breseq  version 0.39.0  
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
RA 92,790 C→T P460S (CCG→TCG)  ftsI → peptidoglycan DD‑transpeptidase FtsI
RA 124,445 C→T P477S (CCG→TCG)  aceE → pyruvate dehydrogenase E1 component
RA 238,884 G→A intergenic (‑148/+535) ykfM ← / ← yafV uncharacterized protein YkfM/2‑oxoglutaramate amidase
RA 239,930 G→A S87F (TCT→TTT)  yafV ← 2‑oxoglutaramate amidase
RA 243,084 G→A R74C (CGC→TGC)  fadE ← acyl‑CoA dehydrogenase
RA 245,766 G→A P14S (CCG→TCG)  dpaA ← peptidoglycan meso‑diaminopimelic acid protein amidase A
RA 246,747 G→T S12S (TCG→TCT)  yafL → NlpC/P60 family protein YafL
RA 251,604 G→A S236N (AGC→AAC)  dinB → DNA polymerase IV
RA 252,349 G→A E17K (GAA→AAA)  yafO → ribosome‑dependent mRNA interferase toxin YafO
JC JC 252,442 IS5 (–) +4 bp coding (142‑145/399 nt) yafO → ribosome‑dependent mRNA interferase toxin YafO
RA 253,658 C→T intergenic (+497/+601) yafP → / ← pepD putative N‑acetyltransferase YafP/peptidase D
RA 253,835 G→A intergenic (+674/+424) yafP → / ← pepD putative N‑acetyltransferase YafP/peptidase D
RA 266,523 G→A L11L (CTG→TTG)  yafY ← inner membrane lipoprotein YafY
RA 267,149 G→A intergenic (‑596/+35) yafY ← / ← yafZ inner membrane lipoprotein YafY/DUF932 domain‑containing protein YafZ
RA 268,709 G→A R84R (CGC→CGT)  ykfA ← putative GTP‑binding protein YkfA
RA 273,450 G→A A202T (GCG→ACG)  ykfC → PF00078 domain‑containing protein YkfC
RA 273,734 G→A Q296Q (CAG→CAA)  ykfC → PF00078 domain‑containing protein YkfC
RA 274,939 G→A A48V (GCT→GTT)  insH1 ← IS5 family transposase and trans‑activator
RA 274,985 G→A P33S (CCA→TCA)  insH1 ← IS5 family transposase and trans‑activator
RA 275,668 G→A G115E (GGA→GAA)  mmuP → S‑methyl‑L‑methionine transporter
RA 277,277 G→A R188H (CGT→CAT)  mmuM → homocysteine S‑methyltransferase
RA 281,053 T→C T311A (ACG→GCG)  yagA ← integrase core domain‑containing protein YagA
RA 281,778 G→A S69F (TCC→TTC)  yagA ← integrase core domain‑containing protein YagA
RA 284,535 T→G A445A (GCT→GCG)  yagF → D‑xylonate dehydratase
RA 285,966 G→A G191D (GGC→GAC)  yagG → putative D‑xylonate transporter YagG
RA 287,324 G→A G179D (GGC→GAC)  yagH → putative xylosidase/arabinosidase
RA 287,348 G→A G187D (GGC→GAC)  yagH → putative xylosidase/arabinosidase
RA 287,946 G→A W386* (TGG→TGA)  yagH → putative xylosidase/arabinosidase
RA 288,641 G→A A174A (GCC→GCT)  xynR ← DNA‑binding transcriptional repressor XynR
RA 305,439 G→A S460F (TCC→TTC)  ecpD ← fimbrial adhesin EcpD
RA 305,990 G→A I276I (ATC→ATT)  ecpD ← fimbrial adhesin EcpD
RA 308,924 G→A R137C (CGC→TGC)  ecpC ← putative fimbrial usher protein EcpC
RA 313,543 G→A intergenic (‑301/‑1748) ykgR ← / → insE1 putative membrane protein YkgR/IS3 element protein InsE
RA 314,622 G→A intergenic (‑1380/‑669) ykgR ← / → insE1 putative membrane protein YkgR/IS3 element protein InsE
RA 316,519 G→A intergenic (+66/+1207) insF1 → / ← rclC IS3 element protein InsF/DUF417 domain‑containing inner membrane protein RclC
RA 316,837 G→A intergenic (+384/+889) insF1 → / ← rclC IS3 element protein InsF/DUF417 domain‑containing inner membrane protein RclC
RA 320,300 G→A S25N (AGT→AAT)  rclR → DNA‑binding transcriptional activator RclR
RA 328,598 C→T V46I (GTC→ATC)  betB ← betaine aldehyde dehydrogenase
RA 339,376 G→A G351E (GGG→GAG)  yahG → DUF1116 domain‑containing protein YahG
RA 339,935 C→T A56V (GCC→GTC)  yahH → putative uncharacterized protein YahH
RA 339,941 C→T T58I (ACT→ATT)  yahH → putative uncharacterized protein YahH
RA 339,958 G→A D64N (GAC→AAC)  yahH → putative uncharacterized protein YahH
RA 343,442 G→A G187R (GGA→AGA)  yahK → aldehyde reductase, NADPH‑dependent
RA 347,833 G→A A204V (GCC→GTC)  prpR ← DNA‑binding transcriptional dual regulator PrpR
RA 352,850 G→A G49S (GGC→AGC)  prpE → propionyl‑CoA synthetase
RA 353,100 G→A G132D (GGC→GAC)  prpE → propionyl‑CoA synthetase
RA 355,006 G→A G29R (GGA→AGA)  codB → cytosine transporter
RA 355,064 G→A S48N (AGC→AAC)  codB → cytosine transporter
RA 355,229 G→A G103E (GGA→GAA)  codB → cytosine transporter
RA 357,285 G→A G372E (GGA→GAA)  codA → cytosine/isoguanine deaminase
RA 358,368 G→A P108L (CCC→CTC)  cynR ← DNA‑binding transcriptional dual regulator CynR
RA 360,082 G→A G31R (GGA→AGA)  cynX → cyanate transporter
RA 360,536 C→T S182F (TCC→TTC)  cynX → cyanate transporter
RA 360,786 G→A M265I (ATG→ATA)  cynX → cyanate transporter
RA 361,489 G→A N124N (AAC→AAT)  lacA ← galactoside O‑acetyltransferase
RA 364,433 G→A Q625* (CAG→TAG)  lacZ ← beta‑galactosidase
RA 365,146 G→A A387V (GCC→GTC)  lacZ ← beta‑galactosidase
RA 365,222 G→A P362S (CCT→TCT)  lacZ ← beta‑galactosidase
RA 365,959 G→A P116L (CCC→CTC)  lacZ ← beta‑galactosidase
RA 366,121 G→A A62V (GCC→GTC)  lacZ ← beta‑galactosidase
RA 372,529 G→A V139M (GTG→ATG)  mhpD → 2‑hydroxypentadienoate hydratase
RA 373,341 G→A A141T (GCG→ACG)  mhpF → acetaldehyde dehydrogenase (acetylating) MhpF
RA 382,571 G→A E300K (GAA→AAA)  insD1 → IS2 element protein
RA 382,943 G→A C331C (TGC→TGT)  yaiP ← putative glucosyltransferase
RA 384,839 G→A intergenic (‑223/‑393) yaiS ← / → tauA putative deacetylase YaiS/taurine ABC transporter periplasmic binding protein
RA 386,290 G→A E28E (GAG→GAA)  tauB → taurine ABC transporter ATP binding subunit
RA 387,624 G→A E218E (GAG→GAA)  tauC → taurine ABC transporter membrane subunit
RA 398,073 G→A G68R (GGG→AGG)  yaiW → surface‑exposed outer membrane lipoprotein
RA 398,494 G→A G208D (GGC→GAC)  yaiW → surface‑exposed outer membrane lipoprotein
RA 400,495 G→A V143V (GTC→GTT)  ddlA ← D‑alanine‑‑D‑alanine ligase A
RA 403,108 G→A L454L (CTG→CTA)  phoA → alkaline phosphatase
RA 431,516 A→C Y166* (TAT→TAG)  tsx ← nucleoside‑specific channel‑forming protein Tsx
RA 480,295 2 bp→AA coding (13‑14/219 nt) hha ← hemolysin expression‑modulating protein Hha
JC JC 480,334 IS5 (+) +4 bp coding (372‑375/375 nt) tomB ← Hha toxicity modulator TomB
RA 487,935 G→A S467N (AGT→AAT)  mscK → potassium dependent, small conductance mechanosensitive channel
MC JC 575,786 Δ1,438 bp IS5‑mediated [nmpC] [nmpC]
RA 598,429 C→T L317L (CTC→CTT)  cusB → copper/silver export system membrane fusion protein
JC JC 607,765 IS150 (+) +3 bp noncoding (26‑28/60 nt) sokE ← small RNA SokE
RA 640,502 C→A L250L (CTC→CTA)  ahpF → alkyl hydroperoxide reductase, AhpF component
RA 690,948 G→A V279V (GTC→GTT)  ybeX ← CorC‑HlyC family protein YbeX
RA 692,073 C→T R90H (CGT→CAT)  ybeY ← endoribonuclease YbeY
RA 700,038 G→A H97Y (CAT→TAT)  umpH ← UMP phosphatase
RA 809,217 2 bp→AG coding (40‑41/1290 nt) bioA ← adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase
RA 825,490 G→A Q207* (CAG→TAG)  ybhR ← ABC exporter membrane subunit YbhR
RA 923,254 G→A intergenic (+21/‑10) clpS → / → clpA specificity factor for ClpA‑ClpP chaperone‑protease complex/ATP‑dependent Clp protease ATP‑binding subunit ClpA
RA 924,040 Δ1 bp coding (777/2277 nt) clpA → ATP‑dependent Clp protease ATP‑binding subunit ClpA
RA 968,837 G→A D158N (GAT→AAT)  lpxK → tetraacyldisaccharide 4'‑kinase
RA 977,287 G→A G321D (GGT→GAT)  mukB → chromosome partitioning protein MukB
RA 1,000,369 C→T A385V (GCC→GTC)  elfC → putative fimbrial usher protein ElfC
RA 1,018,193 C→T S36N (AGT→AAT)  ycbZ ← putative ATP‑dependent protease YcbZ
RA 1,022,002 C→T E628K (GAG→AAG)  yccS ← putative transporter YccS
RA 1,023,148 C→T D246N (GAT→AAT)  yccS ← putative transporter YccS
RA 1,035,862 C→T A31A (GCC→GCT)  hyaD → putative hydrogenase 1 maturation protease HyaD
RA 1,036,085 C→T L106L (CTG→TTG)  hyaD → putative hydrogenase 1 maturation protease HyaD
RA 1,037,810 C→T P24L (CCC→CTC)  appC → cytochrome bd‑II subunit 1
RA 1,040,126 G→T L277L (CTG→CTT)  appB → cytochrome bd‑II subunit 2
RA 1,043,376 C→T V279M (GTG→ATG)  etk ← protein‑tyrosine kinase Etk
RA 1,061,935 G→A S46N (AGC→AAC)  torD → trimethylamine‑N‑oxide reductase‑specific chaperone
RA 1,070,014 A→G L114P (CTG→CCG)  rutF ← FMN reductase RutF
JC JC 1,090,416 IS2 (–) +5 bp coding (1870‑1874/2424 nt) pgaA ← partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export outer membrane porin
JC JC 1,093,120 IS5 (–) +4 bp coding (245‑248/1359 nt) dgcT → putative diguanylate cyclase DgcT
MC JC 1,095,503 Δ10,047 bp IS3‑mediated ycdU–[ymdA] ycdU, serX, ghrA, ycdX, ycdY, ycdZ, csgG, csgF, csgE, csgD, csgB, csgA, csgC, [ymdA]
RA 1,111,727 2 bp→TT coding (865‑866/2544 nt) opgH → osmoregulated periplasmic glucans biosynthesis protein H
RA 1,150,616 C→T L297L (CTG→TTG)  fabD → [acyl‑carrier‑protein] S‑malonyltransferase
RA 1,169,836 A→G L180P (CTG→CCG)  ldtC ← L,D‑transpeptidase LdtC
RA 1,177,891 G→A G191D (GGT→GAT)  lolE → lipoprotein release complex ‑ inner membrane subunit
RA 1,189,980 A→G T156T (ACT→ACC)  phoP ← DNA‑binding transcriptional dual regulator PhoP
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,247 A→G L375M (TTA→CTG)  icd → isocitrate dehydrogenase
JC JC 1,232,148 IS2 (–) +5 bp coding (963‑967/1269 nt) umuC → DNA polymerase V catalytic protein
RA 1,265,367 C→A T119N (ACC→AAC)  prfA → peptide chain release factor RF1
RA 1,276,230 C→T P463P (CCG→CCA)  narX ← sensor histidine kinase NarX
JC JC 1,301,713 IS30 (–) +2 bp coding (532‑533/1632 nt) oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,301,992 A→T N271Y (AAT→TAT)  oppA → oligopeptide ABC transporter periplasmic binding protein
RA 1,306,736 T→G S325A (TCC→GCC)  oppF → murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF
RA 1,310,770 A→G H32H (CAT→CAC)  yciI ← protein YciI
RA 1,315,384 G→A Y129Y (TAC→TAT)  yciF ← DUF892 domain‑containing protein YciF
RA 1,317,129 G→A Q32* (CAG→TAG)  trpA ← tryptophan synthase subunit alpha
RA 1,322,325 G→A L208F (CTC→TTC)  trpE ← anthranilate synthase subunit TrpE
RA 1,337,394 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
RA 1,356,932 G→A T60I (ACC→ATC)  sapA ← putative periplasmic binding protein SapA
RA 1,357,202 C→T intergenic (‑92/+221) sapA ← / ← ymjA putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA
RA 1,358,859 T→C Y110C (TAT→TGT)  puuP ← putrescine:H(+) symporter PuuP
JC JC 1,360,653 IS3 (–) +3 bp coding (254‑256/1419 nt) puuA ← glutamate‑putrescine ligase
RA 1,362,062 C→A T51K (ACG→AAG)  puuR → DNA‑binding transcriptional repressor PuuR
RA 1,366,433 G→A G295D (GGC→GAC)  puuE → 4‑aminobutyrate aminotransferase PuuE
MC JC 1,382,901 Δ13,143 bp IS5‑mediated ycjW–ynaI ycjW, ycjX, ycjF, tyrR, tpx, ycjG, mpaA, ymjC, ymjD, ycjY, pgrR, mppA, ynaI
RA 1,400,978 C→T G266S (GGT→AGT)  abgT ← p‑aminobenzoyl glutamate:H(+) symporter
RA 1,423,272 2 bp→TA coding (521‑522/561 nt) ydaW → putative uncharacterized protein YdaW
RA 1,423,283 2 bp→CC coding (532‑533/561 nt) ydaW → putative uncharacterized protein YdaW
RA 1,423,338 G→C intergenic (+26/‑62) ydaW → / → rzoR putative uncharacterized protein YdaW/putative prophage outer membrane lipoprotein RzoR
RA 1,423,404 G→T R2L (CGA→CTA)  rzoR → putative prophage outer membrane lipoprotein RzoR
RA 1,429,069 T→A G7G (GGT→GGA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,072 A→C V8V (GTA→GTC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,111 A→C T21T (ACA→ACC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,114 C→T I22I (ATC→ATT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,126 A→C A26A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,128 A→G K27R (AAA→AGA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,160 C→G L38V (CTG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,164 C→G A39G (GCC→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,171 A→G E41E (GAA→GAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,204 C→T D52D (GAC→GAT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,207 T→G V53V (GTT→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,225 C→T S59S (AGC→AGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,228 T→C V60V (GTT→GTC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,231 T→C I61I (ATT→ATC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,235 2 bp→CA coding (187‑188/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,240 G→T V64V (GTG→GTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,243 A→C E65D (GAA→GAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,246 A→T G66G (GGA→GGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,249 C→T F67F (TTC→TTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,252 G→A P68P (CCG→CCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,255 G→A P69P (CCG→CCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,258 A→G S70S (TCA→TCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,261 T→C H71H (CAT→CAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,273 T→C I75I (ATT→ATC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,291 T→A S81S (TCT→TCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,297 C→G P83P (CCC→CCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,300 T→G G84G (GGT→GGG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,319 G→T G91C (GGT→TGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,345 T→G R99R (CGT→CGG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,353 2 bp→TG coding (305‑306/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,360 C→T R104R (CGC→CGT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,364 T→C F106L (TTT→CTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,404 C→T A119V (GCG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,416 2 bp→GT coding (368‑369/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,425 C→A A126D (GCC→GAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,435 G→A K129K (AAG→AAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,442 A→G S132G (AGT→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,444 T→C S132G (AGT→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,453 2 bp→TG coding (405‑406/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,462 3 bp→TGC coding (414‑416/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,466 G→C E140Q (GAG→CAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,470 2 bp→TC coding (422‑423/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,474 2 bp→GG coding (426‑427/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,479 A→T H144L (CAT→CTT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,482 C→T A145V (GCG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,484 G→A A146T (GCT→ACT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,492 2 bp→AA coding (444‑445/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,495 G→T A149A (GCG→GCT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,510 A→C A154A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,522 A→C S158S (TCA→TCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,534 C→T A162A (GCC→GCT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,537 G→A A163A (GCG→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,543 G→A S165S (TCG→TCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,550 2 bp→GA coding (502‑503/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,558 T→C S170S (TCT→TCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,562 A→G S172G (AGC→GGC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,569 G→A G174E (GGA→GAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,571 A→G T175A (ACG→GCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,580 A→G T178A (ACA→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,597 3 bp→GGA coding (549‑551/3363 nt) stfR → putative prophage side tail fiber protein StfR
RA 1,429,609 T→C A187A (GCT→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,612 C→A A188A (GCC→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,615 T→C A189A (GCT→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,632 G→A S195N (AGC→AAC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,682 T→G S212A (TCA→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,692 T→A L215Q (CTA→CAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,702 A→C A218A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,708 A→G T220T (ACA→ACG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,714 A→C A222A (GCA→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,724 A→G T226A (ACC→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,732 G→A K228K (AAG→AAA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,735 A→G A229A (GCA→GCG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,741 A→G E231E (GAA→GAG)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,744 T→C A232A (GCT→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,747 G→C A233A (GCG→GCC)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,750 C→T T234T (ACC→ACT)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,753 G→A S235S (TCG→TCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,756 C→A A236A (GCC→GCA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,759 G→A R237R (CGG→CGA)  stfR → putative prophage side tail fiber protein StfR
RA 1,429,767 C→T A240V (GCG→GTG)  stfR → putative prophage side tail fiber protein StfR
RA 1,501,192 C→T P207L (CCT→CTT)  tehA → tellurite resistance protein
JC JC 1,590,457 IS2 (+) +5 bp intergenic (‑456/+393) ydeT ← / ← hipA fimbrial usher domain‑containing protein YdeT/serine/threonine‑protein kinase toxin HipA
RA 1,610,076 T→G D202A (GAT→GCT)  uxaB ← tagaturonate reductase
RA 1,643,679 A→T L209Q (CTG→CAG)  ydfU ← protein YdfU
RA 1,652,331 T→C intergenic (+2346/+397) ydfD → / ← ynfP lysis protein/protein YnfP
RA 1,721,136 C→T L38F (CTT→TTT)  ydhI → DUF1656 domain‑containing protein YdhI
RA 1,776,715 A→T S377C (AGT→TGT)  ydiF → putative acetate‑CoA transferase YdiF
MC JC 1,867,696 Δ7 bp coding (789‑795/1935 nt) yeaG → protein kinase YeaG
RA 1,894,839 T→C L12P (CTC→CCC)  pabB → aminodeoxychorismate synthase subunit 1
JC JC 1,907,451 IS2 (+) +5 bp coding (137‑141/144 nt) yobF ← DUF2527 domain‑containing protein YobF
RA 1,987,499 C→A intergenic (+71/+8) ftnB → / ← yecJ putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ
RA 2,027,288 C→T V244I (GTA→ATA)  dgcQ ← diguanylate cyclase DgcQ
RA 2,040,433 C→A A319D (GCC→GAC)  msrP → protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP
MC JC 2,102,944 Δ1,424 bp IS5‑mediated [wbbL]–[wbbK] [wbbL], [wbbK]
RA 2,188,087 T→C T110A (ACG→GCG)  yehA ← putative fimbrial adhesin YehA
RA 2,195,035 G→A A246T (GCG→ACG)  metG → methionine‑‑tRNA ligase
RA 2,384,808 C→T K305K (AAG→AAA)  yfbK ← IPR002035/DUF3520 domain‑containing protein YfbK
RA 2,410,419 G→A L312L (CTG→TTG)  yfbS ← putative transporter YfbS
RA 2,484,827 C→T L152F (CTT→TTT)  evgS → sensor histidine kinase EvgS
MC JC 2,558,699 Δ6,790 bp intZ–[eutA] intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA]
RA 2,572,542 G→A P322S (CCG→TCG)  eutD ← phosphate acetyltransferase EutD
RA 2,623,776 G→A E245K (GAG→AAG)  ppk → polyphosphate kinase
JC JC 2,737,689 IS150 (+) +3 bp intergenic (+43/‑54) pheL → / → pheA phe operon leader peptide/fused chorismate mutase/prephenate dehydratase
JC JC 2,913,392 IS2 (–) +5 bp coding (256‑260/2235 nt) relA ← GDP/GTP pyrophosphokinase
RA 2,926,292 C→T intergenic (+96/‑16) queF → / → ppnN 7‑cyano‑7‑deazaguanine reductase/nucleotide 5'‑monophosphate nucleosidase
RA 2,942,462 C→A A36S (GCA→TCA)  gcvA ← DNA‑binding transcriptional dual regulator GcvA
RA 2,991,238 G→T intergenic (‑878/‑30) yqeK ← / → ygeG protein YqeK/TPR repeat‑containing putative chaperone YgeG
RA 3,088,010 2 bp→TT intergenic (+150/‑273) metK → / → galP methionine adenosyltransferase/galactose:H(+) symporter
JC JC 3,262,484 IS5 (+) +4 bp coding (1174‑1177/1209 nt) tdcD ← propionate kinase
JC JC 3,308,963 IS150 (–) +3 bp intergenic (‑39/+68) nlpI ← / ← pnp lipoprotein NlpI/polynucleotide phosphorylase
RA 3,336,411 2 bp→AT coding (83‑84/1260 nt) murA ← UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase
RA 3,388,041 T→G T50P (ACG→CCG)  aaeB ← aromatic carboxylic acid efflux pump subunit AaeB
RA 3,436,697 G→A E60E (GAG→GAA)  trkA → NAD‑binding component of Trk potassium transporters
RA 3,474,425 T→C K43R (AAA→AGA)  rpsL ← 30S ribosomal subunit protein S12
RA 3,560,455 +G intergenic (+589/+167) rtcR → / ← glpG DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG
RA 3,629,921 C→T E228K (GAG→AAG)  yhiI ← putative membrane fusion protein YhiI
RA 3,682,515 C→T M311I (ATG→ATA)  dctA ← C4 dicarboxylate/orotate:H(+) symporter
RA 3,707,947 C→A intergenic (‑242/+669) dppA ← / ← proK dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro
MC JC 3,708,467 Δ168 bp [proK] [proK]
RA 3,725,176 T→G E48A (GAG→GCG)  glyQ ← glycine‑‑tRNA ligase subunit alpha
RA 3,761,230 G→A S7F (TCC→TTC)  selA ← selenocysteine synthase
RA 3,771,979 G→T intergenic (‑235/‑302) yibI ← / → mtlA DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
JC 3,822,651 (CAGGAT)1→2 coding (252/2109 nt) spoT → bifunctional (p)ppGpp synthase/hydrolase SpoT
RA 3,823,162 C→T H255Y (CAC→TAC)  spoT → bifunctional (p)ppGpp synthase/hydrolase SpoT
RA 3,869,637 C→A L87L (CTC→CTA)  cbrA → colicin M resistance protein
RA 3,878,536 G→A Y528Y (TAC→TAT)  gyrB ← DNA gyrase subunit B
RA 3,893,688 G→A R308R (CGG→CGA)  yidZ → DNA‑binding transcriptional dual regulator YidZ
RA 3,905,403 G→A N65N (AAC→AAT)  bglF ← beta‑glucoside specific PTS enzyme II/BglG kinase/BglG phosphatase
RA 3,910,111 G→A I96I (ATC→ATT)  pstC ← phosphate ABC transporter membrane subunit PstC
RA 3,912,074 G→A S532F (TCC→TTC)  glmS ← L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase
RA 3,922,092 G→A L117L (CTG→TTG)  atpI ← ATP synthase accessory factor AtpI
RA 3,927,335 G→A A61T (GCT→ACT)  asnA → asparagine synthetase A
RA 3,935,468 G→A V61I (GTC→ATC)  rbsC → ribose ABC transporter membrane subunit
RA 3,935,970 G→A G228D (GGT→GAT)  rbsC → ribose ABC transporter membrane subunit
RA 3,940,141 G→A L158L (CTG→TTG)  hsrA ← putative transporter HsrA
RA 3,950,110 G→A intergenic (‑141/‑212) yifB ← / → ilvL putative magnesium chelatase YifB/ilvXGMEDA operon leader peptide
RA 3,951,022 G→A intergenic (+465/‑1179) ilvX → / → ilvM uncharacterized protein IlvX/acetolactate synthase II subunit IlvM
RA 3,957,469 G→A P118S (CCG→TCG)  ilvY ← DNA‑binding transcriptional dual regulator IlvY
RA 3,961,045 G→A G123G (GGG→GGA)  rep → ATP‑dependent DNA helicase Rep
RA 3,968,491 G→A M192I (ATG→ATA)  rfe → UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase
RA 3,968,779 G→A G288G (GGG→GGA)  rfe → UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase
RA 3,973,964 G→A K119K (AAG→AAA)  rffH → glucose‑1‑phosphate thymidylyltransferase 2
RA 3,977,523 G→A A416T (GCA→ACA)  wzxE → lipid IIIECA flippase
RA 3,981,562 G→A A226T (GCG→ACG)  yifK → putative transporter YifK
RA 3,983,108 G→A E51K (GAA→AAA)  aslB → putative anaerobic sulfatase maturation enzyme AslB
RA 3,986,929 G→A R318R (CGC→CGT)  hemY ← protein HemY
RA 3,993,531 T→C R793R (CGT→CGC)  cyaA → adenylate cyclase
RA 3,993,988 C→T W24* (TGG→TGA) 
P47S (CCA→TCA) 		 cyaY ←
yzcX →		 frataxin CyaY
protein YzcX
RA 3,996,049 T→A L156* (TTG→TAG)  yigA → DUF484 domain‑containing protein YigA
RA 4,011,227 G→A G51D (GGC→GAC)  bioP → biotin transporter
RA 4,011,802 C→T P243S (CCG→TCG)  bioP → biotin transporter
RA 4,034,648 2 bp→GT coding (41‑42/546 nt) hemG → protoporphyrinogen oxidase
RA 4,050,879 G→A intergenic (‑114/‑157) yihA ← / → csrC GTP‑binding protein YihA/small regulatory RNA CsrC
RA 4,084,903 T→G N307T (AAC→ACC)  fdoG ← formate dehydrogenase O subunit alpha
RA 4,086,109 C→T P32S (CCA→TCA)  fdhD → sulfurtransferase for molybdenum cofactor sulfuration
RA 4,092,703 A→G F41L (TTC→CTC)  frvA ← putative PTS enzyme IIA component FrvA
RA 4,113,851 G→A H208Y (CAT→TAT)  fpr ← flavodoxin/ferredoxin‑NADP(+) reductase
RA 4,123,923 +A coding (534/1026 nt) cytR ← DNA‑binding transcriptional repressor CytR
RA 4,143,377 C→T S283L (TCA→TTA)  frwC → putative PTS enzyme IIC component FrwC
RA 4,161,248 G→T G61V (GGC→GTC)  fabR → DNA‑binding transcriptional repressor FabR
RA 4,164,123 C→G A162G (GCA→GGA)  btuB → cobalamin outer membrane transporter
RA 4,164,339 2 bp→AT coding (701‑702/1845 nt) btuB → cobalamin outer membrane transporter
RA 4,172,010 C→T intergenic (+254/‑47) rrfB → / → murB 5S ribosomal RNA/UDP‑N‑acetylenolpyruvoylglucosamine reductase
RA 4,175,988 C→T V15V (GTC→GTT)  tufB → translation elongation factor Tu 2
RA 4,176,012 T→C H23H (CAT→CAC)  tufB → translation elongation factor Tu 2
RA 4,176,021 A→T T26T (ACA→ACT)  tufB → translation elongation factor Tu 2
RA 4,176,024 G→T T27T (ACG→ACT)  tufB → translation elongation factor Tu 2
RA 4,176,042 T→C T33T (ACT→ACC)  tufB → translation elongation factor Tu 2
RA 4,204,268 G→A E317K (GAA→AAA)  zraR → DNA‑binding transcriptional activator ZraR
RA 4,215,347 T→A intergenic (+138/‑131) metA → / → aceB homoserine O‑succinyltransferase/malate synthase A
RA 4,223,638 T→C intergenic (‑10/‑190) iclR ← / → metH DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase
RA 4,282,332 (A)5→6 coding (744/1293 nt) yjcF ← pentapeptide repeat‑containing protein YjcF
RA 4,290,473 C→T S222S (AGC→AGT)  nrfC → putative menaquinol‑cytochrome c reductase 4Fe‑4S subunit
RA 4,293,781 2 bp→AT coding (239‑240/597 nt) nrfG → putative formate‑dependent nitrite reductase complex subunit NrfG
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,325,644 C→T S33N (AGC→AAC)  yjdN ← PF06983 family protein YjdN
RA 4,348,150 C→T D199N (GAT→AAT)  dcuB ← anaerobic C4‑dicarboxylate transporter DcuB
JC JC 4,349,151 IS2 (+) +5 bp intergenic (‑407/+160) dcuB ← / ← dcuR anaerobic C4‑dicarboxylate transporter DcuB/DNA‑binding transcriptional activator DcuR
RA 4,355,811 C→T A201T (GCG→ACG)  dtpC ← dipeptide/tripeptide:H(+) symporter DtpC
RA 4,357,484 G→A I378I (ATC→ATT)  cadA ← lysine decarboxylase 1
RA 4,359,224 C→T A270T (GCT→ACT)  cadB ← lysine:cadaverine antiporter
RA 4,367,656 C→T L224L (CTG→CTA)  aspA ← aspartate ammonia‑lyase
RA 4,378,077 G→A L290L (CTG→TTG)  ampC ← beta‑lactamase
RA 4,392,997 G→A V357V (GTC→GTT)  queG ← epoxyqueuosine reductase
RA 4,393,552 G→A F172F (TTC→TTT)  queG ← epoxyqueuosine reductase
RA 4,396,373 C→T T103T (ACC→ACT)  amiB → N‑acetylmuramoyl‑L‑alanine amidase B
RA 4,396,772 T→C F236F (TTT→TTC)  amiB → N‑acetylmuramoyl‑L‑alanine amidase B
RA 4,399,720 G→A A157T (GCA→ACA)  miaA → tRNA dimethylallyltransferase
RA 4,400,133 G→A W294* (TGG→TGA)  miaA → tRNA dimethylallyltransferase
RA 4,425,688 C→A H57N (CAC→AAC)  priB → primosomal replication protein N
RA 4,425,696 C→A N59K (AAC→AAA)  priB → primosomal replication protein N
RA 4,448,633 G→A A63T (GCC→ACC)  chpS → ChpS antitoxin of the ChpB‑ChpS toxin‑antitoxin system
RA 4,499,661 T→C intergenic (+161/‑1599) insD6 → / → yjgZ IS2 insertion element protein InsB/uncharacterized protein YjgZ
RA 4,510,238 T→G intergenic (+445/+452) insO → / ← fecE IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit
RA 4,519,173 G→A intergenic (+371/+165) insA7 → / ← yjhU IS1 family repressor protein InsA/putative DNA‑binding transcriptional regulator YjhU
RA 4,532,409 T→G intergenic (‑758/+28) sgcX ← / ← yjhP putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP
JC JC 4,542,448 IS5 (–) +4 bp coding (412‑415/597 nt) fimE → regulator for fimA
RA 4,546,601 C→T I502I (ATC→ATT)  fimD → type I fimbriae usher protein
JC JC 4,630,718 IS5 (–) +4 bp intergenic (‑196/‑12) ettA ← / → slt energy‑dependent translational throttle protein EttA/soluble lytic murein transglycosylase
RA 4,636,925 G→C R77P (CGC→CCC)  creC → sensory histidine kinase CreC
RA 4,638,240 G→A L21L (TTG→TTA)  creD → putative inner membrane protein CreD

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 257823 258675–257908 86–853 141 [0] [0] 113 crl–insA9 crl,insB9,insA9
* * ÷ NC_000913 1196266 1211433 15168 39 [34] [36] 37 [icd]–mcrA [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA
* * ÷ NC_000913 1411925 1423254 11330 123 [0] [36] 37 [ttcA]–[ydaW] [ttcA],intR,xisR,rcbA,ralA,ralR,recT,recE,racC,ydaE,kilR,kilS,sieB,ydaF,ydaG,racR,ydaS,ydaT,ydaU,ydaV,[ydaW]
* * ÷ NC_000913 1423487–1423567 1429054 5488–5568 38 [36] [36] 37 [rzoR]–[stfR] [rzoR],trkG,ynaK,ydaY,ynaA,lomR,insH5,lomR,[stfR]
* * ÷ NC_000913 1429777 1434984 5208 38 [36] [12] 135 [stfR]–ynaM [stfR],tfaR,pinR,ynaE,ynaM
* * ÷ NC_000913 1978495 1979270–1978503 9–776 106 [0] [1] 142 insB5–insA5 insB5,insA5
* * ÷ NC_000913 2170322–2171427 2175000 3574–4679 39 [36] [0] 92 [insE5]–[gatA] [insE5],insF5,gatR,gatD,gatB,[gatA]
* * ÷ NC_000913 3423766–3424234 3424551–3424238 5–786 37 [34] [35] 37 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 2578220 (0.000)137 (1.280) 80/598 0.1 100% intergenic (+51/‑7) frsA/crl fermentation‑respiration switch protein/RNA polymerase holoenzyme assembly factor Crl
?NC_000913 = 382590 NA (NA)noncoding (1331/1331 nt) IS2 repeat region
* ? NC_000913 258676 =0 (0.000)81 (1.040)
+81 bp		 58/436 0.1 100% pseudogene (1/331 nt) crl RNA polymerase holoenzyme assembly factor Crl
?NC_000913 = 1469241 NA (NA)intergenic (‑92/‑5) insC2/ydbA IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment
* ? NC_000913 = 498521109 (1.020)78 (0.730) 51/598 0.8 41.5% coding (467/963 nt) hemH ferrochelatase
?NC_000913 498928 = 111 (1.040)coding (874/963 nt) hemH ferrochelatase
* ? NC_000913 = 56677492 (0.860)64 (0.600) 31/594 2.5 38.5% pseudogene (91/93 nt) renD protein RenD
?NC_000913 568036 = 113 (1.060)pseudogene (2/213 nt) renD protein RenD
* ? NC_000913 = 12994980 (0.000)134 (1.270) 78/590 0.1 100% intergenic (+253/‑69) ychE/insH21 MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 = 1397238NA (NA)105 (0.980) 75/598 0.1 100% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 1978494 0 (0.000)intergenic (‑297/+24) flhD/insB5 DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB
* ? NC_000913 = 14119240 (0.000)123 (1.260) 73/546 0.1 100% coding (25/936 nt) ttcA tRNA cytosine(32) 2‑sulfurtransferase TtcA
?NC_000913 1434985 = 0 (0.000)intergenic (‑579/+200) ynaM/uspF protein YnaM/universal stress protein F
* ? NC_000913 1979271 =1 (0.010)142 (1.330) 87/598 0.0 99.3% intergenic (‑56/‑482) insA5/uspC IS1 family protein InsA/universal stress protein C
?NC_000913 = 2102947 NA (NA)pseudogene (443/446 nt) wbbL interrupted rhamnosyltransferase WbbL
* ? NC_000913 = 2102943NA (NA)123 (1.150) 80/598 0.1 99.2% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 2151151 = 1 (0.010)intergenic (‑166/‑34) yegI/yegJ putative serine/threonine‑protein kinase YegI/DUF2314 domain‑containing protein YegJ
* ? NC_000913 = 21511544 (0.040)122 (1.140) 74/598 0.1 96.8% intergenic (‑169/‑31) yegI/yegJ putative serine/threonine‑protein kinase YegI/DUF2314 domain‑containing protein YegJ
?NC_000913 = 2290113 NA (NA)noncoding (1/1195 nt) IS5 repeat region
* ? NC_000913 = 2170611NA (NA)92 (0.870) 69/594 0.2 100% noncoding (441/1258 nt) IS3 repeat region
?NC_000913 2175001 = 0 (0.000)coding (49/453 nt) gatA galactitol‑specific PTS enzyme IIA component