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Method Detail
Submitter Method Handle: SC_JCM
Submitter Method ID: Overlap_SNPs_by_SsahaSNP
Submitted method description:
Clone overlaps from available finished and unfinished public human
genomic sequence were aligned and high quality base discrepancies
(Q>=23) were identified as candidate SNPs. For finished sequence
the quality was assumed to be 40 (1 error in 10,000 bp). For unfinished
sequence, only those with quality values were used in the detection
of SNPs. Clone overlaps were rejected if the total overlap between
them were less than 6000bp. Further restrictions on the candidate
SNPs were that its neighbouring 5 bases all had Phrap quality values
of >=15 and at least 9 of the 10 neighbours match. If the number of
detected SNPs in one clique was greater than 5 in a 500bp interval
then all SNPs were discarded for that interval. If the SNP density
for the entire overlap region was less than 1SNP/4000bp, then all SNPs
detected between those clones were rejected. In some overlap regions,
more than 2 clones overlap. A SNP detected from multiple overlapping
clones were merged and represented as one SNP.

This method was used in the following submission:

Submitter Handle Batch Type Submitter batch id Release build id
SC_JCM Assay 19-JUL-2000 81
SC_JCM Assay 19-JUL-2000b 81
SC_JCM Assay 19-JUL-2000.3 81
SC_JCM Assay 19-JUL-2000.2 81
SC_JCM Assay 19-JUL-2000.4 81
SC_JCM Assay 02-NOV-2000 89
SC_JCM Assay 21-SEP-2001b 100
SC_JCM Assay 21-SEP-2001c 100
SC_JCM Assay 21-SEP-2001d 100
SC_JCM Assay 21-SEP-2001e 100
SC_JCM Assay 21-SEP-2001f 100
SC_JCM Assay 12-OCT-2001 100
SC_JCM Assay 11-FEB-2002 103