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

BMC Microbiology

Table 6 Single nucleotide polymorphisms (SNPs) from F. psychrophilum CSF 259–93 strain passaged with rifampicin (CR)

Reference position^a	Allele frequency (in %)^b	SNP^c	Coverage^d	Annotation^e	Amino acid change^e	Gene/Protein^f
575838	100	C > G	71	FPSM_00502	Val638Leu	Ribonucleoside-diphosphate reductase large chain (nrdA)
824811	94	A > G	50	FPSM_00723	Ile62Thr	GTP-binding protein YihA
1327825	100	G > A	138	FPSM_01200	Asp275Val	Hypothetical protein
2111614	81.9	C > A	144	FPSM_01917	Thr365Lys	Phytoene desaturase (crtI)
2319546	98.8	G > A	167	FPSM_02089	Ser492Phe	DNA-directed RNA polymerase beta chain RpoB
2606236	100	G > T	73	FPSM_02361	Trp4Leu	Putative membrane spanning protein
2606399	100	A > T	65	FPSM_02361	Leu16Phe	Putative membrane spanning protein
2788973	97.1	T > A	105	FPSM_02533	Ile35Phe	Transcriptional regulator, TetR family

^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