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dbVar

Database of genomic structural variation

estd210 (Blake et al. 2014)

Organism:: Human
Study Type:: Case-Set
Submitter:: Jonathon Blake
Description:: Analysis of Structural Variation in a patient with neurodevelopmental disease and balanced chromosomal abnormalities. We have used mate-pair sequencing to investigate the structural variation and possible genetic cause of disorder a high resolution. See Variant Summary counts for estd210 in dbVar Variant Summary.
Publication(s):: Blake et al. 2014

Links

Source: NCBI

Detailed Information: Download 4 Variant Regions, Download 4 Variant Calls, Download Both, FTP

Variant Summary
Samplesets
Experimental Details
Validations

Variant Summary

Assembly used for analysis:
Remapped: GRCh38.p12 (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_000002.12	Chr2	3	3	Remapped	NC_000002.12
NC_000007.14	Chr7	1	1	Remapped	NC_000007.14
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_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_000002.11	Chr2	3	3	Submitted	NC_000002.11
NC_000007.13	Chr7	1	1	Submitted	NC_000007.13
NC_000019.9	Chr19	1	1	Submitted	NC_000019.9

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_000002.11	Chr2	3	1	1	0	0	2	3	1	1	0	0	2
NC_000007.13	Chr7	1	0	0	0	0	2	1	0	0	0	0	2
NC_000019.9	Chr19	1	0	0	0	0	1	1	0	0	0	0	1

Samplesets

Number of Samplesets: 1

Name:: Tralo1
Sampleset Type:: Case
Description:: A patient with Neurodevelopmental Disorder and chromosomal abnormalities
Size:: 1
Organisms:: Homo sapiens
Sampleset Phenotype(s):: None reported
Sex:: Male

Experimental Details

Experiment ID	Type	Method	Analysis	Platforms	Number of Variant Calls
1	Discovery	Sequencing	Split read and paired-end mapping	Illumina GA II	4
2	Validation	Sequencing	Sequence alignment	Sanger	3

Validations

Experiment ID	Method	Analysis	Platform	Number of Variant Calls Validated
2	Sequencing	Sequence alignment	Sanger	3

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