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

BMC Bioinformatics

Table 1 SNP Matrix example

LocusID	Strain A	Strain B	Strain C	Strain D	Strain E
genome123::115::115	A	T	A	A	T
genome123::120::120	G	C	G	G	C
genome123::121::121	T	C	C	C	C
genome123::130::130	C	G	G	G	C
genome123::209::209	A	C	C	N	G
genome123::405::405	-	-	X	C	C
genome123::511::541	10	8	8	10	8
⋮	⋮	⋮	⋮	⋮	⋮

The first column of a variant site matrix contains a genome identifier, a start position, and an end position, each separated by two colons. The start and end position should be the same for SNPs. Each additional column represents a strain and the calls made at each variant site for that strain. The first five rows contain SNPs, the sixth row contains an indel with missing data for Strain C, and the last row contains the lengths of VNTRs (the stopping position is based on the longest repeat of 3 in this case)

ISSN: 1471-2105