Potential mechanisms of attenuation for rifampicin-passaged strains of Flavobacterium psychrophilum

BMC Microbiology

Table 4 Single nucleotide polymorphisms (SNPs) from F. psychrophilum CSF 259-93B.17 strain

Reference position^a	Allele frequency (in %)^b	SNP^c	Coverage^d	Annotation^e	Amino acid change^e	Gene/Protein^f
43576	100	A > T	5	FPSM_00026	Met1Leu	Multimodular transpeptidase-transglycosylase PBP 1A
155877	100	A > T	43	FPSM_00129	Leu71Phe	Putative exported protein
283611	80	A > T	10	FPSM_00250	Asn522Ile	Amino acid permease
325469	100	T > A	4	FPSM_00287	Met1Leu	Thioredoxin
488182	100	A > C	4	FPSM_00425	Gln466Pro	DNA primase
514297	86.4	C > T	162	FPSM_00445	Ala11Thr	Malonyl-CoA-[acyl-carrier-protein] transacylase
548737	100	A > T	5	FPSM_00479	Met1Leu	Ribosome recycling factor (RRF)
846079	100	T > A	4	FPSM_00743	Phe98Tyr	Putative membrane spanning protein
856484	85.7	T > A	7	FPSM_00754	Met13Leu	Hypothetical protein
1334056	100	A > C	39	FPSM_01204	Phe470Cys	Glucose/galactose transporter
1480580	80	A > T	5	FPSM_01337	Asn41Ile	Hypothetical protein
1498680	100	T > A	4	FPSM_01353	Asn123Ile	Phosphoribosyl-ATP cyclohydrolase
1522077	80	T > A	5	FPSM_01375	Met1Leu	Protein translation elongation factor P (EF-P)
1537329	100	C > G	51	FPSM_01388	Arg547Thr	TonB-dependent outer membrane receptor

^aReference position (in bp) for reference sequence (listed under annotation field) are based on CSF 259–93 sequence from ERGO-Integrated genomics
^bAllele frequency refers to the proportion of sequences showing a given single-nucleotide polymorphism (SNP) at the started reference position
^cShows the SNP change represents the change from nucleotide X to Y (X > Y) at the reference position
^dCoverage refers to the total number of sequencing reads that align to each base within the sample DNA
^ePredicted amino acid change for the identified SNP
^fAnnotation shows the name and putative function for the identified gene. Annotation is presented from the CSF 259–93 sequence from ERGO-Integrated genomics

ISSN: 1471-2180