NCBI
dbSNP

dbVar ClinVar GaP PubMed Nucleotide Protein
Search small variations in dbSNP or large structural variations in dbVar
transparent GIF
Spacer gif
Have a question about dbSNP? Try searching the SNP FAQ Archive!

Spacer gif
Method Detail
Submitter Method Handle: SC_SNP
Submitter Method ID: CHR22_NA11321
Submitted method description:
Chromosome 22 specific sequencing libaries were created from the flow
sorted Coriell DNA NA11321 (Chinese origin).
We aligned the sequencing reads 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 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 10-APR-2003 114
SC_SNP Assay CHR22_NA11321_extra 118
SC_SNP Assay SC-CHR22_NA11321-200402 119