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 277,737 C→A 13.8% intergenic (‑43/‑252) yagA ← / → yagE CP4‑6 prophage; putative DNA‑binding transcriptional regulator/2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage
RA 398,946 G→T 11.2% L70F (TTG→TTT)  psiF → PsiF family protein
RA 466,588 G→T 14.8% R166L (CGA→CTA)  mdlB → putative multidrug transporter subunit of ABC superfamily, ATP‑binding component
RA 478,730 A→G 100% L377P (CTC→CCC)  acrB ← multidrug efflux system protein
RA 481,229 A→G 100% T5A (ACC→GCC)  acrR → transcriptional repressor
RA 544,918 G→A 14.3% R369H (CGC→CAC)  ylbE → NO‑induced DUF1116 protein
RA 637,033 G→T 19.3% V97V (GTC→GTA)  uspG ← universal stress protein UP12
RA 885,533 C→A 39.9% intergenic (‑258/‑12) ybjL ← / → ybjM putative transporter/inner membrane protein
RA 970,407 Δ1 bp 10.5% coding (633/1323 nt) mukF → chromosome condensin MukBEF, kleisin‑like subunit, binds calcium
RA 1,047,936 T→C 17.7% T295A (ACC→GCC)  yccM ← putative 4Fe‑4S membrane protein
RA 1,469,551 G→T 16.6% E51* (GAA→TAA)  ydbD → PF10971 family putative periplasmic methylglyoxal resistance protein
RA 1,592,373 C→A 21.3% intergenic (‑129/+501) yneO ← / ← lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
JC JC 1,613,458 IS2 (+) +5 bp 100% coding (82‑86/435 nt) marR → transcriptional repressor of multiple antibiotic resistance
RA 2,083,219 C→A 23.9% intergenic (‑25/‑258) yefM ← / → hisL antitoxin of the YoeB‑YefM toxin‑antitoxin system/his operon leader peptide
RA 2,087,615 G→T 19.3% D223Y (GAC→TAC)  hisB → fused histidinol‑phosphatase/imidazoleglycerol‑phosphate dehydratase
RA 2,183,476 C→A 20.6% G305V (GGA→GTA)  yehB ← putative outer membrane protein
RA 2,313,302 G→A 9.3% F18F (TTC→TTT)  rcsC ← hybrid sensory kinase in two‑component regulatory system with RcsB and YojN
RA 2,468,869 C→A 17.1% S136Y (TCT→TAT)  yfdR → CPS‑53 (KpLE1) prophage; conserved protein
RA 2,511,819 G→T 20.9% intergenic (‑109/‑127) alaW ← / → yfeC tRNA‑Ala/DUF1323 family putative DNA‑binding protein
RA 2,571,219 G→A 17.4% A173V (GCC→GTC)  maeB ← malic enzyme: putative oxidoreductase/putative phosphotransacetylase
RA 2,636,119:1 +A 11.4% coding (85/1014 nt) rodZ ← MreB assembly cytoskeletal protein
RA 2,693,265 C→A 24.1% H82N (CAC→AAC)  yfhL → putative 4Fe‑4S cluster‑containing protein
MC JC 2,809,385 Δ148 bp 100% coding (267‑414/1557 nt) gshA ← glutamate‑cysteine ligase
RA 3,178,061 C→G 11.1% intergenic (‑236/‑138) ribB ← / → yqiC 3,4‑dihydroxy‑2‑butanone‑4‑phosphate synthase/BMFP family putative fusogenic protein
JC 3,320,960 +TTTATC 55.2% coding (64/630 nt) rlmE ← 23S rRNA U2552 2'‑O‑ribose methyltransferase, SAM‑dependent
RA 3,370,347 G→A 9.7% Q145* (CAG→TAG)  sspA ← stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog
RA 3,445,831 G→A 100% P152L (CCG→CTG)  rplC ← 50S ribosomal subunit protein L3
RA 3,448,179 G→A 12.9% G193G (GGC→GGT)  gspA ← general secretory pathway component, cryptic
RA 3,505,544 C→A 15.1% E54* (GAA→TAA)  yhfZ ← putative DNA‑binding transcriptional regulator
RA 3,544,630 G→A 11.3% H401H (CAC→CAT)  malP ← maltodextrin phosphorylase
RA 3,629,125 C→A 14.1% L309I (CTT→ATT)  yhiM → acid resistance protein, inner membrane
RA 3,671,509 C→A 15.4% G68C (GGC→TGC)  yhjG ← putative inner membrane‑anchored periplasmic AsmA family protein
RA 3,679,656 C→T 11.1% G960S (GGC→AGC)  bcsC ← cellulose synthase subunit
RA 3,688,515 C→A 14.4% G28C (GGT→TGT)  bcsA ← cellulose synthase, catalytic subunit
RA 3,706,007 A→G 10.5% N96N (AAT→AAC)  yhjY ← autotransporter beta‑domain protein
RA 3,845,175 G→T 15.5% Q324K (CAG→AAG)  ilvB ← acetolactate synthase 2 large subunit
RA 3,910,911 C→A 14.7% E239* (GAG→TAG)  atpG ← F1 sector of membrane‑bound ATP synthase, gamma subunit
RA 3,962,311 C→A 14.6% R346S (CGC→AGC)  wecA → UDP‑GlcNAc:undecaprenylphosphate GlcNAc‑1‑phosphate transferase
RA 3,963,453 G→C 14.3% intergenic (+16/‑40) wzzE → / → wecB Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein/UDP‑N‑acetyl glucosamine‑2‑epimerase
RA 3,994,519 G→A 40.3% intergenic (‑103/‑267) yigE ← / → corA DUF2233 family protein/magnesium/nickel/cobalt transporter
RA 4,216,855 G→A 8.9% E1034K (GAA→AAA)  metH → homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,244,145 G→T 13.7% F750L (TTC→TTA)  plsB ← glycerol‑3‑phosphate O‑acyltransferase
MC JC 4,285,799 Δ452 bp 100% intergenic (+77/+3) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,295,913 G→C 12.5% R168G (CGT→GGT)  yjcS ← metallo‑beta‑lactamase superfamily protein
RA 4,584,335 G→T 17.3% R69S (CGT→AGT)  yjjL ← L‑galactonate transporter

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 233674 233762 89 6 [4] [3] 6 aspV/yafT tRNA‑Asp/lipoprotein
* * ÷ CP009273 327495 327548 54 6 [5] [5] 6 betT/yahA choline transporter of high affinity/c‑di‑GMP‑specific phosphodiesterase
* * ÷ CP009273 533001 533056 56 6 [5] [5] 7 glxR/ybbW tartronate semialdehyde reductase, NADH‑dependent/putative allantoin transporter
* * ÷ CP009273 579903 579963 61 6 [4] [5] 6 appY/ompT global transcriptional activator; DLP12 prophage/DLP12 prophage; outer membrane protease VII (outer membrane protein 3b)
* * ÷ CP009273 716362 716491 130 6 [5] [5] 6 ybfK/kdpE uncharacterized protein/response regulator in two‑component regulatory system with KdpD
* * ÷ CP009273 716510 716576 67 6 [5] [5] 6 [kdpE] [kdpE]
* * ÷ CP009273 748505 748584 80 6 [4] [5] 6 ybgD/gltA putative fimbrial‑like adhesin protein/citrate synthase
* * ÷ CP009273 955682 955702 21 6 [4] [4] 7 aroA/ycaL 5‑enolpyruvylshikimate‑3‑phosphate synthetase/putative peptidase‑related chaperone
* * ÷ CP009273 993135 993245 111 6 [5] [5] 6 ssuE/elfA NAD(P)H‑dependent FMN reductase/laminin‑binding fimbrin subunit
* * ÷ CP009273 1206614 1206707 94 6 [5] [5] 6 [mcrA] [mcrA]
* * ÷ CP009273 1225844 1225943 100 8 [5] [5] 6 [hlyE] [hlyE]
* * ÷ CP009273 1459326 1459625 300 6 [5] [5] 6 ynbG ynbG
* * ÷ CP009273 1521862 1521946 85 6 [5] [5] 6 yncH/rhsE IPR020099 family protein/pseudogene, Rhs family protein
* * ÷ CP009273 1524300 1524473 174 7 [5] [3] 6 ydcD uncharacterized protein
* * ÷ CP009273 1524575 1524672 98 6 [5] [5] 6 [ydcD] [ydcD]
* * ÷ CP009273 1538678 1538783 106 6 [5] [5] 6 yddK pseudogene, leucine‑rich protein; putative glycoportein
* * ÷ CP009273 1540413 1540474 62 6 [5] [5] 6 yddL/yddG putative lipoprotein;putative membrane; Not classified; putative outer membrane porin protein/aromatic amino acid exporter
* * ÷ CP009273 1592511 1592558 48 6 [4] [5] 6 yneO/lsrK pseudogene, AidA homolog/autoinducer‑2 (AI‑2) kinase
* * ÷ CP009273 1618869 1618977 109 6 [5] [5] 7 ydeI/ydeJ hydrogen peroxide resistance OB fold protein; putative periplasmic protein/inactive PncC family protein
* * ÷ CP009273 1807469 1807565 97 6 [5] [4] 6 ydjO/cedA uncharacterized protein/cell division modulator
* * ÷ CP009273 1952500 1952635 136 8 [5] [5] 6 torY/cutC TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
* * ÷ CP009273 2061904 2062133 230 6 [5] [4] 6 [yoeA] [yoeA]
* * ÷ CP009273 2097488 2097592 105 6 [5] [5] 7 wbbK lipopolysaccharide biosynthesis protein
* * ÷ CP009273 2144422 2144542 121 6 [5] [5] 6 [yegI] [yegI]
* * ÷ CP009273 2161815 2161881 67 6 [3] [5] 6 yegR/yegS uncharacterized protein/phosphatidylglycerol kinase, metal‑dependent
* * ÷ CP009273 2197689 2197768 80 6 [5] [4] 6 yehK uncharacterized protein
* * ÷ CP009273 2379161 2379377 217 6 [4] [5] 6 [yfbK]–[yfbL] [yfbK],[yfbL]
* * ÷ CP009273 2449478 2449514 37 6 [5] [5] 6 yfcV/sixA putative fimbrial‑like adhesin protein/phosphohistidine phosphatase
* * ÷ CP009273 2463165 2463268 104 6 [5] [5] 6 gtrS serotype‑specific glucosyl transferase, CPS‑53 (KpLE1) prophage
* * ÷ CP009273 2476767 2476826 60 6 [5] [4] 6 [emrK] [emrK]
* * ÷ CP009273 2569260 2569354 95 7 [5] [5] 7 eutS/maeB putative ethanol utilization carboxysome structural protein/malic enzyme: putative oxidoreductase/putative phosphotransacetylase
* * ÷ CP009273 2779381 2779450 70 7 [3] [5] 6 ileY/ygaQ tRNA‑Ile/uncharacterized protein; putative enzyme
* * ÷ CP009273 2798154 2798236 83 6 [5] [5] 8 [proV] [proV]
* * ÷ CP009273 2877631 2877790 160 6 [4] [5] 7 casA/ygcB CRISP RNA (crRNA) containing Cascade antiviral complex protein/R‑loop helicase‑annealase Cas3 needed for Cascade anti‑viral activity
* * ÷ CP009273 2898894 2898998 105 7 [5] [5] 6 [yqcG] [yqcG]
* * ÷ CP009273 2984443 2984586 144 6 [5] [4] 6 ygeF/ygeG pseudogene/SycD‑like chaperone family TPR‑repeat‑containing protein
* * ÷ CP009273 2988480 2988809 330 6 [5] [5] 6 [ygeN] [ygeN]
* * ÷ CP009273 3246079 3246189 111 6 [5] [5] 9 yhaH/yhaI DUF805 family inner membrane protein/DUF805 family inner membrane protein
* * ÷ CP009273 3260530 3260587 58 6 [4] [5] 6 tdcA/tdcR tdc operon transcriptional activator/L‑threonine dehydratase operon activator protein
* * ÷ CP009273 3354466 3354532 67 6 [5] [4] 6 gltD/gltF glutamate synthase, 4Fe‑4S protein, small subunit/periplasmic protein
* * ÷ CP009273 3378674 3378785 112 6 [5] [5] 6 argR/yhcN l‑arginine‑responsive arginine metabolism regulon transcriptional regulator/cadmium and peroxide resistance protein, stress‑induced
* * ÷ CP009273 3463283 3463426 144 6 [4] [5] 6 chiA/tufA periplasmic endochitinase/translation elongation factor EF‑Tu 1
* * ÷ CP009273 3575995 3576051 57 7 [5] [5] 6 yhhZ putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
* * ÷ CP009273 3762922 3763274 353 6 [5] [5] 6 [yibV]–yibV [yibV],yibV
* * ÷ CP009273 3790357 3790466 110 7 [5] [5] 6 waaL O‑antigen ligase
* * ÷ CP009273 3792413 3792711 299 6 [5] [5] 6 [waaU]–[waaZ] [waaU],[waaZ]
* * ÷ CP009273 3797779 3797894 116 6 [5] [4] 6 waaS lipopolysaccharide core biosynthesis protein
* * ÷ CP009273 3943498 3943581 84 6 [5] [5] 6 yifB/ilvL bifunctional magnesium chelatase family protein and putative transcriptional regulator/ilvG operon leader peptide
* * ÷ CP009273 4037378 4037487 110 6 [5] [5] 7 [dsbA] [dsbA]
* * ÷ CP009273 4211921 4212015 95 8 [5] [5] 6 arpA ankyrin repeat protein
* * ÷ CP009273 4212398 4212514 117 6 [4] [5] 7 [arpA] [arpA]
* * ÷ CP009273 4241381 4241492 112 6 [5] [5] 6 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ CP009273 4241607 4241633 27 6 [5] [5] 6 yjbI pseudogene, SopA‑related, pentapeptide repeats‑containing
* * ÷ CP009273 4250314 4250406 93 6 [4] [5] 6 yjbL uncharacterized protein
* * ÷ CP009273 4272710 4272747 38 6 [3] [4] 8 yjcF pentapeptide repeats protein
* * ÷ CP009273 4469496 4469513 18 7 [5] [4] 6 yjgM/yjgN putative acetyltransferase/DUF898 family inner membrane protein
* * ÷ CP009273 4546332 4546459 128 6 [5] [4] 6 yjiC/iraD uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor
* * ÷ CP009273 4561740 4561828 89 6 [5] [4] 10 yjiS/yjiT DUF1127 family protein/pseudogene
* * ÷ CP009273 4561992 4562153 162 6 [5] [5] 6 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)12 (0.440) 11/226 NT 30.8% noncoding (1/768 nt) IS1 repeat region
?CP009273 = 879040 27 (0.990)intergenic (‑196/‑89) ybjG/mdfA undecaprenyl pyrophosphate phosphatase/multidrug efflux system protein
* ? CP009273 360104 =28 (1.020)39 (1.430) 31/226 NT 61.9% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 = 360286 20 (0.730)intergenic (‑220/+375) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
* ? CP009273 = 4542552 (0.070)26 (0.990) 24/218 NT 93.1% 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 =20 (0.730)6 (0.220) 5/226 NT 23.1% 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 =8 (0.290)26 (1.110) 22/194 NT 80.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 6 (0.260)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032618 (0.290)10 (0.430) 8/194 NT 60.9% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 6 (0.260)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related