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Method Detail
Submitter Method Handle: WI_SSAHASNP
Submitter Method ID: WIBR_FOSMID_END_SNPS
Submitted method description:
We aligned 2,298,789 human Fosmid end reads, available at
http://www.ncbi.nih.gov/Traces, to build31 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 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 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 Whitehead Institute for Biomedical
Research through a grant from NIH. This SNP analysis was performed with
permission from WIBR. The Fosmid library was prepared from a female sample,
NA15510, in the Coriell Institute Polymorphism Discovery Resource
collection. The DNA was prepped from white blood cells immortalized with EBV.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
WI_SSAHASNP Assay 11-FEB-2003 112