| | We realigned all available chromosome 9 clone based shotgun sequences collected at |
| | The Sanger Centre onto the NCBI build 33 Genomic Reference Sequence for chromosome 9, |
| | detecting SNPs using ssahaSNP. |
| | Since the depth of shotgun sequencing for these clones was greater than 4X, only those |
| | regions of chromosome 9 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. |
