Table 3. The SNVs of penicillin regulatory Proteins in all Lineages.

Gene	Annotation	SNV	Mutation	Mutation type	Lineage	Strain	SIFT Scorea
TPANIC_0500	penicillin-binding protein (pbp-1)	C537571T	P564L	nonsynonymous	2,3	Strain C-0, D-R, E-V, G-I2, B3, C3, K3, Q3 and SS14	0.2
TPANIC_0547	4-hydroxy-3-methylbut-2-enyl diphosphate reductase/penicillin tolerance protein (lytB)	T592290C	/	synonymous	2,3	Strain C-0, D-R, E-V, G-I2, B3, C3, K3, Q3, SS14 and Mexico A	/
		T592614C	/	synonymous	2,3	Strain C-0, D-R, E-V, G-I2, B3, C3, K3, Q3, SS14 and Mexico A	/
TPANIC_0705	penicillin-binding protein (pbp-2)	G773571A	A506V	nonsynonymous	2	Strain C-0, D-R, E-V, G-I2, B3, C3, K3 and Q3	0.03
TPANIC_0760	penicillin-binding protein (pbp-3)	G824922A	A366T	nonsynonymous	2	Strain C-0, and B3	0.14
		A825069T	I415F	nonsynonymous	2	Strain C-0, D-R, E-V, G-I2, B3, C3 and Q3	0.03
		C825071G	I415M	nonsynonymous	2	Strain K3	0.17

^afunctional SNVs predicted using SIFT (SIFT score ≤0.05 as the deleterious effect).