The Bacillus anthracis database presents published genotyping data compiled from the litterature. While we have done our best to harmonize the typing conventions, the database is provided as is.
Two categories of data are included, MLVA data derived from the analysis of variable number of tandem repeats (VNTRs), and single nucleotide polymorphisms (SNPs).
Data from one collection of 13 SNPs is presented, canSNP13 set-up by van Ert et al., 2007, comprising 13 SNPs.
A number of MLVA panels are defined in the database, selected among 31 VNTR loci :
MLVA8Keim2000, MLVA15vanErt2007, MLVA25Lista2006, MLVA31Beyer2012.
The typing convention for each of the 31 loci is presented as supplementary file S1 in Thierry 2014 et al. :
The convention indicates for each locus the repeat unit size and the corresponding repeat copy number in the Ames ancestor sequenced genome refseq NC_007530 (chromosome), NC_007322 and NC_007323 (two plasmids, containing the four loci pXO1, pXO2, VNTR16 and VNTR17).
It is important to keep in mind that this copy number is a convention. The "true" repeat copy number at a given locus may be 4.5, 5.5 etc. A convention is a decision on how to round up such values. The convention has no impact on data quality, only the same convention needs to be applied before merging data sets produced by different groups. Also different groups might want to use different primers, for good reasons such as PCR multiplexing. This is likely to change the expected PCR product size, but should not change the corresponding repeat copy number.
The source for each data is indicated in the database in the "publication" column, the "contact" column is a suggestion for further inquiries.
