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Method Detail
Submitter Method Handle: CSHL-HAPMAP
Submitter Method ID: CSHL-HUCC-200402
Submitted method description:
We aligned 1,728,270 human reads, individual C (see Venter JC, et al, The Sequence of the Human Genome, Science Feb 16 2001: 1304-1351), 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 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 det
ected 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.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
CSHL-HAPMAP Assay CSHL-HuCC-200402 119