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
MC JC 182,235 Δ3 bp 100% coding (198‑200/825 nt) dapD ← 2,3,4,5‑tetrahydropyridine‑2‑carboxylate N‑succinyltransferase
RA 481,777:1 +A 100% coding (561/648 nt) acrR → transcriptional repressor
RA 490,165 C→G 6.1% S102* (TCA→TGA)  recR → gap repair protein
RA 490,473 G→T 8.6% intergenic (+7/‑103) recR → / → htpG gap repair protein/protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase
RA 668,380 C→G 13.9% M620I (ATG→ATC)  leuS ← leucyl‑tRNA synthetase
RA 689,185 C→A 6.3% V409V (GTG→GTT)  miaB ← tRNA‑i(6)A37 methylthiotransferase
RA 690,821 G→T 6.5% E89* (GAA→TAA)  ubiF → 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol oxygenase
RA 710,088 Δ1 bp 8.0% coding (1075/1641 nt) pgm → phosphoglucomutase
RA 710,089 Δ1 bp 8.0% coding (1076/1641 nt) pgm → phosphoglucomutase
RA 710,555 Δ1 bp 18.4% coding (1542/1641 nt) pgm → phosphoglucomutase
RA 905,314 G→T 9.3% R398S (CGC→AGC)  poxB ← pyruvate dehydrogenase (pyruvate oxidase), thiamine triphosphate‑binding, FAD‑binding
RA 982,347 Δ1 bp 100% coding (92/1089 nt) ompF ← outer membrane porin 1a (Ia;b;F)
RA 1,167,913 C→T 11.9% G503D (GGC→GAC)  mfd ← transcription‑repair coupling factor
RA 1,335,140 C→T 7.0% A109V (GCG→GTG)  yciM → envelope integrity maintenance protein; EnvC‑interacting protein
RA 1,514,608 A→G 7.3% K30K (AAA→AAG)  mcbR → colanic acid and biofilm gene transcriptional regulator, MqsR‑controlled
JC 1,737,646 Δ13 bp 100% intergenic (‑147/‑56) ribC ← / → mdtK riboflavin synthase, alpha subunit/multidrug efflux system transporter
RA 1,870,939 C→A 12.4% S337* (TCG→TAG)  yeaN → putative transporter
RA 1,888,277 T→C 7.5% intergenic (+309/‑113) yoaB → / → yoaC putative reactive intermediate deaminase/DUF1889 family protein
RA 1,973,147 C→A 19.0% intergenic (‑693/‑87) flhD ← / → uspC flagellar class II regulon transcriptional activator, with FlhC/universal stress protein
RA 2,098,354 G→A 8.6% S71F (TCC→TTC)  wbbJ ← putative lipopolysaccharide biosynthesis O‑acetyl transferase
RA 2,241,421 Δ1 bp 12.8% coding (591/1470 nt) lysP ← lysine transporter
RA 2,241,422 Δ1 bp 12.8% coding (590/1470 nt) lysP ← lysine transporter
JC 2,305,901 Δ5 bp 85.7% coding (324‑328/1104 nt) ompC ← outer membrane porin protein C
RA 2,332,544 G→T 100% A119E (GCA→GAA)  gyrA ← DNA gyrase (type II topoisomerase), subunit A
RA 2,402,179 Δ1 bp 76.9% coding (1140/1218 nt) alaA → valine‑pyruvate aminotransferase 2
RA 2,402,180 Δ1 bp 76.9% coding (1141/1218 nt) alaA → valine‑pyruvate aminotransferase 2
RA 2,430,495 C→A 6.8% G279V (GGG→GTG)  pdxB ← erythronate‑4‑phosphate dehydrogenase
RA 2,497,021 G→T 11.0% P315Q (CCG→CAG)  fryA ← putative PTS enzyme, Hpr component/enzyme I component/enzyme IIA component
RA 2,679,445:1 +C 10.5% coding (252/1191 nt) hmp → fused nitric oxide dioxygenase/dihydropteridine reductase 2
RA 2,711,945 G→A 10.8% intergenic (‑58/‑149) yfiF ← / → trxC putative methyltransferase/thioredoxin 2
JC 2,768,985 +GGC 15.5% pseudogene (82/180 nt) ypjI → pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related
RA 2,974,946 G→T 8.6% P199Q (CCA→CAA)  araE ← arabinose transporter
RA 3,159,093 G→T 81.0% S80R (AGC→AGA)  parC ← DNA topoisomerase IV, subunit A
RA 3,167,252 G→A 7.9% L502F (CTC→TTC)  parE ← DNA topoisomerase IV, subunit B
RA 3,251,001 C→A 5.6% L123L (CTG→CTT)  yhaO ← putative transporter
RA 3,276,567 Δ1 bp 100% coding (66/861 nt) kbaY → tagatose 6‑phosphate aldolase 1, kbaY subunit
JC 3,390,836 +CTG 70.3% coding (319/1470 nt) rng ← ribonuclease G
JC 3,478,011 +CGATCC 25.4% coding (163/870 nt) prkB → putative phosphoribulokinase
JC 3,505,342 Δ4 bp 7.8% coding (359‑362/906 nt) yhfZ ← putative DNA‑binding transcriptional regulator
RA 3,530,413 Δ1 bp 7.4% coding (243/477 nt) greB → transcript cleavage factor
RA 3,616,126 C→A 7.5% P1192Q (CCG→CAG)  rhsB → Rhs family putative polymorphic toxin, putative neighboring cell growth inhibitor
RA 3,641,071 C→A 8.6% L26L (CTG→CTT)  dinQ ← UV‑inducible membrane toxin, DinQ‑AgrB type I toxin‑antitoxin system
RA 3,880,673:1 +C 100% coding (486/1365 nt) mnmE → tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA 3,880,673:2 +T 70.6% coding (486/1365 nt) mnmE → tRNA U34 5‑methylaminomethyl‑2‑thiouridine modification GTPase
RA 3,928,650 G→T 8.5% M1M (ATG→ATT) † rbsC → D‑ribose transporter subunit
JC 3,993,264 Δ11 bp 7.3% coding (1922‑1932/2163 nt) uvrD → DNA‑dependent ATPase I and helicase II
RA 4,015,041 G→A 25.3% A486T (GCC→ACC)  ubiB → regulator of octaprenylphenol hydroxylation, ubiquinone synthesis; regulator of 2'‑N‑acetyltransferase; putative ABC1 family protein kinase
RA 4,032,803 Δ1 bp 39.5% noncoding (1925/2905 nt) rrlA → 23S ribosomal RNA of rrnA operon
RA 4,081,388 A→G 11.7% M343V (ATG→GTG)  yiiG → DUF3829 family lipoprotein
JC 4,212,946 Δ3 bp 7.0% coding (609‑611/825 nt) iclR ← transcriptional repressor
RA 4,267,455 G→A 100% R20H (CGC→CAC)  soxR → redox‑sensitive transcriptional activator of soxS; autorepressor
RA 4,361,451 T→C 9.5% F204L (TTC→CTC)  groL → Cpn60 chaperonin GroEL, large subunit of GroESL
RA 4,385,173 G→T 10.6% G431* (GGA→TGA)  nnr → bifunctional NAD(P)H‑hydrate repair enzyme; C‑terminal domain ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase and N‑terminal domain NAD(P)H‑hydrate epimerase
RA 4,476,060 G→T 8.8% R9L (CGG→CTG)  lptF → lipopolysaccharide export ABC permease of the LptBFGC export complex
RA 4,522,553 C→A 15.5% E150* (GAA→TAA)  yjhP ← putative methyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ CP009273 269431 269619 189 11 [9] [8] 10 ykfC CP4‑6 prophage; conserved protein;Phage or Prophage Related
* * ÷ CP009273 271054 271945 892 10 [9] [9] 10 mmuP CP4‑6 prophage; putative S‑methylmethionine transporter
* * ÷ CP009273 276791 277413 623 10 [9] [9] 10 yagA CP4‑6 prophage; putative DNA‑binding transcriptional regulator
* * ÷ CP009273 279217 279828 612 10 [9] [9] 10 yagF CP4‑6 prophage; dehydratase family protein
* * ÷ CP009273 279832 280170 339 10 [9] [9] 10 yagF CP4‑6 prophage; dehydratase family protein
* * ÷ CP009273 280871 281263 393 10 [9] [9] 11 [yagF]–[yagG] [yagF],[yagG]
* * ÷ CP009273 281565 282000 436 10 [9] [9] 12 yagG CP4‑6 prophage; putative sugar transporter
* * ÷ CP009273 287687 288012 326 10 [9] [8] 10 [yagJ] [yagJ]
* * ÷ CP009273 290498 290699 202 10 [9] [9] 10 [yagM] [yagM]
* * ÷ CP009273 293060 293163 104 10 [8] [9] 10 [yagP] [yagP]
* * ÷ CP009273 295778 296146 369 10 [9] [9] 10 paoC PaoABC aldehyde oxidoreductase, Moco‑containing subunit
* * ÷ CP009273 300649 301077 429 10 [9] [8] 10 [ecpE]–[ecpD] [ecpE],[ecpD]
* * ÷ CP009273 303838 304549 712 10 [9] [9] 10 ecpC ECP production outer membrane protein
* * ÷ CP009273 314129 314519 391 10 [9] [9] 11 [rclB]–[rclA] [rclB],[rclA]
* * ÷ CP009273 315541 315780 240 10 [9] [9] 10 [rclA] [rclA]
* * ÷ CP009273 321201 321486 286 10 [9] [9] 10 [betA] [betA]
* * ÷ CP009273 326213 326644 432 10 [9] [8] 10 betT choline transporter of high affinity
* * ÷ CP009273 327351 327597 247 10 [9] [9] 10 betT/yahA choline transporter of high affinity/c‑di‑GMP‑specific phosphodiesterase
* * ÷ CP009273 329113 330514 1402 11 [9] [9] 10 [yahA]–[yahC] [yahA],yahB,[yahC]
* * ÷ CP009273 339573 339831 259 10 [9] [9] 10 [yahK] [yahK]
* * ÷ CP009273 342503 342814 312 10 [8] [9] 10 [prpR] [prpR]
* * ÷ CP009273 344192 344914 723 10 [8] [9] 10 [prpB] [prpB]
* * ÷ CP009273 348898 349450 553 10 [9] [9] 10 prpE propionate‑‑CoA ligase
* * ÷ CP009273 358405 358979 575 10 [9] [9] 10 [lacY]–[lacZ] [lacY],[lacZ]
* * ÷ CP009273 361953 362596 644 11 [9] [9] 10 mhpR mhp operon transcriptional activator
* * ÷ CP009273 363943 364590 648 10 [9] [9] 10 [mhpA]–[mhpB] [mhpA],[mhpB]
* * ÷ CP009273 365524 365891 368 10 [9] [9] 10 mhpC pseudogene, IS30 insertion
* * ÷ CP009273 569784 569872 89 11 [7] [8] 11 [quuD] [quuD]
* * ÷ CP009273 1566409 1566480 72 10 [8] [9] 11 gadB/pqqL glutamate decarboxylase B, PLP‑dependent/putative periplasmic M16 family zinc metalloendopeptidase
* * ÷ CP009273 1952446 1952609 164 10 [9] [9] 10 torY/cutC TMAO reductase III (TorYZ), cytochrome c‑type subunit/copper homeostasis protein
* * ÷ CP009273 2050160 2050288 129 10 [9] [9] 13 amn/yeeN AMP nucleosidase/UPF0082 family protein
* * ÷ CP009273 2097482 2097590 109 10 [6] [9] 11 wbbK lipopolysaccharide biosynthesis protein
* * ÷ CP009273 2100643 2100711 69 12 [8] [9] 10 [wbbH]–[glf] [wbbH],[glf]
* * ÷ CP009273 2297248 2297311 64 11 [9] [9] 10 napF/eco ferredoxin‑type protein, role in electron transfer to periplasmic nitrate reductase NapA/ecotin, a serine protease inhibitor
* * ÷ CP009273 2753665 2753775 111 10 [8] [6] 12 [yfjI] [yfjI]
* * ÷ CP009273 2768271 2768354 84 12 [4] [6] 11 yfjW CP4‑57 prophage; putative inner membrane protein
* * ÷ CP009273 2792277 2792331 55 10 [9] [9] 10 stpA/alaE DNA binding protein, nucleoid‑associated/alanine exporter, alanine‑inducible, stress‑responsive
* * ÷ CP009273 3178603 3178772 170 10 [9] [9] 10 yqiC/ygiL BMFP family putative fusogenic protein/putative fimbrial‑like adhesin protein
* * ÷ CP009273 3262562 3262712 151 10 [9] [6] 10 yhaC pentapetide repeats‑related protein
* * ÷ CP009273 3575996 3576033 38 15 [8] [7] 12 yhhZ putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
* * ÷ CP009273 3792508 3792701 194 10 [9] [7] 10 [waaU] [waaU]
* * ÷ CP009273 3797711 3797858 148 14 [8] [9] 11 waaS lipopolysaccharide core biosynthesis protein

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP009273 360104 =2 (0.050)8 (0.200)
+AATTCC		 8/258 NT 28.5% intergenic (‑38/+557) lacZ/lacI pseudogene, truncated/DNA‑binding transcriptional repressor
?CP009273 4161677 = 40 (0.960)noncoding (113/120 nt) rrfB 5S ribosomal RNA of rrnB operon
* ? CP009273 1203246 =3 (0.070)45 (1.230) 33/238 NT 97.1% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 1205075 = 0 (0.000)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 = 12032613 (0.070)30 (0.820) 26/238 NT 95.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?CP009273 = 1205058 0 (0.000)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? CP009273 2962330 =30 (0.720)18 (0.440) 15/268 NT 37.7% coding (7/531 nt) rppH RNA pyrophosphohydrolase
?CP009273 3576789 = NA (NA)intergenic (+11/‑54) yrhA/insA pseudogene, interrupted by IS1E/IS1 repressor TnpA
* ? CP009273 = 296233927 (0.650)10 (0.240) 9/268 NT 27.2% intergenic (‑3/‑682) rppH/mutH RNA pyrophosphohydrolase/methyl‑directed mismatch repair protein
?CP009273 = 3577554 NA (NA)intergenic (+14/‑2) insB1/yrhA IS1 transposase B/pseudogene, interrupted by IS1E
* ? CP009273 = 431147434 (0.820)3 (0.080) 3/252 NT 8.9% coding (40/453 nt) phnG ribophosphonate triphosphate synthase subunit
?CP009273 = 4311483 30 (0.780)coding (31/453 nt) phnG ribophosphonate triphosphate synthase subunit