A new approach to in silico SNP detection and some new SNPs in the Bacillus anthracis genome

BMC Research Notes

Table 2 Distribution of SNPs in Ames Ancestor, Ames, and Sterne genomes.

sequence	strain homology	SNP spacing (average)	SNP spacing (adjusted for indels)
Chromosome (AA-S)	99.96%	40.3	40.3
Chromosome (AA-A)	100.00%	277.8	277.8
Chromosome (A-S)	99.94%	34.5	34.5
pXO1 (AA-S)	72.38%	13.0	9.4
pXO2 (AA-P)	98.49%	4.5	4.4

The average SNP spacing, given in Kbp, is computed by dividing the sequence length by the number of SNPs. Non-indel SNP spacing is computed similarly, except that the lengths of all indels and polymorphic regions (SNP clusters, i.e. regions where average SNP spacing is greater than one in every twenty bases) are subtracted from the total sequence length.

ISSN: 1756-0500