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Method Detail
Submitter Method Handle: BCM_SSAHASNP
Submitter Method ID: BAYLOR-WGS-200306
Submitted method description:
We aligned 2,812,455 human reads, available at
http://www.ncbi.nih.gov/Traces, to build33 of the human genome,
available at ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/, 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 generated 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 samples 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
represent 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 -
www.cardiogene.org.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
BCM_SSAHASNP Assay Baylor-WGS-200306-1 116
BCM_SSAHASNP Assay Baylor-WGS-200306-2 116
BCM_SSAHASNP Assay Baylor-WGS-200306-3 116
BCM_SSAHASNP Assay Baylor-WGS-200306-4 116
BCM_SSAHASNP Validation doubleHit_May2003 116
BCM_SSAHASNP Validation doubleHit_Jul2003 116
BCM_SSAHASNP Validation doubleHit_Oct2003 117
BCM_SSAHASNP Validation doubleHit_Jan2004 119
BCM_SSAHASNP Validation doubleHit_Mar2004 120
BCM_SSAHASNP Validation doubleHit_2004Apr21 121
NCBI Validation doubleHit_ncbi 116