Table 3.

List of chromosomal mutations identified in the genome of the SCV morphotype (n°2) when compared to the genome of morphotype n°1.

Gene	Protein	Mutation	Effect on the protein	Impact on the protein function
Hypothetical protein	Unknown	99T > C	synonymous variant	Unlikely
sdhA	Succinate dehydrogenase flavoprotein subunit	1673A > G	missense variant: His558Arg	Unlikely: same family of aminoacids
serA	Phosphoglycerate deshydrogenase	40T > C	missense variant: Phe14Leu	Possible: different families of aminoacids
Hypothetical protein	Unknown	739A > C	missense variant: Thr247Pro	Unknown
pbuE	Purine efflux pump PbuE	605G > AT	missence variant: insertion of Arg in 202	Unlikely (end of protein)
nodD2	Nodulation protein	303G > T	synonymous variant	Unlikely
lgrD	non-ribosomal peptide synthetase	2668A > T	stop gained Lys890*	Possible: truncated protein of 890 amino acids versus 991

Variant calling was performed using the Snippy software (https://github.com/tseemann/snippy) after annotation of the reference genome of morphotype n°1 (Prokka software).