breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 12,125 A→C intergenic (‑339/‑38) yaaI ← / → dnaK DUF2541 family protein/molecular chaperone DnaK
RA 44,049 A→G I288V (ATC→GTC)  fixB → electron transfer flavoprotein subunit alpha/FixB family protein
RA 100,843 T→C H125H (CAT→CAC ftsA → cell division protein FtsA
RA 136,175 T→C E513G (GAA→GGA)  gcd ← quinoprotein glucose dehydrogenase
RA 232,843 T→C I97T (ATC→ACC)  dnaQ → DNA polymerase III subunit epsilon
RA 245,728 A→G pseudogene (830/1713 nt) BW25113_RS01160 ← flagellar biosynthesis protein FlhA
RA 258,435 A→G I408V (ATC→GTC)  proA → glutamate‑5‑semialdehyde dehydrogenase
RA 392,218 T→C S42P (TCC→CCC)  sbmA → peptide antibiotic transporter SbmA
RA 427,262 A→C F70V (TTC→GTC)  tsx ← nucleoside‑specific channel‑forming protein Tsx
RA 444,604 T→C A498A (GCA→GCG cyoB ← cytochrome o ubiquinol oxidase subunit I
RA 450,563 G→A intergenic (+318/‑26) bolA → / → tig transcriptional regulator BolA/trigger factor
RA 454,444 A→G E34G (GAA→GGA)  lon → endopeptidase La
RA 500,156 A→G intergenic (‑4/‑214) fsr ← / → ushA fosmidomycin MFS transporter/bifunctional UDP‑sugar hydrolase/5'‑nucleotidase
RA 538,997 T→C D169G (GAT→GGT)  allE ← (S)‑ureidoglycine aminohydrolase
RA 656,002 T→C E278G (GAA→GGA)  ybeF ← YbeF family transcriptional regulator
RA 710,687 T→C intergenic (+33/‑181) pgm → / → BW25113_RS03560 phosphoglucomutase (alpha‑D‑glucose‑1,6‑bisphosphate‑dependent)/lipoprotein
RA 797,607 A→C T89P (ACC→CCC)  ybhI → anion permease
RA 838,798 A→G V713V (GTT→GTC ybiO ← mechanosensitive channel protein
RA 847,509 T→C D182G (GAT→GGT)  opgE ← phosphoethanolamine transferase
RA 933,331 T→C D168D (GAT→GAC lolA → outer membrane lipoprotein chaperone LolA
RA 989,508 C→G A261P (GCC→CCC)  ssuC ← aliphatic sulfonate ABC transporter permease SsuC
RA 1,015,359 T→C T51A (ACC→GCC)  ompA ← porin OmpA
RA 1,056,010 T→C I433I (ATT→ATC torA → trimethylamine‑N‑oxide reductase TorA
RA 1,067,094 A→G V43A (GTC→GCC)  rutD ← pyrimidine utilization protein D
RA 1,077,067 T→C pseudogene (256/830 nt) BW25113_RS05295 → FTR1 family protein
RA 1,084,094 T→C D407G (GAT→GGT)  pgaB ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase PgaB
RA 1,185,332 T→A D191V (GAT→GTT)  phoP ← two‑component system response regulator PhoP
RA 1,201,334 T→C pseudogene (148/408 nt) BW25113_RS05975 → phage portal protein
RA 1,343,839 T→C T176A (ACA→GCA)  yciW ← CMD domain‑containing protein
RA 1,364,361 T→C intergenic (+101/‑112) pspE → / → ycjM thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase
RA 1,393,322 A→T D154E (GAT→GAA fnr ← fumarate/nitrate reduction transcriptional regulator Fnr
RA 1,443,321 (T)7→6 intergenic (+46/+12) feaB → / ← tynA phenylacetaldehyde dehydrogenase/primary‑amine oxidase
RA 1,473,944 (G)6→7 coding (550/1758 nt) ynbC → bifunctional alpha/beta hydrolase/class I SAM‑dependent methyltransferase
RA 1,494,141 A→G F189S (TTT→TCT)  ydcK ← YdcK family protein
RA 1,749,862 A→C H37P (CAC→CCC)  BW25113_RS26160 → protein YnhH
RA 1,759,822 A→G F23S (TTC→TCC)  menI ← 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase
RA 1,764,071 A→G L247L (TTA→TTG ydiK → AI‑2E family transporter YdiK
RA 1,841,981 (C)6→5 coding (285/1044 nt) selD ← selenide, water dikinase SelD
RA 1,907,320 A→G F585S (TTC→TCC)  prc ← carboxy terminal‑processing peptidase
RA 1,943,712 T→G E356D (GAA→GAC aspS ← aspartate‑‑tRNA ligase
RA 2,090,333 A→G D80G (GAC→GGC)  hisIE → bifunctional phosphoribosyl‑AMP cyclohydrolase/phosphoribosyl‑ATP diphosphatase HisIE
MC JC 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA
RA 2,449,226 A→G intergenic (‑101/+580) yfcV ← / ← sixA fimbrial protein/phosphohistidine phosphatase SixA
RA 2,495,699 A→G S756P (TCC→CCC)  ptsP ← phosphoenolpyruvate‑‑protein phosphotransferase
RA 2,545,923 A→G G71G (GGA→GGG amiA → N‑acetylmuramoyl‑L‑alanine amidase AmiA
RA 2,549,285 T→G T159P (ACC→CCC)  eutL ← ethanolamine utilization microcompartment protein EutL
RA 2,550,898 T→C I381V (ATC→GTC)  eutB ← ethanolamine ammonia‑lyase subunit alpha
RA 2,769,064 A→G pseudogene (74/185 nt) BW25113_RS24190 → DUF905 domain‑containing protein
RA 2,929,425 C→T R161R (CGC→CGT fucI → L‑fucose isomerase
RA 2,968,720 T→C G218G (GGA→GGG aas ← bifunctional acyl‑ACP‑‑phospholipid O‑acyltransferase/long‑chain‑fatty‑acid‑‑ACP ligase
RA 2,972,615 A→G D79G (GAT→GGT)  lysR → DNA‑binding transcriptional regulator LysR
RA 3,095,787 A→G F142S (TTC→TCC)  trmB ← tRNA (guanosine(46)‑N7)‑methyltransferase TrmB
RA 3,255,828 +G coding (1192/1209 nt) tdcD ← propionate kinase
RA 3,427,745 A→G E58G (GAA→GGA)  fmt → methionyl‑tRNA formyltransferase
RA 3,620,259 A→T D880E (GAT→GAA rbbA ← ribosome‑associated ATPase/putative transporter RbbA
RA 3,736,824 A→G A244A (GCA→GCG yiaK → 3‑dehydro‑L‑gulonate 2‑dehydrogenase
RA 3,758,726 G→C A1062P (GCC→CCC)  rhsA → RHS element protein RhsA
RA 3,845,141 A→G I335T (ATC→ACC)  ilvB ← acetolactate synthase large subunit
RA 3,935,432 G→A noncoding (265/1542 nt) BW25113_RS19520 → 16S ribosomal RNA
RA 4,004,376 T→C intergenic (+16/‑60) yigL → / → bioP sugar/pyridoxal phosphate phosphatase YigL/biotin transporter
RA 4,006,495 C→G A28G (GCG→GGG)  metE → 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase
RA 4,087,432 A→G intergenic (‑82/‑232) rhaD ← / → rhaS rhamnulose‑1‑phosphate aldolase/HTH‑type transcriptional activator RhaS
RA 4,258,591 (T)6→5 intergenic (+356/+146) tyrB → / ← BW25113_RS26020 aromatic amino acid transaminase/hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 356981 357567 587 4 [0] [0] 3 lacA galactoside O‑acetyltransferase
* * ÷ NZ_CP009273 2505244 2505302 59 3 [2] [2] 3 mntH Nramp family divalent metal transporter

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 360104 =NA (NA)47 (1.330) 26/164 0.2 NA intergenic (‑35/+251) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
?NZ_CP009273 = 360286 NA (NA)intergenic (‑217/+69) lacZ/BW25113_RS23320 beta‑galactosidase/relaxase/mobilization nuclease domain‑containing protein
* ? NZ_CP009273 = 1391494NA (NA)23 (0.660) 12/162 1.0 79.5% intergenic (+145/‑128) BW25113_RS06980/ynaJ IS5‑like element IS5 family transposase/DUF2534 family protein
?NZ_CP009273 1972747 = 6 (0.170)intergenic (‑293/‑487) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
* ? NZ_CP009273 = 19727510 (0.000)52 (1.470) 33/164 0.1 100% intergenic (‑297/‑483) flhD/uspC flagellar transcriptional regulator FlhD/universal stress protein UspC
?NZ_CP009273 = 2283592 NA (NA)intergenic (‑68/‑387) BW25113_RS11435/narP IS5‑like element IS5 family transposase/nitrate/nitrite response regulator protein NarP
* ? NZ_CP009273 = 453250720 (0.570)12 (0.380) 7/146 1.5 34.4% intergenic (+57/‑425) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA
?NZ_CP009273 = 4532803 28 (0.890)intergenic (+353/‑129) fimE/fimA type 1 fimbria switch DNA invertase FimE/type 1 fimbrial major subunit FimA