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Method Detail
Submitter Method Handle: WI_SSAHASNP
Submitter Method ID: WI-WGS-200306
Submitted method description:
We aligned 3,047,741 human reads, available at, to build33 of the human genome, available at, using ssahaSNP. The settings for ssahaSNP were such that the candidate SNP base in the
read was at least Phred Q=23, that its neighbouring 5 bases on either side of the candidate SNP all had Phred quality values of >=15 and at least 9 of the 10 neighbours match. If the number of detected SNPs for the aligned segment of a read exceeded a ra
te of 15 SNPs per 1000 bases then that read alignment was ignored. If a read aligned to more than one place in the genome, then only the longest alignment with the fewest SNPs was reported. Trace data was generated by Whitehead Institute for Biomedical Re
search through a grant from NIH. This SNP analysis was performed with permission from WIBR.
The SNP reads are from a pool of 8 unrelated adult African Americans, 4 male and 4 female enrolled in Houston, TX. The pool does not have a name. The 8 samples were derived from the Baylor Polymorphism Reource which includes >500 ethnically diverse sample
s used as controls for allele frequency estimates and mutation analysis.
The DNA was prepped from lymphoblastoid cell lines developed from 8 unrelated African American adults. The genomic DNA was then pooled with equal quantities from each subject and the pooled DNA used to construct the genomic libraries. The cell lines repre
sent a subset of anonymous samples from healthy adults included in the Baylor Polymorphism Resource.
There is a URL for reference to the Baylor Polymorphism Resource -

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
WI_SSAHASNP Assay WI-WGS-200306-A 116
WI_SSAHASNP Assay WI-WGS-200306-B 116
WI_SSAHASNP Assay WI-WGS-200306-C 116
WI_SSAHASNP Assay WI-WGS-200306-A.2 116
WI_SSAHASNP Assay WI-WGS-200306-B.2 116
WI_SSAHASNP Assay WI-WGS-200306-C.2 116