estd49 - Gusev et al 2008 - dbVar Study

estd49 (Gusev et al. 2008)

Organism:: Human
Study Type:: Control Set
Submitter:: Itsik Pe'er
Description:: We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. We use GERMLINE to comprehensively survey hidden relatedness both in the HapMap as well as in a densely typed island population of 3000 individuals. We bolster these results by demonstrating novel applications of precise analysis of hidden relatedness for identification and resolution of phasing errors and exposing polymorphic deletions that are otherwise challenging to detect. See Variant Summary counts for estd49 in dbVar Variant Summary.
Publication(s):: Gusev et al. 2008

Links

Source: NCBI

Detailed Information: Download 225 Variant Regions, Download 225 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: NCBI36 (hg18)

Variant Summary for:

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.11	Chr1	12	12	Remapped	NC_000001.11
NC_000002.12	Chr2	20	20	Remapped	NC_000002.12
NC_000003.12	Chr3	15	15	Remapped	NC_000003.12
NC_000004.12	Chr4	11	11	Remapped	NC_000004.12
NC_000005.10	Chr5	12	12	Remapped	NC_000005.10
NC_000006.12	Chr6	11	11	Remapped	NC_000006.12
NC_000007.14	Chr7	9	9	Remapped	NC_000007.14
NC_000008.11	Chr8	10	10	Remapped	NC_000008.11
NC_000009.12	Chr9	8	8	Remapped	NC_000009.12
NC_000010.11	Chr10	16	16	Remapped	NC_000010.11
NC_000011.10	Chr11	25	25	Remapped	NC_000011.10
NC_000012.12	Chr12	8	8	Remapped	NC_000012.12
NC_000013.11	Chr13	8	8	Remapped	NC_000013.11
NC_000014.9	Chr14	7	7	Remapped	NC_000014.9
NC_000015.10	Chr15	13	13	Remapped	NC_000015.10
NC_000016.10	Chr16	8	8	Remapped	NC_000016.10
NC_000017.11	Chr17	5	5	Remapped	NC_000017.11
NC_000018.10	Chr18	9	9	Remapped	NC_000018.10
NC_000019.10	Chr19	6	6	Remapped	NC_000019.10
NC_000020.11	Chr20	6	6	Remapped	NC_000020.11
NC_000021.9	Chr21	1	1	Remapped	NC_000021.9
NC_000022.11	Chr22	5	5	Remapped	NC_000022.11
NT_167246.2	Chr6\|NT_167246.2	2	2	Remapped	NT_167246.2
NT_167249.2	Chr6\|NT_167249.2	2	2	Remapped	NT_167249.2
NT_187562.1	Chr7\|NT_187562.1	1	1	Remapped	NT_187562.1
NW_018654717.1	Chr8\|NW_018654717.1	2	2	Remapped	NW_018654717.1
NT_187580.1	Chr10\|NT_187580.1	2	2	Remapped	NT_187580.1
NW_019805495.1	Chr11\|NW_019805495.1	2	2	Remapped	NW_019805495.1
NT_187601.1	Chr14\|NT_187601.1	1	1	Remapped	NT_187601.1
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_187607.1	Chr16\|NT_187607.1	1	1	Remapped	NT_187607.1
NW_003315956.1	Chr18\|NW_003315956.1	1	1	Remapped	NW_003315956.1
NT_187693.1	Chr19\|NT_187693.1	1	1	Remapped	NT_187693.1
NW_003571061.2	Chr19\|NW_003571061.2	1	1	Remapped	NW_003571061.2
NW_003571057.2	Chr19\|NW_003571057.2	1	1	Remapped	NW_003571057.2
NW_003571058.2	Chr19\|NW_003571058.2	1	1	Remapped	NW_003571058.2
NW_003571059.2	Chr19\|NW_003571059.2	1	1	Remapped	NW_003571059.2
NW_003571060.1	Chr19\|NW_003571060.1	1	1	Remapped	NW_003571060.1
NW_003571056.2	Chr19\|NW_003571056.2	1	1	Remapped	NW_003571056.2
NW_003571055.2	Chr19\|NW_003571055.2	1	1	Remapped	NW_003571055.2
NW_003571054.1	Chr19\|NW_003571054.1	1	1	Remapped	NW_003571054.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	12	12	Remapped	NC_000001.10
NC_000002.11	Chr2	20	20	Remapped	NC_000002.11
NC_000003.11	Chr3	15	15	Remapped	NC_000003.11
NC_000004.11	Chr4	11	11	Remapped	NC_000004.11
NC_000005.9	Chr5	12	12	Remapped	NC_000005.9
NC_000006.11	Chr6	11	11	Remapped	NC_000006.11
NC_000007.13	Chr7	9	9	Remapped	NC_000007.13
NC_000008.10	Chr8	10	10	Remapped	NC_000008.10
NC_000009.11	Chr9	8	8	Remapped	NC_000009.11
NC_000010.10	Chr10	16	16	Remapped	NC_000010.10
NC_000011.9	Chr11	25	25	Remapped	NC_000011.9
NC_000012.11	Chr12	8	8	Remapped	NC_000012.11
NC_000013.10	Chr13	8	8	Remapped	NC_000013.10
NC_000014.8	Chr14	7	7	Remapped	NC_000014.8
NC_000015.9	Chr15	13	13	Remapped	NC_000015.9
NC_000016.9	Chr16	8	8	Remapped	NC_000016.9
NC_000017.10	Chr17	5	5	Remapped	NC_000017.10
NC_000018.9	Chr18	9	9	Remapped	NC_000018.9
NC_000019.9	Chr19	5	5	Remapped	NC_000019.9
NC_000020.10	Chr20	6	6	Remapped	NC_000020.10
NC_000021.8	Chr21	1	1	Remapped	NC_000021.8
NC_000022.10	Chr22	5	5	Remapped	NC_000022.10
NT_167246.1	Chr6\|NT_167246.1	2	2	Remapped	NT_167246.1
NT_167249.1	Chr6\|NT_167249.1	2	2	Remapped	NT_167249.1
NW_003571040.1	Chr7\|NW_003571040.1	1	1	Remapped	NW_003571040.1
NW_003315956.1	Chr18\|NW_003315956.1	1	1	Remapped	NW_003315956.1
NW_003571061.1	Chr19\|NW_003571061.1	1	1	Remapped	NW_003571061.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.9	Chr1	12	12	Submitted	NC_000001.9
NC_000002.10	Chr2	20	20	Submitted	NC_000002.10
NC_000003.10	Chr3	15	15	Submitted	NC_000003.10
NC_000004.10	Chr4	11	11	Submitted	NC_000004.10
NC_000005.8	Chr5	12	12	Submitted	NC_000005.8
NC_000006.10	Chr6	11	11	Submitted	NC_000006.10
NC_000007.12	Chr7	9	9	Submitted	NC_000007.12
NC_000008.9	Chr8	10	10	Submitted	NC_000008.9
NC_000009.10	Chr9	8	8	Submitted	NC_000009.10
NC_000010.9	Chr10	16	16	Submitted	NC_000010.9
NC_000011.8	Chr11	25	25	Submitted	NC_000011.8
NC_000012.10	Chr12	8	8	Submitted	NC_000012.10
NC_000013.9	Chr13	8	8	Submitted	NC_000013.9
NC_000014.7	Chr14	7	7	Submitted	NC_000014.7
NC_000015.8	Chr15	13	13	Submitted	NC_000015.8
NC_000016.8	Chr16	8	8	Submitted	NC_000016.8
NC_000017.9	Chr17	5	5	Submitted	NC_000017.9
NC_000018.8	Chr18	9	9	Submitted	NC_000018.8
NC_000019.8	Chr19	6	6	Submitted	NC_000019.8
NC_000020.9	Chr20	6	6	Submitted	NC_000020.9
NC_000021.7	Chr21	1	1	Submitted	NC_000021.7
NC_000022.9	Chr22	5	5	Submitted	NC_000022.9

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_000001.9	Chr1	12	11	0	1	0	0	12	11	0	1	0	0
NC_000002.10	Chr2	20	19	1	0	0	0	20	19	1	0	0	0
NC_000003.10	Chr3	15	14	1	0	0	0	15	14	1	0	0	0
NC_000004.10	Chr4	11	11	0	0	0	0	11	11	0	0	0	0
NC_000005.8	Chr5	12	12	0	0	0	0	12	12	0	0	0	0
NC_000006.10	Chr6	11	8	0	0	0	3	11	8	0	0	0	3
NC_000007.12	Chr7	9	8	0	0	0	1	9	8	0	0	0	1
NC_000008.9	Chr8	10	10	0	0	0	0	10	10	0	0	0	0
NC_000009.10	Chr9	8	8	0	0	0	0	8	8	0	0	0	0
NC_000010.9	Chr10	16	16	0	0	0	0	16	16	0	0	0	0
NC_000011.8	Chr11	25	25	0	0	0	0	25	25	0	0	0	0
NC_000012.10	Chr12	8	7	0	1	0	0	8	7	0	1	0	0
NC_000013.9	Chr13	8	8	0	0	0	0	8	8	0	0	0	0
NC_000014.7	Chr14	7	7	0	0	0	0	7	7	0	0	0	0
NC_000015.8	Chr15	13	13	0	0	0	0	13	13	0	0	0	0
NC_000016.8	Chr16	8	8	0	0	0	0	8	8	0	0	0	0
NC_000017.9	Chr17	5	5	0	0	0	0	5	5	0	0	0	0
NC_000018.8	Chr18	9	8	0	0	0	1	9	8	0	0	0	1
NC_000019.8	Chr19	6	5	0	1	0	0	6	5	0	1	0	0
NC_000020.9	Chr20	6	6	0	0	0	0	6	6	0	0	0	0
NC_000021.7	Chr21	1	1	0	0	0	0	1	1	0	0	0	0
NC_000022.9	Chr22	5	5	0	0	0	0	5	5	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_000001.9	Chr1	12	11	0	1	0	0	12	11	0	1	0	0
NC_000002.10	Chr2	20	20	0	0	0	0	20	20	0	0	0	0
NC_000003.10	Chr3	15	14	1	0	0	0	15	14	1	0	0	0
NC_000004.10	Chr4	11	11	0	0	0	0	11	11	0	0	0	0
NC_000005.8	Chr5	12	12	0	0	0	0	12	12	0	0	0	0
NC_000006.10	Chr6	11	8	0	0	0	3	11	8	0	0	0	3
NC_000007.12	Chr7	9	8	0	0	0	1	9	8	0	0	0	1
NC_000008.9	Chr8	10	8	0	0	0	2	10	8	0	0	0	2
NC_000009.10	Chr9	8	8	0	0	0	0	8	8	0	0	0	0
NC_000010.9	Chr10	16	13	1	0	0	2	16	13	1	0	0	2
NC_000011.8	Chr11	25	23	0	0	0	2	25	23	0	0	0	2
NC_000012.10	Chr12	8	7	0	1	0	0	8	7	0	1	0	0
NC_000013.9	Chr13	8	8	0	0	0	0	8	8	0	0	0	0
NC_000014.7	Chr14	7	6	0	0	0	1	7	6	0	0	0	1
NC_000015.8	Chr15	13	11	1	0	0	1	13	11	1	0	0	1
NC_000016.8	Chr16	8	7	0	0	0	1	8	7	0	0	0	1
NC_000017.9	Chr17	5	5	0	0	0	0	5	5	0	0	0	0
NC_000018.8	Chr18	9	8	0	0	0	1	9	8	0	0	0	1
NC_000019.8	Chr19	6	5	0	0	0	1	6	5	0	0	0	1
NC_000020.9	Chr20	6	6	0	0	0	0	6	6	0	0	0	0
NC_000021.7	Chr21	1	1	0	0	0	0	1	1	0	0	0	0
NC_000022.9	Chr22	5	2	3	0	0	0	5	2	3	0	0	0

Samplesets

Number of Samplesets: 2

Sampleset ID:: 1
Name:: Kosrae Samples
Description:: 2906 Islandes from Kosrae
Size:: 2,906 (sample data not available)
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Sampleset ID:: 2
Name:: HapMap270
Description:: HapMap 270 30 trio parent pairs from the CEU and YRI populations, and 45 unrelated individuals from the JPT and CHB populations.
Size:: 270
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported

Samples for sampleset 2 (displaying 100 of the 270 samples)
Sample ID	Cell Type	Subject ID	Sex	Ethnicity	Subject Age	Subject Phenotype
NA12812	DNA	NA12812	Male	Caucasian		Not reported
NA07348	DNA	NA07348	Female	Caucasian	45 Years	Not reported
NA18502	DNA	NA18502	Female			Not reported
NA11993	DNA	NA11993	Female	Caucasian	80 Years	Not reported
NA12813	DNA	NA12813	Female	Caucasian		Not reported
NA12761	DNA	NA12761	Female	Caucasian		Not reported
NA12154	DNA	NA12154	Male	Caucasian	92 Years	Not reported
NA12057	DNA	NA12057	Female	Caucasian	75 Years	Not reported
NA10857	DNA	NA10857	Male	Caucasian	47 Years	Not reported
NA11839	DNA	NA11839	Male	Caucasian	67 Years	Not reported
NA12156	DNA	NA12156	Female	Caucasian	81 Years	Not reported
NA11881	DNA	NA11881	Male	Caucasian	62 Years	Not reported
NA11831	DNA	NA11831	Male	Caucasian	73 Years	Not reported
NA06993	DNA	NA06993	Male	Caucasian	74 Years	Not reported
NA10830	DNA	NA10830	Male	Caucasian	66 Years	Not reported
NA10856	DNA	NA10856	Male	Caucasian	46 Years	Not reported
NA07048	DNA	NA07048	Male	Caucasian	43 Years	Not reported
NA12056	DNA	NA12056	Male	Caucasian	79 Years	Not reported
NA12236	DNA	NA12236	Female	Caucasian	86 Years	Not reported
NA12751	DNA	NA12751	Female	Caucasian		Not reported
NA12155	DNA	NA12155	Male	Caucasian	86 Years	Not reported
NA12146	DNA	NA12146	Male	Caucasian	61 Years	Not reported
NA12872	DNA	NA12872	Male	Caucasian		Not reported
NA12865	DNA	NA12865	Female	Caucasian		Not reported
NA12249	DNA	NA12249	Female	Caucasian	77 Years	Not reported
NA11830	DNA	NA11830	Female	Caucasian	63 Years	Not reported
NA12892	DNA	NA12892	Female	Caucasian		Not reported
NA12716	DNA	NA12716	Male	Caucasian		Not reported
NA10859	DNA	NA10859	Female	Caucasian	41 Years	Not reported
NA10838	DNA	NA10838	Male	Caucasian	60 Years	Not reported
NA06991	DNA	NA06991	Female	Caucasian	42 Years	Not reported
NA12760	DNA	NA12760	Male	Caucasian		Not reported
NA12763	DNA	NA12763	Female	Caucasian		Not reported
NA11995	DNA	NA11995	Female	Caucasian	84 Years	Not reported
NA10831	DNA	NA10831	Female	Caucasian	59 Years	Not reported
NA11829	DNA	NA11829	Male	Caucasian	72 Years	Not reported
NA11992	DNA	NA11992	Male	Caucasian	86 Years	Not reported
NA12815	DNA	NA12815	Female	Caucasian		Not reported
NA12043	DNA	NA12043	Male	Caucasian	74 Years	Not reported
NA12003	DNA	NA12003	Male	Caucasian	97 Years	Not reported
NA18501	DNA	NA18501	Male			Not reported
NA07022	DNA	NA07022	Male	Caucasian	63 Years	Not reported
NA10860	DNA	NA10860	Male	Caucasian	50 Years	Not reported
NA06985	DNA	NA06985	Female	Caucasian	69 Years	Not reported
NA18508	DNA	NA18508	Female			Not reported
NA18505	DNA	NA18505	Female			Not reported
NA12044	DNA	NA12044	Female	Caucasian	70 Years	Not reported
NA18500	DNA	NA18500	Male			Not reported
NA12234	DNA	NA12234	Female	Caucasian	74 Years	Not reported
NA12264	DNA	NA12264	Male	Caucasian	72 Years	Not reported
NA12874	DNA	NA12874	Male	Caucasian		Not reported
NA10851	DNA	NA10851	Male	Caucasian	52 Years	Not reported
NA12145	DNA	NA12145	Female	Caucasian	70 Years	Not reported
NA12752	DNA	NA12752	Male	Caucasian		Not reported
NA07029	DNA	NA07029	Male	Caucasian	47 Years	Not reported
NA12004	DNA	NA12004	Female	Caucasian	92 Years	Not reported
NA07357	DNA	NA07357	Male	Caucasian	69 Years	Not reported
NA06994	DNA	NA06994	Male	Caucasian	68 Years	Not reported
NA12878	DNA	NA12878	Female	Caucasian		Not reported
NA11840	DNA	NA11840	Female	Caucasian	67 Years	Not reported
NA12864	DNA	NA12864	Male	Caucasian		Not reported
NA18506	DNA	NA18506	Male			Not reported
NA07034	DNA	NA07034	Male	Caucasian	71 Years	Not reported
NA12753	DNA	NA12753	Female	Caucasian		Not reported
NA11994	DNA	NA11994	Male	Caucasian	80 Years	Not reported
NA12248	DNA	NA12248	Male	Caucasian	89 Years	Not reported
NA12005	DNA	NA12005	Male	Caucasian	77 Years	Not reported
NA07345	DNA	NA07345	Female	Caucasian	69 Years	Not reported
NA10847	DNA	NA10847	Female	Caucasian	38 Years	Not reported
NA10839	DNA	NA10839	Female	Caucasian	55 Years	Not reported
NA12762	DNA	NA12762	Male	Caucasian		Not reported
NA12006	DNA	NA12006	Female	Caucasian	75 Years	Not reported
NA12144	DNA	NA12144	Male	Caucasian	71 Years	Not reported
NA12891	DNA	NA12891	Male	Caucasian		Not reported
NA12814	DNA	NA12814	Male	Caucasian		Not reported
NA12801	DNA	NA12801	Male	Caucasian		Not reported
NA07055	DNA	NA07055	Female	Caucasian	70 Years	Not reported
NA10863	DNA	NA10863	Female	Caucasian	43 Years	Not reported
NA10855	DNA	NA10855	Female	Caucasian	37 Years	Not reported
NA10854	DNA	NA10854	Female	Caucasian	42 Years	Not reported
NA11882	DNA	NA11882	Female	Caucasian	61 Years	Not reported
NA07019	DNA	NA07019	Female	Caucasian	45 Years	Not reported
NA12717	DNA	NA12717	Female	Caucasian		Not reported
NA12707	DNA	NA12707	Male	Caucasian		Not reported
NA10835	DNA	NA10835	Male	Caucasian	39 Years	Not reported
NA12873	DNA	NA12873	Female	Caucasian		Not reported
NA18503	DNA	NA18503	Male			Not reported
NA18507	DNA	NA18507	Male			Not reported
NA07056	DNA	NA07056	Female	Caucasian	65 Years	Not reported
NA12875	DNA	NA12875	Female	Caucasian		Not reported
NA10861	DNA	NA10861	Female	Caucasian	49 Years	Not reported
NA10846	DNA	NA10846	Male	Caucasian	43 Years	Not reported
NA12750	DNA	NA12750	Male	Caucasian		Not reported
NA12802	DNA	NA12802	Female	Caucasian		Not reported
NA07000	DNA	NA07000	Female	Caucasian	66 Years	Not reported
NA12740	DNA	NA12740	Female	Caucasian		Not reported
NA11832	DNA	NA11832	Female	Caucasian	58 Years	Not reported
NA12239	DNA	NA12239	Female	Caucasian	61 Years	Not reported
NA18504	DNA	NA18504	Male			Not reported
NA18515	DNA	NA18515	Male			Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	SNP array	SNP genotyping analysis	[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array, [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array	29
2	Discovery	SNP array	SNP genotyping analysis	Not reported	196

dbVar

Database of genomic structural variation

estd49 (Gusev et al. 2008)

Links

Detailed Information: Download 225 Variant Regions, Download 225 Variant Calls, Download Both, FTP

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (hg38)
Remapped: GRCh37.p13 (hg19)
Submitted: NCBI36 (hg18)

Variant Summary for:

Remapping summary:

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

dbVar

Database of genomic structural variation

estd49 (Gusev et al. 2008)

Links

Detailed Information: Download 225 Variant Regions, Download 225 Variant Calls, Download Both, FTP

Variant Summary

Variant Summary for: GRCh38.p12 (hg38)GRCh37.p13 (hg19)NCBI36 (hg18)

Remapping summary: NCBI36->GRCh37.p13NCBI36->GRCh38.p12

Samplesets

Number of Samplesets: 2

Experimental Details

Validations

No validation data were submitted for this study.

Variant Summary for:

Remapping summary: