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Method Detail
Submitter Method Handle: SC_JCM
Submitter Method ID: SNPS_DETECTED_BY_GENOMIC_ALIGNMENT_OF_TSC_READS
Submitted method description:
The TSC read set (available from ftp.snp.cshl.org) were clipped using ssahaCLIP
( ftp://ftp.ensembl.org/pub/traces/homo_sapiens/clip/README-clip; reads also available
here as ftp://ftp.ensembl.org/pub/traces/homo_sapiens/clip/cshl-human-wgs-*.clip.gz.)
which set a usable read length for each read. The reads were aligned using SsahaSNP to
build 30 of NCBI the Reference Sequences. Quality values were not used for this genomic
sequence. Where reads matched the genome more than once, the best quality match was used.
High quality base discrepancies (Q>=23) were identified as candidate SNPs. Further
restrictions on the candidate SNPs were that its neighbouring 5 bases all had Phred
quality values of >=15 and at least 9 of the 10 neighbours match.
When both the Q>=23 threshold and the neighbourhood restrictions are met, the base then
meets the Neighbourhood Quality Standard (NQS).
If the (number of SNPs detected for a read)/(number of NQS aligned bases for that read)
is determined to have a ratio > 15SNPs/1kb of sequence then all SNPs were discarded for
that read alignment.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
SC_JCM Assay 02-JAN-2003 111