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Table 1 Interpretation of the output of stringMLST and SRST2 with “*”

From: STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data

 

Capability to identify correct alleles

Capability to identify new alleles

SRST2 / stringMLST output

High stringency

Low stringency

High stringency

Low stringency

allele_1*

Missed the correct allele

Hit the correct allele

(this case doesn’t exist because allele_1 is not present)

(this case doesn’t exist because allele_1 is not present)

allele_2* to allele_100*

Missed the correct allele

Missed the correct allele

Hit a new allele is present

Missed a new allele is present

  1. Synoptic table describing differences in the interpretation of output containing “*” with high and low stringency criteria for both capability to identify correct and new alleles. To measure the capability to identify new alleles, in this example “allele_1” has been removed from the set of reference alleles