Fig. 1

Schematic diagram of error-prone SSR typing caused by variations in SSR or flanking regions. Take a site with CAGCC SSR motif as an example, for Seq1 (from reference genome), it’s clear that its SSR region is with three times repeats of CAGCC; for Seq2 with a G- > A variation in SSR region, the regular exact matching algorithm will type it as two repeats of CAGCC, while fault-tolerant algorithm could recognize it as three repeats; for Seq3 with a T- > C variation in right flanking region, flanking boundary-based algorithm will treat it as three repeats of CAGCC, however, the regular exact matching algorithm will recognize it as four times of repeat. When comparing different samples, especially different varieties, this discordance of SSR typing will cause misunderstanding of genetic information