nstd39 - Schuster et al 2010 - dbVar Study

nstd39 (Schuster et al. 2010)

Organism:: Human
Study Type:: Control Set
Submitter:: Evan Eichler
Description:: Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. See Variant Summary counts for nstd39 in dbVar Variant Summary.
Publication(s):: Schuster et al. 2010

Links

Source: NCBI

Detailed Information: Download 187 Variant Regions, Download 187 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	27	27	Remapped	NC_000001.11
NC_000002.12	Chr2	14	14	Remapped	NC_000002.12
NC_000003.12	Chr3	5	5	Remapped	NC_000003.12
NC_000004.12	Chr4	4	4	Remapped	NC_000004.12
NC_000005.10	Chr5	3	3	Remapped	NC_000005.10
NC_000006.12	Chr6	5	5	Remapped	NC_000006.12
NC_000007.14	Chr7	17	17	Remapped	NC_000007.14
NC_000008.11	Chr8	9	9	Remapped	NC_000008.11
NC_000009.12	Chr9	6	6	Remapped	NC_000009.12
NC_000010.11	Chr10	8	8	Remapped	NC_000010.11
NC_000011.10	Chr11	10	10	Remapped	NC_000011.10
NC_000012.12	Chr12	2	2	Remapped	NC_000012.12
NC_000013.11	Chr13	2	2	Remapped	NC_000013.11
NC_000014.9	Chr14	4	4	Remapped	NC_000014.9
NC_000015.10	Chr15	6	6	Remapped	NC_000015.10
NC_000016.10	Chr16	18	18	Remapped	NC_000016.10
NC_000017.11	Chr17	5	5	Remapped	NC_000017.11
NC_000019.10	Chr19	27	27	Remapped	NC_000019.10
NC_000020.11	Chr20	6	6	Remapped	NC_000020.11
NC_000022.11	Chr22	8	8	Remapped	NC_000022.11
NT_187528.1	Chr2\|NT_187528.1	2	2	Remapped	NT_187528.1
NT_187539.1	Chr3\|NT_187539.1	1	1	Remapped	NT_187539.1
NT_167248.2	Chr6\|NT_167248.2	1	1	Remapped	NT_167248.2
NT_167245.2	Chr6\|NT_167245.2	1	1	Remapped	NT_167245.2
NT_113891.3	Chr6\|NT_113891.3	1	1	Remapped	NT_113891.3
NT_167244.2	Chr6\|NT_167244.2	1	1	Remapped	NT_167244.2
NW_018654714.1	Chr7\|NW_018654714.1	1	1	Remapped	NW_018654714.1
NW_018654715.1	Chr7\|NW_018654715.1	1	1	Remapped	NW_018654715.1
NW_018654716.1	Chr8\|NW_018654716.1	1	1	Remapped	NW_018654716.1
NW_018654717.1	Chr8\|NW_018654717.1	4	4	Remapped	NW_018654717.1
NT_187681.1	Chr11\|NT_187681.1	1	1	Remapped	NT_187681.1
NT_187656.1	Chr11\|NT_187656.1	1	1	Remapped	NT_187656.1
NW_015148966.1	Chr11\|NW_015148966.1	1	1	Remapped	NW_015148966.1
NT_187658.1	Chr12\|NT_187658.1	1	1	Remapped	NT_187658.1
NT_187588.1	Chr12\|NT_187588.1	1	1	Remapped	NT_187588.1
NW_018654722.1	Chr14\|NW_018654722.1	2	2	Remapped	NW_018654722.1
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
NT_187603.1	Chr15\|NT_187603.1	1	1	Remapped	NT_187603.1
NT_187604.1	Chr15\|NT_187604.1	1	1	Remapped	NT_187604.1
NW_011332701.1	Chr15\|NW_011332701.1	1	1	Remapped	NW_011332701.1
NW_018654723.1	Chr16\|NW_018654723.1	2	2	Remapped	NW_018654723.1
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1
NT_167251.2	Chr17\|NT_167251.2	1	1	Remapped	NT_167251.2
NW_009646206.1	Chr19\|NW_009646206.1	1	1	Remapped	NW_009646206.1
NT_187633.1	Chr22\|NT_187633.1	3	3	Remapped	NT_187633.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.10	Chr1	27	27	Remapped	NC_000001.10
NC_000002.11	Chr2	14	14	Remapped	NC_000002.11
NC_000003.11	Chr3	5	5	Remapped	NC_000003.11
NC_000004.11	Chr4	3	3	Remapped	NC_000004.11
NC_000005.9	Chr5	3	3	Remapped	NC_000005.9
NC_000006.11	Chr6	5	5	Remapped	NC_000006.11
NC_000007.13	Chr7	17	17	Remapped	NC_000007.13
NC_000008.10	Chr8	9	9	Remapped	NC_000008.10
NC_000009.11	Chr9	6	6	Remapped	NC_000009.11
NC_000010.10	Chr10	8	8	Remapped	NC_000010.10
NC_000011.9	Chr11	10	10	Remapped	NC_000011.9
NC_000012.11	Chr12	2	2	Remapped	NC_000012.11
NC_000013.10	Chr13	2	2	Remapped	NC_000013.10
NC_000014.8	Chr14	4	4	Remapped	NC_000014.8
NC_000015.9	Chr15	6	6	Remapped	NC_000015.9
NC_000016.9	Chr16	18	18	Remapped	NC_000016.9
NC_000017.10	Chr17	5	5	Remapped	NC_000017.10
NC_000019.9	Chr19	27	27	Remapped	NC_000019.9
NC_000020.10	Chr20	6	6	Remapped	NC_000020.10
NC_000022.10	Chr22	9	9	Remapped	NC_000022.10
NW_003571032.1	Chr2\|NW_003571032.1	1	1	Remapped	NW_003571032.1
NW_003571034.1	Chr4\|NW_003571034.1	1	1	Remapped	NW_003571034.1
NT_113891.2	Chr6\|NT_113891.2	1	1	Remapped	NT_113891.2
NT_167244.1	Chr6\|NT_167244.1	1	1	Remapped	NT_167244.1
NT_167245.1	Chr6\|NT_167245.1	1	1	Remapped	NT_167245.1
NT_167248.1	Chr6\|NT_167248.1	1	1	Remapped	NT_167248.1
NW_003871064.1	Chr7\|NW_003871064.1	3	3	Remapped	NW_003871064.1
NW_003315924.1	Chr8\|NW_003315924.1	1	1	Remapped	NW_003315924.1
NW_003871068.1	Chr10\|NW_003871068.1	2	2	Remapped	NW_003871068.1
NW_003871080.1	Chr11\|NW_003871080.1	1	1	Remapped	NW_003871080.1
NT_167251.1	Chr17\|NT_167251.1	1	1	Remapped	NT_167251.1
NW_004775434.1	Chr19\|NW_004775434.1	1	1	Remapped	NW_004775434.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.8	Chr1	27	27	Submitted	NC_000001.8
NC_000002.9	Chr2	14	14	Submitted	NC_000002.9
NC_000003.9	Chr3	5	5	Submitted	NC_000003.9
NC_000004.9	Chr4	4	4	Submitted	NC_000004.9
NC_000005.8	Chr5	3	3	Submitted	NC_000005.8
NC_000006.9	Chr6	5	5	Submitted	NC_000006.9
NC_000007.11	Chr7	17	17	Submitted	NC_000007.11
NC_000008.9	Chr8	9	9	Submitted	NC_000008.9
NC_000009.9	Chr9	6	6	Submitted	NC_000009.9
NC_000010.8	Chr10	8	8	Submitted	NC_000010.8
NC_000011.8	Chr11	10	10	Submitted	NC_000011.8
NC_000012.9	Chr12	2	2	Submitted	NC_000012.9
NC_000013.9	Chr13	2	2	Submitted	NC_000013.9
NC_000014.7	Chr14	4	4	Submitted	NC_000014.7
NC_000015.8	Chr15	6	6	Submitted	NC_000015.8
NC_000016.8	Chr16	18	18	Submitted	NC_000016.8
NC_000017.9	Chr17	5	5	Submitted	NC_000017.9
NC_000019.8	Chr19	27	27	Submitted	NC_000019.8
NC_000020.9	Chr20	6	6	Submitted	NC_000020.9
NC_000022.8	Chr22	9	9	Submitted	NC_000022.8

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	27	25	2	0	0	0	27	25	2	0	0	0
NC_000002.9	Chr2	14	13	0	0	0	1	14	13	0	0	0	1
NC_000003.9	Chr3	5	5	0	0	0	0	5	5	0	0	0	0
NC_000004.9	Chr4	4	4	0	0	0	0	4	4	0	0	0	0
NC_000005.8	Chr5	3	3	0	0	0	0	3	3	0	0	0	0
NC_000006.9	Chr6	5	4	0	0	0	1	5	4	0	0	0	1
NC_000007.11	Chr7	17	12	1	1	0	3	17	12	1	1	0	3
NC_000008.9	Chr8	9	8	0	0	0	1	9	8	0	0	0	1
NC_000009.9	Chr9	6	6	0	0	0	0	6	6	0	0	0	0
NC_000010.8	Chr10	8	6	0	0	0	2	8	6	0	0	0	2
NC_000011.8	Chr11	10	9	0	0	0	1	10	9	0	0	0	1
NC_000012.9	Chr12	2	2	0	0	0	0	2	2	0	0	0	0
NC_000013.9	Chr13	2	2	0	0	0	0	2	2	0	0	0	0
NC_000014.7	Chr14	4	4	0	0	0	0	4	4	0	0	0	0
NC_000015.8	Chr15	6	6	0	0	0	0	6	6	0	0	0	0
NC_000016.8	Chr16	18	18	0	0	0	0	18	18	0	0	0	0
NC_000017.9	Chr17	5	4	0	0	0	1	5	4	0	0	0	1
NC_000019.8	Chr19	27	26	0	0	0	1	27	26	0	0	0	1
NC_000020.9	Chr20	6	6	0	0	0	0	6	6	0	0	0	0
NC_000022.8	Chr22	9	9	0	0	0	0	9	9	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	27	25	2	0	0	0	27	25	2	0	0	0
NC_000002.9	Chr2	14	12	0	0	0	2	14	12	0	0	0	2
NC_000003.9	Chr3	5	4	0	0	0	1	5	4	0	0	0	1
NC_000004.9	Chr4	4	4	0	0	0	0	4	4	0	0	0	0
NC_000005.8	Chr5	3	3	0	0	0	0	3	3	0	0	0	0
NC_000006.9	Chr6	5	3	1	0	0	1	5	3	1	0	0	1
NC_000007.11	Chr7	17	10	5	0	0	2	17	10	5	0	0	2
NC_000008.9	Chr8	9	4	0	0	0	5	9	4	0	0	0	5
NC_000009.9	Chr9	6	5	1	0	0	0	6	5	1	0	0	0
NC_000010.8	Chr10	8	8	0	0	0	0	8	8	0	0	0	0
NC_000011.8	Chr11	10	8	1	0	0	1	10	8	1	0	0	1
NC_000012.9	Chr12	2	0	0	0	0	2	2	0	0	0	0	2
NC_000013.9	Chr13	2	2	0	0	0	0	2	2	0	0	0	0
NC_000014.7	Chr14	4	2	0	0	0	2	4	2	0	0	0	2
NC_000015.8	Chr15	6	3	0	0	0	3	6	3	0	0	0	3
NC_000016.8	Chr16	18	16	0	0	0	2	18	16	0	0	0	2
NC_000017.9	Chr17	5	4	0	0	0	1	5	4	0	0	0	1
NC_000019.8	Chr19	27	25	1	0	0	1	27	25	1	0	0	1
NC_000020.9	Chr20	6	6	0	0	0	0	6	6	0	0	0	0
NC_000022.8	Chr22	9	7	0	0	0	2	9	7	0	0	0	2

Samplesets

Number of Samplesets: 1

Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Male

Samples for sampleset 1
Sample ID	Subject ID	Sex	Ethnicity	Subject Phenotype
KB1	KB1	Male	San	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Data	Number of Variant Calls
1	Discovery	Sequencing	Read depth	Illumina Genome Analyzer and Roche/454 sequencer. For arrayCGH validation experiments we used Nimblegen	SRA, http://main.g2.bx.psu.edu/bushman	187
2	Validation	Oligo aCGH	Probe signal intensity			187

Validations

Experiment ID	Method	Analysis	Number of Variant Calls Validated
2	Oligo aCGH	Probe signal intensity	187

dbVar

Database of genomic structural variation

nstd39 (Schuster et al. 2010)

Links

Detailed Information: Download 187 Variant Regions, Download 187 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: 1

Experimental Details

Validations

Variant Summary for:

Remapping summary: