NCBI
dbSNP

dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
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Method Detail
Submitter Method Handle: CSHL-HAPMAP
Submitter Method ID: CSHL-HUAA-200402
Submitted method description:
We aligned 2,783,661 human reads, individual A (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 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 a
ll 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 ge
nome, 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-HuAA-200402 119