nstd1 - Tuzun et al 2005 - dbVar Study

nstd1 (Tuzun et al. 2005)

Organism:: Human
Study Type:: Control Set
Submitter:: Evan Eichler
Submitter URL:: http://hgsv.washington.edu
Description:: We systematically compared the human genome reference sequence with a second genome (represented by GM15510 fosmid paired-end sequences) to detect intermediate-sized structural variants >8 kb in length. See Variant Summary counts for nstd1 in dbVar Variant Summary.
Project:: PRJNA29893
Publication(s):: Tuzun et al. 2005

Links

Source: NCBI

Detailed Information: Download 297 Variant Regions, Download 297 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	22	22	Remapped	NC_000001.11
NC_000002.12	Chr2	15	15	Remapped	NC_000002.12
NC_000003.12	Chr3	20	20	Remapped	NC_000003.12
NC_000004.12	Chr4	13	13	Remapped	NC_000004.12
NC_000005.10	Chr5	15	15	Remapped	NC_000005.10
NC_000006.12	Chr6	7	7	Remapped	NC_000006.12
NC_000007.14	Chr7	21	21	Remapped	NC_000007.14
NC_000008.11	Chr8	20	20	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	16	16	Remapped	NC_000011.10
NC_000012.12	Chr12	12	12	Remapped	NC_000012.12
NC_000014.9	Chr14	6	6	Remapped	NC_000014.9
NC_000015.10	Chr15	34	34	Remapped	NC_000015.10
NC_000016.10	Chr16	17	17	Remapped	NC_000016.10
NC_000017.11	Chr17	12	12	Remapped	NC_000017.11
NC_000018.10	Chr18	1	1	Remapped	NC_000018.10
NC_000019.10	Chr19	14	14	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	7	7	Remapped	NC_000022.11
NC_000023.11	ChrX	20	20	Remapped	NC_000023.11
NT_187515.1	Chr1\|NT_187515.1	1	1	Remapped	NT_187515.1
NW_003315906.1	Chr1\|NW_003315906.1	2	2	Remapped	NW_003315906.1
NW_003315907.2	Chr1\|NW_003315907.2	1	1	Remapped	NW_003315907.2
NW_018654707.1	Chr1\|NW_018654707.1	1	1	Remapped	NW_018654707.1
NT_187523.1	Chr2\|NT_187523.1	1	1	Remapped	NT_187523.1
NT_187647.1	Chr2\|NT_187647.1	1	1	Remapped	NT_187647.1
NW_003315909.1	Chr2\|NW_003315909.1	1	1	Remapped	NW_003315909.1
NW_012132915.1	Chr2\|NW_012132915.1	1	1	Remapped	NW_012132915.1
NT_187539.1	Chr3\|NT_187539.1	1	1	Remapped	NT_187539.1
NW_003315913.1	Chr3\|NW_003315913.1	1	1	Remapped	NW_003315913.1
NW_018654711.1	Chr3\|NW_018654711.1	1	1	Remapped	NW_018654711.1
NW_019805492.1	Chr3\|NW_019805492.1	1	1	Remapped	NW_019805492.1
NT_187542.1	Chr4\|NT_187542.1	1	1	Remapped	NT_187542.1
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_003571036.1	Chr5\|NW_003571036.1	1	1	Remapped	NW_003571036.1
NW_016107297.1	Chr5\|NW_016107297.1	1	1	Remapped	NW_016107297.1
NW_016107298.1	Chr5\|NW_016107298.1	2	2	Remapped	NW_016107298.1
NT_167247.2	Chr6\|NT_167247.2	2	2	Remapped	NT_167247.2
NT_167248.2	Chr6\|NT_167248.2	2	2	Remapped	NT_167248.2
NT_167249.2	Chr6\|NT_167249.2	2	2	Remapped	NT_167249.2
NT_167245.2	Chr6\|NT_167245.2	2	2	Remapped	NT_167245.2
NT_113891.3	Chr6\|NT_113891.3	1	1	Remapped	NT_113891.3
NT_187561.1	Chr7\|NT_187561.1	1	1	Remapped	NT_187561.1
NT_187562.1	Chr7\|NT_187562.1	2	2	Remapped	NT_187562.1
NW_018654714.1	Chr7\|NW_018654714.1	2	2	Remapped	NW_018654714.1
NT_187565.1	Chr8\|NT_187565.1	1	1	Remapped	NT_187565.1
NT_187566.1	Chr8\|NT_187566.1	1	1	Remapped	NT_187566.1
NT_187576.1	Chr8\|NT_187576.1	1	1	Remapped	NT_187576.1
NT_187654.1	Chr8\|NT_187654.1	1	1	Remapped	NT_187654.1
NW_018654717.1	Chr8\|NW_018654717.1	3	3	Remapped	NW_018654717.1
NW_019805494.1	Chr8\|NW_019805494.1	1	1	Remapped	NW_019805494.1
NW_009646201.1	Chr9\|NW_009646201.1	1	1	Remapped	NW_009646201.1
NT_187681.1	Chr11\|NT_187681.1	1	1	Remapped	NT_187681.1
NW_015148966.1	Chr11\|NW_015148966.1	1	1	Remapped	NW_015148966.1
NW_019805495.1	Chr11\|NW_019805495.1	1	1	Remapped	NW_019805495.1
NW_019805496.1	Chr11\|NW_019805496.1	1	1	Remapped	NW_019805496.1
NW_003315939.2	Chr12\|NW_003315939.2	1	1	Remapped	NW_003315939.2
NW_009646204.1	Chr12\|NW_009646204.1	1	1	Remapped	NW_009646204.1
NW_018654718.1	Chr12\|NW_018654718.1	1	1	Remapped	NW_018654718.1
NW_019805499.1	Chr12\|NW_019805499.1	1	1	Remapped	NW_019805499.1
NT_187600.1	Chr14\|NT_187600.1	1	1	Remapped	NT_187600.1
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
NW_003315944.2	Chr15\|NW_003315944.2	1	1	Remapped	NW_003315944.2
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_018654723.1	Chr16\|NW_018654723.1	1	1	Remapped	NW_018654723.1
NT_187663.1	Chr17\|NT_187663.1	1	1	Remapped	NT_187663.1
NW_003871093.1	Chr17\|NW_003871093.1	1	1	Remapped	NW_003871093.1
NT_167251.2	Chr17\|NT_167251.2	1	1	Remapped	NT_167251.2
NT_187616.1	Chr17\|NT_187616.1	1	1	Remapped	NT_187616.1
NW_017363819.1	Chr17\|NW_017363819.1	1	1	Remapped	NW_017363819.1
NW_019805501.1	Chr17\|NW_019805501.1	1	1	Remapped	NW_019805501.1
NT_187693.1	Chr19\|NT_187693.1	2	2	Remapped	NT_187693.1
NW_003571061.2	Chr19\|NW_003571061.2	2	2	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	2	2	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_003315963.1	Chr19\|NW_003315963.1	1	1	Remapped	NW_003315963.1
NW_003571054.1	Chr19\|NW_003571054.1	2	2	Remapped	NW_003571054.1
NW_009646206.1	Chr19\|NW_009646206.1	2	2	Remapped	NW_009646206.1
NW_014040929.1	Chr19\|NW_014040929.1	1	1	Remapped	NW_014040929.1
NW_003315970.2	Chr21\|NW_003315970.2	1	1	Remapped	NW_003315970.2
NT_187629.1	Chr22\|NT_187629.1	2	2	Remapped	NT_187629.1
NT_187633.1	Chr22\|NT_187633.1	1	1	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	22	22	Remapped	NC_000001.10
NC_000002.11	Chr2	15	15	Remapped	NC_000002.11
NC_000003.11	Chr3	20	20	Remapped	NC_000003.11
NC_000004.11	Chr4	13	13	Remapped	NC_000004.11
NC_000005.9	Chr5	15	15	Remapped	NC_000005.9
NC_000006.11	Chr6	7	7	Remapped	NC_000006.11
NC_000007.13	Chr7	21	21	Remapped	NC_000007.13
NC_000008.10	Chr8	22	22	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	16	16	Remapped	NC_000011.9
NC_000012.11	Chr12	12	12	Remapped	NC_000012.11
NC_000014.8	Chr14	6	6	Remapped	NC_000014.8
NC_000015.9	Chr15	34	34	Remapped	NC_000015.9
NC_000016.9	Chr16	17	17	Remapped	NC_000016.9
NC_000017.10	Chr17	13	13	Remapped	NC_000017.10
NC_000018.9	Chr18	1	1	Remapped	NC_000018.9
NC_000019.9	Chr19	13	13	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	7	7	Remapped	NC_000022.10
NC_000023.10	ChrX	18	18	Remapped	NC_000023.10
NW_003315906.1	Chr1\|NW_003315906.1	2	2	Remapped	NW_003315906.1
NW_003315907.1	Chr1\|NW_003315907.1	1	1	Remapped	NW_003315907.1
NW_003871055.3	Chr1\|NW_003871055.3	3	3	Remapped	NW_003871055.3
NW_003315909.1	Chr2\|NW_003315909.1	1	1	Remapped	NW_003315909.1
NW_003315913.1	Chr3\|NW_003315913.1	1	1	Remapped	NW_003315913.1
NW_003315914.1	Chr4\|NW_003315914.1	1	1	Remapped	NW_003315914.1
NW_004775427.1	Chr4\|NW_004775427.1	1	1	Remapped	NW_004775427.1
NW_003571036.1	Chr5\|NW_003571036.1	1	1	Remapped	NW_003571036.1
NW_004775428.1	Chr5\|NW_004775428.1	1	1	Remapped	NW_004775428.1
NT_113891.2	Chr6\|NT_113891.2	1	1	Remapped	NT_113891.2
NT_167245.1	Chr6\|NT_167245.1	2	2	Remapped	NT_167245.1
NT_167247.1	Chr6\|NT_167247.1	2	2	Remapped	NT_167247.1
NT_167248.1	Chr6\|NT_167248.1	2	2	Remapped	NT_167248.1
NT_167249.1	Chr6\|NT_167249.1	2	2	Remapped	NT_167249.1
NW_003571038.1	Chr7\|NW_003571038.1	1	1	Remapped	NW_003571038.1
NW_003571040.1	Chr7\|NW_003571040.1	2	2	Remapped	NW_003571040.1
NW_003571042.1	Chr8\|NW_003571042.1	1	1	Remapped	NW_003571042.1
NW_003315925.1	Chr9\|NW_003315925.1	1	1	Remapped	NW_003315925.1
NW_003871068.1	Chr10\|NW_003871068.1	1	1	Remapped	NW_003871068.1
NW_003315939.1	Chr12\|NW_003315939.1	1	1	Remapped	NW_003315939.1
NW_004166863.1	Chr14\|NW_004166863.1	1	1	Remapped	NW_004166863.1
NW_003315944.1	Chr15\|NW_003315944.1	1	1	Remapped	NW_003315944.1
NT_167251.1	Chr17\|NT_167251.1	1	1	Remapped	NT_167251.1
NW_003871087.1	Chr17\|NW_003871087.1	1	1	Remapped	NW_003871087.1
NW_003871093.1	Chr17\|NW_003871093.1	1	1	Remapped	NW_003871093.1
NW_003315963.1	Chr19\|NW_003315963.1	1	1	Remapped	NW_003315963.1
NW_003571060.1	Chr19\|NW_003571060.1	1	1	Remapped	NW_003571060.1
NW_003871094.1	Chr19\|NW_003871094.1	2	2	Remapped	NW_003871094.1
NW_003315970.1	Chr21\|NW_003315970.1	1	1	Remapped	NW_003315970.1
NW_003871103.3	ChrX\|NW_003871103.3	3	3	Remapped	NW_003871103.3
NW_004070880.2	ChrX\|NW_004070880.2	2	2	Remapped	NW_004070880.2
NW_004070883.1	ChrX\|NW_004070883.1	1	1	Remapped	NW_004070883.1
NW_004070885.1	ChrX\|NW_004070885.1	3	3	Remapped	NW_004070885.1
NW_004070890.2	ChrX\|NW_004070890.2	2	2	Remapped	NW_004070890.2
NW_004070892.1	ChrX\|NW_004070892.1	2	2	Remapped	NW_004070892.1
NW_004166866.1	ChrX\|NW_004166866.1	1	1	Remapped	NW_004166866.1

Sequence ID	Chr	Number of Variant Regions	Number of Variant Calls	Placement type	Link to graphical display
NC_000001.8	Chr1	22	22	Submitted	NC_000001.8
NC_000002.9	Chr2	15	15	Submitted	NC_000002.9
NC_000003.9	Chr3	20	20	Submitted	NC_000003.9
NC_000004.9	Chr4	13	13	Submitted	NC_000004.9
NC_000005.8	Chr5	15	15	Submitted	NC_000005.8
NC_000006.9	Chr6	7	7	Submitted	NC_000006.9
NC_000007.11	Chr7	22	22	Submitted	NC_000007.11
NC_000008.9	Chr8	22	22	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	16	16	Submitted	NC_000011.8
NC_000012.9	Chr12	12	12	Submitted	NC_000012.9
NC_000014.7	Chr14	6	6	Submitted	NC_000014.7
NC_000015.8	Chr15	34	34	Submitted	NC_000015.8
NC_000016.8	Chr16	17	17	Submitted	NC_000016.8
NC_000017.9	Chr17	13	13	Submitted	NC_000017.9
NC_000018.8	Chr18	1	1	Submitted	NC_000018.8
NC_000019.8	Chr19	14	14	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_000022.8	Chr22	7	7	Submitted	NC_000022.8
NC_000023.8	ChrX	20	20	Submitted	NC_000023.8

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	22	15	1	1	0	5	22	15	1	1	0	5
NC_000002.9	Chr2	15	13	0	0	0	2	15	13	0	0	0	2
NC_000003.9	Chr3	20	16	1	2	0	1	20	16	1	2	0	1
NC_000004.9	Chr4	13	11	0	0	0	2	13	11	0	0	0	2
NC_000005.8	Chr5	15	13	0	0	0	2	15	13	0	0	0	2
NC_000006.9	Chr6	7	4	0	1	0	2	7	4	0	1	0	2
NC_000007.11	Chr7	22	17	2	1	0	2	22	17	2	1	0	2
NC_000008.9	Chr8	22	15	3	3	0	1	22	15	3	3	0	1
NC_000009.9	Chr9	6	5	0	0	0	1	6	5	0	0	0	1
NC_000010.8	Chr10	8	7	0	0	0	1	8	7	0	0	0	1
NC_000011.8	Chr11	16	16	0	0	0	0	16	16	0	0	0	0
NC_000012.9	Chr12	12	11	0	0	0	1	12	11	0	0	0	1
NC_000014.7	Chr14	6	5	0	0	0	1	6	5	0	0	0	1
NC_000015.8	Chr15	34	31	0	2	0	1	34	31	0	2	0	1
NC_000016.8	Chr16	17	17	0	0	0	0	17	17	0	0	0	0
NC_000017.9	Chr17	13	10	0	0	0	3	13	10	0	0	0	3
NC_000018.8	Chr18	1	1	0	0	0	0	1	1	0	0	0	0
NC_000019.8	Chr19	14	9	0	2	0	3	14	9	0	2	0	3
NC_000020.9	Chr20	6	6	0	0	0	0	6	6	0	0	0	0
NC_000021.7	Chr21	1	0	0	0	0	1	1	0	0	0	0	1
NC_000022.8	Chr22	7	7	0	0	0	0	7	7	0	0	0	0
NC_000023.8	ChrX	20	5	2	1	0	12	20	5	2	1	0	12

			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	22	11	5	1	0	5	22	11	5	1	0	5
NC_000002.9	Chr2	15	8	2	2	0	3	15	8	2	2	0	3
NC_000003.9	Chr3	20	13	2	1	0	4	20	13	2	1	0	4
NC_000004.9	Chr4	13	9	1	0	0	3	13	9	1	0	0	3
NC_000005.8	Chr5	15	11	0	0	0	4	15	11	0	0	0	4
NC_000006.9	Chr6	7	3	0	2	0	2	7	3	0	2	0	2
NC_000007.11	Chr7	22	15	1	2	0	4	22	15	1	2	0	4
NC_000008.9	Chr8	22	9	3	3	1	6	22	9	3	3	1	6
NC_000009.9	Chr9	6	5	0	0	0	1	6	5	0	0	0	1
NC_000010.8	Chr10	8	7	0	1	0	0	8	7	0	1	0	0
NC_000011.8	Chr11	16	13	0	0	0	3	16	13	0	0	0	3
NC_000012.9	Chr12	12	8	0	0	0	4	12	8	0	0	0	4
NC_000014.7	Chr14	6	3	0	1	0	2	6	3	0	1	0	2
NC_000015.8	Chr15	34	29	0	3	0	2	34	29	0	3	0	2
NC_000016.8	Chr16	17	15	0	0	0	2	17	15	0	0	0	2
NC_000017.9	Chr17	13	5	1	1	1	5	13	5	1	1	1	5
NC_000018.8	Chr18	1	1	0	0	0	0	1	1	0	0	0	0
NC_000019.8	Chr19	14	5	3	0	0	6	14	5	3	0	0	6
NC_000020.9	Chr20	6	5	0	1	0	0	6	5	0	1	0	0
NC_000021.7	Chr21	1	0	0	0	0	1	1	0	0	0	0	1
NC_000022.8	Chr22	7	2	2	0	0	3	7	2	2	0	0	3
NC_000023.8	ChrX	20	7	6	7	0	0	20	7	6	7	0	0

Samplesets

Number of Samplesets: 1

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

Samples for sampleset 1
Sample ID	Subject ID	Sex	Subject Phenotype
SAMN00000376	GM15510	Female	Not reported

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Data	Number of Variant Calls
1	Discovery	Sequencing	Paired-end mapping	Capillary	WI2	297
2	Validation	Sequencing	Sequence alignment			34
3	Validation	PCR	Manual observation			7
4	Validation	BAC aCGH	Probe signal intensity			30

Validations

Experiment ID	Method	Analysis	Number of Variant Calls Validated
2	Sequencing	Sequence alignment	34
3	PCR	Manual observation	7
4	BAC aCGH	Probe signal intensity	30

dbVar

Database of genomic structural variation

nstd1 (Tuzun et al. 2005)

Links

Detailed Information: Download 297 Variant Regions, Download 297 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: