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Method Detail
Submitter Method Handle: SC_SNP
Submitter Method ID: CHR20_NA10470
Submitted method description:
Chromosome 20 specific sequencing libaries were created from the flow
sorted Coriell DNA NA10470 (Pygmy origin).
We aligned the sequencing reads to build33 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 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.
Note: Flow sorting of chromosomes also includes a small percentage of
unintended chromosomal material. Therefore some reads for this flow
sorted library may generate SNPs on other chromosomes.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
SC_SNP Assay 11-APR-2003a 114
SC_SNP Assay CHR20_NA10470 118