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

Predicted mutations
evidence position mutation freq annotation gene description
RA 88,049 G→T 13.4% P50P (CCG→CCT)  ftsI → transpeptidase involved in septal peptidoglycan synthesis (penicillin‑binding protein 3)
RA 130,455 Δ1 bp 11.8% coding (2354/2598 nt) acnB → bifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase
RA 352,772 G→A 10.8% T297T (ACG→ACA)  codA → cytosine/isoguanine deaminase
RA 477,958 C→A 100% W634C (TGG→TGT)  acrB ← multidrug efflux system protein
JC JC 481,667 IS1 (–) +9 bp 100% coding (451‑459/648 nt) acrR → transcriptional repressor
RA 512,167 G→T 12.1% A43A (GCG→GCT)  fetB → iron exporter permease subunit, ABC transporter FetAB; peroxide resistance protein
RA 774,634 G→T 17.1% G38C (GGT→TGT)  pal → peptidoglycan‑associated outer membrane lipoprotein
RA 879,117 C→A 100% intergenic (‑273/‑12) ybjG ← / → mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
RA 1,098,628 G→T 16.0% H9N (CAT→AAT)  csgD ← csgBAC operon transcriptional regulator
RA 1,285,744:1 +G 100% coding (47/1014 nt) rssB → PcnB‑degradosome interaction factor; response regulator
RA 1,389,706 C→A 20.8% M158I (ATG→ATT)  ynaI ← mechanosensitive channel protein, very small conductance
RA 1,458,375 G→T 25.3% E194* (GAA→TAA)  paaX → transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer
RA 1,472,568 Δ1 bp 14.8% coding (86/897 nt) ynbB → putative CDP‑diglyceride synthase
RA 1,514,467 T→C 10.6% intergenic (+146/‑52) curA → / → mcbR curcumin/dihydrocurcumin reductase, NADPH‑dependent/colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled
MC JC 1,613,357 Δ20 bp 100% intergenic (‑192/‑1) marC ← / → marR UPF0056 family inner membrane protein/transcriptional repressor of multiple antibiotic resistance
RA 1,649,631 G→T 14.4% I100I (ATC→ATA)  ynfA ← UPF0060 family inner membrane protein
RA 1,847,184 C→A 12.9% A351A (GCG→GCT)  ydjE ← putative transporter
RA 2,022,234 C→A 12.1% W205L (TGG→TTG)  yedI ← DUF808 family inner membrane protein
RA 2,128,324 G→T 12.6% A270A (GCC→GCA)  wzc ← colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase
RA 2,245,742 G→T 14.5% A188A (GCG→GCT)  yeiI → putative kinase
RA 2,482,690 G→C 11.5% intergenic (‑43/+31) yfdE ← / ← yfdV acetyl‑CoA:oxalate CoA‑transferase/putative transporter
RA 2,501,687 G→T 11.5% P12Q (CCG→CAG)  fryB ← putative enzyme IIB component of PTS
RA 2,752,380 C→A 15.4% P13T (CCT→ACT)  yfjI → CP4‑57 prophage; uncharacterized protein
RA 3,010,901 C→A 13.9% L495M (CTG→ATG)  ygfK → putative Fe‑S subunit oxidoreductase subunit
RA 3,055,107 C→A 11.5% A300E (GCG→GAG)  scpA → methylmalonyl‑CoA mutase
RA 3,160,274 C→A 12.2% P268P (CCG→CCT)  ygiS ← putative inner membrane ABC superfamily transporter permease
RA 3,256,708 G→T 21.0% V104V (GTC→GTA)  tdcD ← propionate kinase/acetate kinase C, anaerobic
RA 3,880,370 G→T 18.1% Q61H (CAG→CAT)  mnmE → tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA 3,968,096 G→T 11.2% E90D (GAG→GAT)  wecD → TDP‑fucosamine acetyltransferase
RA 4,266,090 C→A 16.5% S231* (TCA→TAA)  yjcC → putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase
RA 4,608,070 C→A 12.9% R9S (CGT→AGT)  deoA → thymidine phosphorylase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 80473 80589 117 4 [2] [3] 4 leuL/leuO leu operon leader peptide/global transcription factor
* * ÷ CP009273 153538 153747 210 4 [2] [2] 4 [folK] [folK]
* * ÷ CP009273 234718 234751 34 4 [3] [2] 4 [ykfM] [ykfM]
* * ÷ CP009273 234982 235063 82 4 [3] [3] 4 ykfM lethality reduction protein, putative inner membrane protein
* * ÷ CP009273 249121 249278 158 4 [3] [3] 5 [yafO]–[yafP] [yafO],[yafP]
* * ÷ CP009273 578965 579140 176 4 [3] [1] 4 [appY] [appY]
* * ÷ CP009273 581127 581169 43 4 [3] [3] 4 ompT/pauD DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)/tRNA‑OTHER
* * ÷ CP009273 703459 703529 71 4 [3] [3] 4 glnS/chiP glutamyl‑tRNA synthetase/chitoporin, uptake of chitosugars
* * ÷ CP009273 724407 724446 40 4 [2] [3] 4 kdpF/ybfA potassium ion accessory transporter subunit/DUF2517 family protein
* * ÷ CP009273 731781 731866–731841 61–86 4 [2] [2] 4 ybfC/ybfQ putative periplasmic protein/pseudogene, H repeat‑associated protein
* * ÷ CP009273 993093 993203 111 4 [3] [3] 4 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ CP009273 1193174 1193256 83 4 [3] [3] 4 ymfE e14 prophage; putative inner membrane protein
* * ÷ CP009273 1207780 1207796 17 4 [1] [3] 4 iraM/ycgX RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein
* * ÷ CP009273 1211122 1211171 50 4 [2] [1] 4 bluF/ycgZ anti‑repressor for YcgE, blue light‑responsive; FAD‑binding; has c‑di‑GMP phosphodiesterase‑like EAL domain, but does not degrade c‑di‑GMP/RcsB connector protein for regulation of biofilm and acid‑resistance
* * ÷ CP009273 1427988–1428235 1428268 34–281 4 [3] [2] 4 [ynaE] [ynaE]
* * ÷ CP009273 1459357 1459560 204 4 [3] [3] 5 ynbG ynbG
* * ÷ CP009273 1524362 1524473 112 4 [2] [1] 4 ydcD uncharacterized protein
* * ÷ CP009273 1566646 1566687 42 4 [3] [3] 4 [pqqL] [pqqL]
* * ÷ CP009273 1631637 1631656 20 4 [3] [3] 4 ydfO Qin prophage; uncharacterized protein
* * ÷ CP009273 1631929 1632001 73 4 [3] [3] 4 gnsB Qin prophage; multicopy suppressor of secG(Cs) and fabA6(Ts)
* * ÷ CP009273 1635178 1635309 132 5 [3] [3] 4 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock protein
* * ÷ CP009273 1902192 1902294 103 4 [2] [3] 4 yobF/yebO DUF2527 family heat‑induced protein/putative inner membrane protein
* * ÷ CP009273 1952497 1952619 123 4 [2] [3] 5 torY/cutC TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
* * ÷ CP009273 1980188 1980234 47 4 [3] [3] 4 araF/ftnB L‑arabinose transporter subunit/ferritin B, putative ferrous iron reservoir
* * ÷ CP009273 2027056 2027119 64 5 [3] [3] 4 yedR/rseX inner membrane protein/sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent
* * ÷ CP009273 2027299 2027464 166 4 [3] [3] 4 rseX/yedS sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology; putative outer membrane protein
* * ÷ CP009273 2051096 2051161 66 4 [3] [3] 4 yeeN/asnW UPF0082 family protein/tRNA‑Asn
* * ÷ CP009273 2061974 2062133 160 4 [3] [3] 7 [yoeA] [yoeA]
* * ÷ CP009273 2078958 2079025 68 4 [3] [3] 4 [yeeE] [yeeE]
* * ÷ CP009273 2097480 2097579 100 4 [3] [2] 4 wbbK lipopolysaccharide biosynthesis protein
* * ÷ CP009273 2131137 2131248 112 4 [3] [3] 4 wza/yegH colanic acid export protein; outer membrane auxillary lipoprotein/inner membrane protein
* * ÷ CP009273 2337800 2337870 71 4 [2] [2] 5 yfaL/nrdA adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit
* * ÷ CP009273 2357876 2357947 72 4 [3] [2] 4 yfaZ/nudI outer membrane protein, putative porin/nucleoside triphosphatase
* * ÷ CP009273 2379299 2379388 90 4 [3] [3] 4 [yfbL] [yfbL]
* * ÷ CP009273 2400551 2400631 81 4 [3] [3] 4 lrhA/alaA transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2
* * ÷ CP009273 2462802 2462841 40 4 [3] [3] 4 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2462875 2463001 127 4 [3] [3] 5 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2584470 2584520 51 4 [3] [3] 4 ypfM/yffB stress‑induced small enterobacterial protein/putative ArsC family reductase
* * ÷ CP009273 2766940 2766960 21 4 [2] [2] 4 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ CP009273 2984454 2984498 45 4 [3] [3] 4 ygeF/ygeG pseudogene/SycD‑like chaperone family TPR‑repeat‑containing protein
* * ÷ CP009273 2988498 2988649 152 4 [3] [3] 5 ygeK/ygeN pseudogene; putative 2‑component transcriptional regulator/pseudogene
* * ÷ CP009273 3262656 3262719 64 4 [3] [3] 4 yhaC pentapetide repeats‑related protein
* * ÷ CP009273 3463349 3463439 91 5 [3] [3] 5 chiA/tufA periplasmic endochitinase/translation elongation factor EF‑Tu 1
* * ÷ CP009273 3490288 3490323 36 5 [3] [3] 4 nirD/nirC nitrite reductase, NAD(P)H‑binding, small subunit/nitrite transporter
* * ÷ CP009273 3625534 3625568 35 4 [3] [3] 7 yhiJ DUF4049 family protein
* * ÷ CP009273 3763095 3763277 183 4 [3] [2] 4 [yibV] [yibV]
* * ÷ CP009273 3797756 3797850 95 4 [3] [3] 4 waaS lipopolysaccharide core biosynthesis protein
* * ÷ CP009273 4466762 4466898 137 4 [2] [3] 4 yjgL uncharacterized protein
* * ÷ CP009273 4508097 4508178 82 4 [3] [1] 4 fecI/insA RNA polymerase, sigma 19 factor/IS1 repressor TnpA
* * ÷ CP009273 4532574 4532752 179 4 [2] [3] 6 fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* * ÷ CP009273 4561738 4561825 88 4 [3] [3] 5 yjiS/yjiT DUF1127 family protein/pseudogene

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 = 20563NA (NA)24 (0.930) 20/294 NT 100% noncoding (1/768 nt) IS1 repeat region
?CP009273 = 879039 0 (0.000)intergenic (‑195/‑90) ybjG/mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
* ? CP009273 360104 =16 (0.620)32 (1.240) 30/294 NT 60.4% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 26 (1.000)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 454243 =1 (0.040)36 (1.420) 27/288 NT 97.4% intergenic (+87/‑101) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?CP009273 603467 = NA (NA)intergenic (+23/‑54) hokE/insL1 toxic polypeptide, small/IS186 transposase
* ? CP009273 = 4542550 (0.000)27 (1.070) 23/286 NT 100% intergenic (+99/‑89) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?CP009273 = 604803 NA (NA)intergenic (+170/+112) insL1/entD IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex
* ? CP009273 879032 =1 (0.040)34 (1.310) 28/294 NT 97.1% intergenic (‑188/‑97) ybjG/mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
?CP009273 = 3577555 NA (NA)intergenic (+15/‑1) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E
* ? CP009273 1203246 =40 (1.550)9 (0.390) 9/262 NT 28.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 9 (0.390)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 120326141 (1.580)6 (0.260) 6/262 NT 20.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 9 (0.390)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related