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Method Detail
Submitter Method Handle: SC_SNP
Submitter Method ID: CHRX_NA11321
Submitted method description:
Chromosome X specific sequencing libaries were created from the flow
sorted Coriell DNA NA11321 (Chinese origin).
We aligned the sequencing reads to build31 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 CHRX_NA11321 115
SC_SNP Assay CHRX_NA11321.2 118
SC_SNP Assay SC-CHRX_NA11321-200402 119