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Method Detail
Submitter Method Handle: SC_SNP
Submitter Method ID: CHR1_OVERLAP_SNPS
Submitted method description:
We realigned all available chromosome 1 clone based shotgun sequences collected at
The Sanger Centre onto the NCBI build 33 Genomic Reference Sequence for chromosome 1,
detecting SNPs using ssahaSNP.
Since the depth of shotgun sequencing for these clones was greater than 4X, only those
regions of chromosome 1 where a SNP was detected by at least 4 reads was considered valid.
The phred quality value of at least 4 of the reads at the SNP location had to be at least
30 (phred base calling error probability of 1/1000 or less). Further restrictions on the
candidate SNPs for a read alignment were that its neighbouring 5 bases all had Phred quality
values of >=15 and at least 9 of the 10 neighbours match.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
SC_SNP Assay CHR1_Overlap_SNPs 118