| | We aligned 2,298,789 human Fosmid end reads, available at |
| | http://www.ncbi.nih.gov/Traces, to build31 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. |
| | Trace data was generated by Whitehead Institute for Biomedical |
| | Research through a grant from NIH. This SNP analysis was performed with |
| | permission from WIBR. The Fosmid library was prepared from a female sample, |
| | NA15510, in the Coriell Institute Polymorphism Discovery Resource |
| | collection. The DNA was prepped from white blood cells immortalized with EBV. |
