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Method Detail
Submitter Method Handle: BCM_SSAHASNP
Submitter Method ID: BAYLOR-WGS-200310
Submitted method description:
We aligned 2,812,455 human reads, available at, to build34 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 neighboring 5 bases on either side of the candidate SNP all had Phred quality values of >=15 and at least 9 of the 10 neighbors match. If the number of detected SNPs
for the aligned segment of a read exceeded a rate 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 g
enerated by the Human Genome
Sequencing Center, Baylor College of Medicine, through a grant from NIH.
This SNP analysis was performed with permission from HGSC.
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 Resource which includes >500 ethnically diverse sampl
es 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
BCM_SSAHASNP Assay Baylor-WGS-200310 118