Table 3. Determination of putative variants in the genomes sequenced in this study.

Strain	No. putative variants (LQ + HQ)	No. HQ putative variants	No. unique HQ putative variants*	No. Sanger verified unique HQ putative variants (TP)
ΔANR	71	1	1	1
HS-2-1	150	18	17	4
HS-2-5	23	5	4	4
HS-2-5-6	44	8	4	3
34F2	101	48	48	39
gerH::ery **	425	97	17	1
AP50R	65	44	2	2

LQ Low quality. HQ High quality. TP True positive.

*Does not include identity by descent variants from descendant strains.

**Includes both FLX and Titanium runs.