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

BMC Microbiology

Table 3 Analysis of single nucleotide polymorphisms (SNPs) from F. psychrophilum CSF 259–93 used in our laboratory

Reference position^a	Allele frequency (in %)^b	SNP^c	Coverage^d	Annotation^e	Amino acid change^e	Gene/Protein^f
721449	100	C > A	72	FPSM_00632	Gly111Trp	Hypothetical protein
742016	100	A > G	70	FPSM_00646	Ser615Gly	Type II restriction-modification system methylation subunit
899151	100	C > A	84	FPSM_00800	Phe215Leu	RmuC family protein
899152	100	G > A	92	FPSM_00800	Gly216Glu
921140	96.7	C > A	90	FPSM_00823	Pro254Thr	Hypothetical protein (similar to FP1973-GldK gliding motility protein)
1257208	100	C > G	98	FPSM_01126	Trp148Ser	Putative membrane spanning protein
1333946	97.7	A > T	43	FPSM_01204	Phe507Ile	Glucose/galactose transporter
1334321	98.7	A > C	78	FPSM_01204	Tyr382Asp
1387849	95.1	T > G	61	FPSM_01258	Leu133Arg	Phage related protein
1387851	100	T > G	99	FPSM_01258	Tyr134Asn
1537329	98.7	C > G	75	FPSM_01388	Arg547Thr	TonB-dependent outer membrane receptor
1630279	92	A > C	25	FPSM_01473	Thr160Pro	Transposase
1664395	100	C > G	81	FPSM_01493	Val213Leu	Cation efflux system plasma membrane protein (similar to FP0880 – probable multidrug resistance protein precursor AcrB/D/F family)
1664410	99	G > C	96	FPSM_01493	Pro208Ala
1970401	97.4	T > C	116	FPSM_01788	Ser383Gly	Von Willebrand factor type A domain protein (FP0550 – yfbK probable outer membrane protein precursor)
1970443	100	C > T	122	FPSM_01788	Asp369Asn
2066236	100	C > A	76	FPSM_01870	His300Asn	Hypothetical protein
2514049	98.5	C > G	130	FPSM_02290	Leu293Val	3-oxoacyl-(acyl carrier-protein) synthase III (FP1374 fabH1)
2737510	100	C > G	119	FPSM_02485	Leu163Phe	tRNA pseudouridine synthase B (FP2357 truB)

^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

ISSN: 1471-2180