None
NA18498	B-Lymphocyte	NA18498	Male	YORUBA	None
NA12813	B-Lymphocyte	NA12813	Female	UTAH/MORMON	None
NA12761	B-Lymphocyte	NA12761	Female	UTAH/MORMON	None
NA12154	B-Lymphocyte	NA12154	Male	UTAH/MORMON	None
NA12156	B-Lymphocyte	NA12156	Female	UTAH/MORMON	None
NA18486	B-Lymphocyte	NA18486	Male	YORUBA	None
NA11881	B-Lymphocyte	NA11881	Male	UTAH/MORMON	None
NA11831	B-Lymphocyte	NA11831	Male	UTAH/MORMON	None
NA18532	B-Lymphocyte	NA18532	Female	HAN CHINESE	None
NA18489	B-Lymphocyte	NA18489	Female	YORUBA	None
NA18566	B-Lymphocyte	NA18566	Female	HAN CHINESE	None
NA12751	B-Lymphocyte	NA12751	Female	UTAH/MORMON	None
NA12155	B-Lymphocyte	NA12155	Male	UTAH/MORMON	None
NA18563	B-Lymphocyte	NA18563	Male	HAN CHINESE	None
NA18537	B-Lymphocyte	NA18537	Female	HAN CHINESE	None
NA11920	B-Lymphocyte	NA11920	Female	UTAH/MORMON	None
NA12872	B-Lymphocyte	NA12872	Male	UTAH/MORMON	None
NA18511	B-Lymphocyte	NA18511	Female	YORUBA	None
NA12249	B-Lymphocyte	NA12249	Female	UTAH/MORMON	None
NA11830	B-Lymphocyte	NA11830	Female	UTAH/MORMON	None
NA12892	B-Lymphocyte	NA12892	Female	UTAH/MORMON	None
NA12716	B-Lymphocyte	NA12716	Male	UTAH/MORMON	None
NA18555	B-Lymphocyte	NA18555	Female	HAN CHINESE	None
NA12760	B-Lymphocyte	NA12760	Male	UTAH/MORMON	None
NA12763	B-Lymphocyte	NA12763	Female	UTAH/MORMON	None
NA11995	B-Lymphocyte	NA11995	Female	UTAH/MORMON	None
NA18526	B-Lymphocyte	NA18526	Female	HAN CHINESE	None
NA11931	B-Lymphocyte	NA11931	Female	UTAH/MORMON	None
NA18564	B-Lymphocyte	NA18564	Female	HAN CHINESE	None
NA11829	B-Lymphocyte	NA11829	Male	UTAH/MORMON	None
NA11894	B-Lymphocyte	NA11894	Female	UTAH/MORMON	None
NA11992	B-Lymphocyte	NA11992	Male	UTAH/MORMON	None
NA12815	B-Lymphocyte	NA12815	Female	UTAH/MORMON	None
NA12749	B-Lymphocyte	NA12749	Female	UTAH/MORMON	None
NA12043	B-Lymphocyte	NA12043	Male	UTAH/MORMON	None
NA18542	B-Lymphocyte	NA18542	Female	HAN CHINESE	None
NA12003	B-Lymphocyte	NA12003	Male	UTAH/MORMON	None
NA18501	B-Lymphocyte	NA18501	Male	YORUBA	None
NA06985	B-Lymphocyte	NA06985	Female	UTAH/MORMON	None
NA18520	B-Lymphocyte	NA18520	Female	YORUBA	None
NA18508	B-Lymphocyte	NA18508	Female	YORUBA	None
NA18505	B-Lymphocyte	NA18505	Female	YORUBA	None
NA12044	B-Lymphocyte	NA12044	Female	UTAH/MORMON	None
NA18519	B-Lymphocyte	NA18519	Male	YORUBA	None
NA12234	B-Lymphocyte	NA12234	Female	UTAH/MORMON	None
NA18561	B-Lymphocyte	NA18561	Male	HAN CHINESE	None
NA10851	B-Lymphocyte	NA10851	Male	UTAH/MORMON	None
NA12874	B-Lymphocyte	NA12874	Male	UTAH/MORMON	None
NA12004	B-Lymphocyte	NA12004	Female	UTAH/MORMON	None
NA07347	B-Lymphocyte	NA07347	Male	UTAH/MORMON	None
NA07357	B-Lymphocyte	NA07357	Male	UTAH/MORMON	None
NA12776	B-Lymphocyte	NA12776	Female	UTAH/MORMON	None
NA06994	B-Lymphocyte	NA06994	Male	UTAH/MORMON	None
NA18550	B-Lymphocyte	NA18550	Female	HAN CHINESE	None
NA18510	B-Lymphocyte	NA18510	Male	YORUBA	None
NA12489	B-Lymphocyte	NA12489	Female	UTAH/MORMON	None
NA11919	B-Lymphocyte	NA11919	Male	UTAH/MORMON	None
NA18562	B-Lymphocyte	NA18562	Male	HAN CHINESE	None
NA11840	B-Lymphocyte	NA11840	Female	UTAH/MORMON	None
NA12878	B-Lymphocyte	NA12878	Female	UTAH/MORMON	None
NA07051	B-Lymphocyte	NA07051	Male	UTAH/MORMON	None
NA18573	B-Lymphocyte	NA18573	Female	HAN CHINESE	None
NA18499	B-Lymphocyte	NA18499	Female	YORUBA	None
NA11918	B-Lymphocyte	NA11918	Female	UTAH/MORMON	None
NA11994	B-Lymphocyte	NA11994	Male	UTAH/MORMON	None
NA18571	B-Lymphocyte	NA18571	Female	HAN CHINESE	None
NA12005	B-Lymphocyte	NA12005	Male	UTAH/MORMON	None
NA06986	B-Lymphocyte	NA06986	Male	UTAH/MORMON	None
NA10847	B-Lymphocyte	NA10847	Female	UTAH/MORMON	None
NA18545	B-Lymphocyte	NA18545	Female	HAN CHINESE	None
NA12287	B-Lymphocyte	NA12287	Female	UTAH/MORMON	None
NA12006	B-Lymphocyte	NA12006	Female	UTAH/MORMON	None
NA12762	B-Lymphocyte	NA12762	Male	UTAH/MORMON	None
NA18522	B-Lymphocyte	NA18522	Male	YORUBA	None
NA12144	B-Lymphocyte	NA12144	Male	UTAH/MORMON	None
NA12891	B-Lymphocyte	NA12891	Male	UTAH/MORMON	None
NA12814	B-Lymphocyte	NA12814	Male	UTAH/MORMON	None
NA12045	B-Lymphocyte	NA12045	Male	UTAH/MORMON	None
NA18523	B-Lymphocyte	NA18523	Female	YORUBA	None
NA18516	B-Lymphocyte	NA18516	Male	YORUBA	None
NA18547	B-Lymphocyte	NA18547	Female	HAN CHINESE	None
NA07346	B-Lymphocyte	NA07346	Female	UTAH/MORMON	None
NA18572	B-Lymphocyte	NA18572	Male	HAN CHINESE	None
NA12717	B-Lymphocyte	NA12717	Female	UTAH/MORMON	None
NA12873	B-Lymphocyte	NA12873	Female	UTAH/MORMON	None
NA07037	B-Lymphocyte	NA07037	Female	UTAH/MORMON	None
NA18507	B-Lymphocyte	NA18507	Male	YORUBA	None
NA18552	B-Lymphocyte	NA18552	Female	HAN CHINESE	None
NA12750	B-Lymphocyte	NA12750	Male	UTAH/MORMON	None
NA07000	B-Lymphocyte	NA07000	Female	UTAH/MORMON	None
NA18517	B-Lymphocyte	NA18517	Female	YORUBA	None
NA11832	B-Lymphocyte	NA11832	Female	UTAH/MORMON	None
NA12828	B-Lymphocyte	NA12828	Female	UTAH/MORMON	None
NA18504	B-Lymphocyte	NA18504	Male	YORUBA	None
NA12414	B-Lymphocyte	NA12414	Female	UTAH/MORMON	None

Sampleset ID:: 2
Name:: HapMap_Trios
Description:: Two HapMap trios, one CEU, one YRI
Size:: 6
Sampleset Phenotype(s):: None

Samples for sampleset 2
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Phenotype
NA19240	B-Lymphocyte	NA19240	Female	YORUBA	None
NA12892	B-Lymphocyte	NA12892	Female	UTAH/MORMON	None
NA19239	B-Lymphocyte	NA19239	Male	YORUBA	None
NA19238	B-Lymphocyte	NA19238	Female	YORUBA	None
NA12878	B-Lymphocyte	NA12878	Female	UTAH/MORMON	None
NA12891	B-Lymphocyte	NA12891	Male	UTAH/MORMON	None

Experimental Details

Methods
Number of Discovery Experiments: 17

Method ID:1
Method type:Sequencing
Description:
Fragment libraries or paired-end libraries were constructed for each of the assigned samplesaccording to manuals "Genome Sequencer FLX and Genome Sequencer FLX Titanium Methods Manual" and "GS FLX Paired End DNA Library Preparation Method Manual". Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by Ribo/PicoGreen assays. Libraries were then sequenced on the 454 FLX/Titanium platform using standard vendor emPCR, enrichment and sequencing methods.
Platforms:454 GS FLX

Method ID:2
Method type:Sequencing
Description:
A combination of fragment and mate-paired libraries were utilized for sequencing on the SOLiD System V2.0 platform. SOLiD fragment libraries were constructed with 30ug of input DNA and an average insert size of 160 bp following standard vendor protocols (SOLiD System 2.0 Fragment Library Preparation) and sequenced as unidirectional reads of 25bp. DNA input ranged from 30 to 50ug for mate-paired libraries to insure library complexity (SOLiD System 2.0 Mate-Paired Library Preparation). Insert sizes of 1.5 and 2.5 kb were utilized for sequencing in the 2 X 25 bp format providing both sequence coverage and structural information. Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by PicoGreen assays. Each fragment and mate-paired library was then sequenced on the SOLiD V2.0 platform following standard vendor methods for emPCR, enrichment, 3’ end modification and ligation sequencing (Applied Biosystems SOLiD System 2.0 User Guide).
Platforms:ABI SOLiD System

Method ID:3
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:4
Method type:Sequencing
Description:
Fragment libraries or paired-end libraries were constructed for each of the assigned samplesaccording to manuals "Genome Sequencer FLX and Genome Sequencer FLX Titanium Methods Manual" and "GS FLX Paired End DNA Library Preparation Method Manual". Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by Ribo/PicoGreen assays. Libraries were then sequenced on the 454 FLX/Titanium platform using standard vendor emPCR, enrichment and sequencing methods.
Platforms:454 GS FLX

Method ID:5
Method type:Sequencing
Description:
A combination of fragment and mate-paired libraries were utilized for sequencing on the SOLiD System V2.0 platform. SOLiD fragment libraries were constructed with 30ug of input DNA and an average insert size of 160 bp following standard vendor protocols (SOLiD System 2.0 Fragment Library Preparation) and sequenced as unidirectional reads of 25bp. DNA input ranged from 30 to 50ug for mate-paired libraries to insure library complexity (SOLiD System 2.0 Mate-Paired Library Preparation). Insert sizes of 1.5 and 2.5 kb were utilized for sequencing in the 2 X 25 bp format providing both sequence coverage and structural information. Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by PicoGreen assays. Each fragment and mate-paired library was then sequenced on the SOLiD V2.0 platform following standard vendor methods for emPCR, enrichment, 3’ end modification and ligation sequencing (Applied Biosystems SOLiD System 2.0 User Guide).
Platforms:ABI SOLiD System

Method ID:6
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:7
Method type:Sequencing
Description:
Fragment libraries or paired-end libraries were constructed for each of the assigned samples according to manuals "Genome Sequencer FLX and Genome Sequencer FLX Titanium Methods Manual" and "GS FLX Paired End DNA Library Preparation Method Manual". Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by Ribo/PicoGreen assays. Libraries were then sequenced on the 454 FLX/Titanium platform using standard vendor emPCR, enrichment and sequencing methods.
Platforms:454 GS FLX

Method ID:8
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:9
Method type:Sequencing
Description:
Fragment libraries or paired-end libraries were constructed for each of the assigned samples according to manuals "Genome Sequencer FLX and Genome Sequencer FLX Titanium Methods Manual" and "GS FLX Paired End DNA Library Preparation Method Manual". Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by Ribo/PicoGreen assays. Libraries were then sequenced on the 454 FLX/Titanium platform using standard vendor emPCR, enrichment and sequencing methods.
Platforms:454 GS FLX

Method ID:10
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:11
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:12
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:13
Method type:Sequencing
Description:
Fragment libraries or paired-end libraries were constructed for each of the assigned samples according to manuals "Genome Sequencer FLX and Genome Sequencer FLX Titanium Methods Manual" and "GS FLX Paired End DNA Library Preparation Method Manual". Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by Ribo/PicoGreen assays. Libraries were then sequenced on the 454 FLX/Titanium platform using standard vendor emPCR, enrichment and sequencing methods.
Platforms:454 GS FLX

Method ID:14
Method type:Sequencing
Description:
A combination of fragment and mate-paired libraries were utilized for sequencing on the SOLiD System V2.0 platform. SOLiD fragment libraries were constructed with 30ug of input DNA and an average insert size of 160 bp following standard vendor protocols (SOLiD System 2.0 Fragment Library Preparation) and sequenced as unidirectional reads of 25bp. DNA input ranged from 30 to 50ug for mate-paired libraries to insure library complexity (SOLiD System 2.0 Mate-Paired Library Preparation). Insert sizes of 1.5 and 2.5 kb were utilized for sequencing in the 2 X 25 bp format providing both sequence coverage and structural information. Each fragment and paired-end library was run on the Agilent Bioanalyzer 2100 to determine the library size, and the concentration determined by PicoGreen assays. Each fragment and mate-paired library was then sequenced on the SOLiD V2.0 platform following standard vendor methods for emPCR, enrichment, 3’ end modification and ligation sequencing (Applied Biosystems SOLiD System 2.0 User Guide).
Platforms:ABI SOLiD System

Method ID:15
Method type:Sequencing
Description:
Illumina fragment libraries were prepared using 1 ug of high molecular weight genomic DNA according to manufacturer’s instructions, and the resulting libraries were sequenced on Illumina GA sequencers.
Platforms:Illumina Genome Analyzer II

Method ID:16
Method type:Sequencing
Description:
Combined Illumina and 454 Sequencing
Platforms:Illumina Genome Analyzer II and 454 GS FLX

Method ID:17
Method type:Sequencing
Description:
Combined Illumina and SOLiD Sequencing
Platforms:Illumina Genome Analyzer II and ABI SOLiD System

Analyses

Analysis ID: 1
Method ID(s): 1
Sampleset ID(s): 1
Description:
Sequencing platform: 454. Mapping algorithm: MOSAIK. Type of computational approach: split read alignment.
Detection method:MOSAIK
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 2
Method ID(s): 3
Sampleset ID(s): 1
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MAQ. Type of computational approach: read depth analysis.
Detection method:MAQ
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 3
Method ID(s): 3
Sampleset ID(s): 1
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MAQ. Type of computational approach: read pair mapping.
Detection method:MAQ
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 4
Method ID(s): 3
Sampleset ID(s): 1
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: A combination of MAQ and PINDEL. Type of computational approach: split read alignment.
Detection method:MAQ_And_PINDEL
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 5
Method ID(s): 3
Sampleset ID(s): 1
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MOSAIK. Type of computational approach: read pair mapping.
Detection method:MOSAIK
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 6
Method ID(s): 2
Sampleset ID(s): 1
Description:
Sequencing platform: SOLiD. Mapping algorithm: Corona. Type of computational approach: read pair mapping.
Detection method:CORONA
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 7
Method ID(s): 3
Sampleset ID(s): 1
Merged Analysis ID(s) 2
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read depth analysis.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 8
Method ID(s): 2, 3
Sampleset ID(s): 1
Merged Analysis ID(s) 3, 5, 6
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair mapping.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 9
Method ID(s): 1, 3
Sampleset ID(s): 1
Merged Analysis ID(s) 1, 4
Description:
Merging of all supporting structural variant calls generated by type of computational approach: split read alignments.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 10
Method ID(s): 1, 2, 3
Sampleset ID(s): 1
Merged Analysis ID(s) 7, 8, 9
Description:
Discovery structural variant merging of all analysis structural variants generated by each of the types of computational approaches (RP, RD, and SR).
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 11
Method ID(s): 4
Sampleset ID(s): 2
Description:
Sequencing platform 454. Mapping algorithm: BLAT. Type of computational approach: split read alignment.
Detection method:BLAT
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 12
Method ID(s): 4
Sampleset ID(s): 2
Description:
Sequencing platform: 454. Mapping algorithm: MOSAIK. Type of computational approach: split read alignment.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 13
Method ID(s): 4
Sampleset ID(s): 2
Description:
Sequencing platform: 454. Mapping algorithm: paired-end mapping. Type of computational approach: read pair mapping.
Detection method:PEM
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 14
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MAQ. Type of computational approach: read depth analysis.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 15
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MAQ. Type of computational approach: read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 16
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: A combination of MAQ and PINDEL. Type of computational approach: split read alignment.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 17
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MOSAIK. Type of computational approach: read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 18
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: mrFAST. Type of computational approach: read depth analysis.
Detection method:MRFAST
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 19
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: mrFAST. Type of computational approach: read pair mapping.
Detection method:MRFAST
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 20
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: Combination of mrFAST and ABySS. Type of computational approach: assembly.
Detection method:MRFAST,ABYSS
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 21
Method ID(s): 6
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: SOAPdenovo. Type of computational approach: assembly
Detection method:SOAP
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 22
Method ID(s): 5
Sampleset ID(s): 2
Description:
Sequencing platform: SOLiD. Mapping algorithm: MAPREADS. Type of computational approach: read pair mapping.
Detection method:MAPREADS
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 23
Method ID(s): 4, 6
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX. Type of compuational approach: assembly.
Detection method:CORTEX
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 24
Method ID(s): 6
Sampleset ID(s): 2
Merged Analysis ID(s) 14, 18
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read depth analysis.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 25
Method ID(s): 4, 5, 6
Sampleset ID(s): 2
Merged Analysis ID(s) 13, 15, 17, 19, 22
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair mapping.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 26
Method ID(s): 4, 6
Sampleset ID(s): 2
Merged Analysis ID(s) 11, 12, 16
Description:
Merging of all supporting structural variant calls generated by type of computational approach: split read alignments.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 27
Method ID(s): 6
Sampleset ID(s): 2
Merged Analysis ID(s) 20, 21, 23
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: assembly.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 28
Method ID(s): 4, 5, 6
Sampleset ID(s): 2
Merged Analysis ID(s) 24, 25, 26, 27
Description:
Discovery structural variant merging of all analysis structtural variants generated by each of the types of computational approaches (AS, RP, RD, and SR).
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 29
Method ID(s): 8
Sampleset ID(s): 1
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MOSAIK. Type of computational approach: read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 30
Method ID(s): 7
Sampleset ID(s): 1
Description:
Sequencing platform: 454. Mapping algorithm: MOSAIK. Type of computational approach: split read alignment.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 31
Method ID(s): 7, 8
Sampleset ID(s): 1
Description:
Sequencing platform: 454 and Illumina. Mapping algorithm: MOSAIK. Type of computational approach: read pair mapping and split read alignment.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 32
Method ID(s): 7, 8
Sampleset ID(s): 1
Merged Analysis ID(s) 29, 30, 31
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair mapping and split read alignment.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 33
Method ID(s): 10
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: MOSAIK. Type of computational approach: read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 34
Method ID(s): 9
Sampleset ID(s): 2
Description:
Sequencing platform: 454. Mapping algorithm: MOSAIK. Type of computational approach: split read alignment.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 35
Method ID(s): 9, 10
Sampleset ID(s): 2
Description:
Sequencing platform: 454 and Illumina. Mapping algorithm: MOSAIK. Type of computational approach: read pair mapping and split read alignment.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 36
Method ID(s): 9, 10
Sampleset ID(s): 2
Merged Analysis ID(s) 33, 34, 35
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair mapping and split read alignment.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 37
Method ID(s): 11
Sampleset ID(s): 1
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: SPANNER. Type of computational approach: read pair mapping.
Detection method:SPANNER
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 38
Method ID(s): 11
Sampleset ID(s): 1
Merged Analysis ID(s) 37
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair mapping.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 39
Method ID(s): 12
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: SPANNER. Type of computational approach: read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 40
Method ID(s): 12
Sampleset ID(s): 2
Merged Analysis ID(s) 39
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair mapping.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 41
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX. Type of compuational approach:read pair mapping.
Detection method:Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 42
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX and SOAP. Type of compuational approach:read pair mapping.
Detection method:SOAP_And_Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 43
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX on reference. Type of compuational approach:read pair mapping.
Detection method:Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 44
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX on reference and CORTEX de novo. Type of compuational approach:read pair mapping.
Detection method:Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 45
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX on reference, CORTEX de novo, and SOAP. Type of compuational approach:read pair mapping.
Detection method:SOAP_And_Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 46
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX on reference and SOAP. Type of compuational approach:read pair mapping.
Detection method:SOAP_And_Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 47
Method ID(s): 14
Sampleset ID(s): 2
Description:
Sequencing platform: SOLiD. Mapping algorithm: MAPREADS. Type of computational approach: read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 48
Method ID(s): 15
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina: Mapping algorithm: NovelSeq. Type of compuational approach:read pair mapping.
Detection method:NovelSeq
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 49
Method ID(s): 16
Sampleset ID(s): 2
Description:
Sequencing platform: Combination of Whole Genome Illumina and 454. Mapping algorithm: CORTEX on reference and NovelSeq. Type of compuational approach:read pair mapping.
Detection method:NovelSeq_And_Cortex
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 50
Method ID(s): 15
Sampleset ID(s): 2
Description:
Sequencing platform: Whole Genome Illumina. Mapping algorithm: SOAP. Type of compuational approach:read pair mapping.
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 51
Method ID(s): 17
Sampleset ID(s): 2
Description:
Combination of Whole Genome Illumina and SOLiD. Mapping algorithm: SOAP and MAPREADS. Type of compuational approach:read pair mapping.
Detection method:SOAP_And_MAPREADS
Sample level: Yes
Reference organism: Human
Reference assembly:NCBI36 (hg18)

Analysis ID: 52
Method ID(s): 14, 15, 16, 17
Sampleset ID(s): 2
Merged Analysis ID(s) 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51
Description:
Analysis structural variant merging of all supporting structural variant calls generated by type of computational approach: read pair analysis.
Sample level: No
Reference organism: Human
Reference assembly:NCBI36 (hg18)

dbVar

Database of genomic structural variation

estd59

Links

Detailed Information: Download 218039 Variant Regions, Download 2150366 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh37 (hg19)
Remapped: GRCh37.p5 GRCh37.p5 contains hg19 and PATCH updates released by the GRC (Click to go to GRC website).
Submitted: NCBI36 (hg18)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 2

Experimental Details

Methods
Number of Discovery Experiments: 17

Analyses

Validations

There are no validation data for this study.

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information

dbVar

Database of genomic structural variation

estd59

Links

Detailed Information: Download 218039 Variant Regions, Download 2150366 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh37 (hg19)GRCh37.p5NCBI36 (hg18)

Remapping summary: NCBI36->GRCh37.p5

Samplesets

Number of Samplesets: 2

Experimental Details

MethodsNumber of Discovery Experiments: 17

Analyses

Validations

There are no validation data for this study.

Simple NCBI Directory

Getting Started

Resources

Popular

Featured

NCBI Information

Variant Summary for:

Remapping summary:

Methods
Number of Discovery Experiments: 17