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. 2015 Sep 16;15:179. doi: 10.1186/s12866-015-0518-1

Table 4.

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

Reference positiona Allele frequency (in %)b SNPc Coveraged Annotatione Amino acid changee Gene/Proteinf
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