Variant site strain typer (VaST): efficient strain typing using a minimal number of variant genomic sites

BMC Bioinformatics

Table 3 New strains that were not used to build the minimum spanning set are identified as closely related strains

Assembly accession	Strain name	Patristic distance	In same clade	Clade size
GCA_000255875.1 [61]	Biovar Orientalis AS200901434	2	Yes	3
GCA_000186725.1 [62]	Biovar Medievalis Harbin 35	7	Yes	2
GCA_000182545.1 [63]	Pestoides A	1	Yes	3
GCA_000006645.1 [64]	KIM10	9	Yes	2
GCA_000013805.1 [65]	Nepal516	10	Yes	3

The Y. pestis minimum spanning set was regenerated with 5 of the original strains removed. These strains were then treated as samples and identified using the new minimum spanning set. In each case, the strain that most closely matched the sample strain’s haplotype was closely related. The table shows the assembly accession and name of each of the strains that were removed. The patristic distance between the sample strain and the strain it was identified as was calculated using the full tree. The clade size is the size of the clade that included both strains

ISSN: 1471-2105