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

Predicted mutations
evidence seq id position mutation freq annotation gene description
RA NZ_CP022686 119,184 T→G 15.8% F47V (TTT→GTT)  marB → multiple antibiotic resistance protein MarB
RA NZ_CP022686 264,457 A→C 12.2% V591G (GTC→GGC)  ppsA ← phosphoenolpyruvate synthase
RA NZ_CP022686 269,554 A→C 12.9% G269G (GGT→GGG)  selO ← protein adenylyltransferase SelO
RA NZ_CP022686 340,516 A→C 12.2% F31V (TTT→GTT)  ydjK ← MFS transporter
RA NZ_CP022686 372,574 A→C 12.0% N275T (AAC→ACC)  sdaA → L‑serine ammonia‑lyase
RA NZ_CP022686 418,374 T→G 13.0% F48V (TTT→GTT)  znuB → zinc ABC transporter permease subunit ZnuB
RA NZ_CP022686 442,342 A→C 11.2% S80A (TCG→GCG)  CIW80_RS02340 ← phage tail protein
RA NZ_CP022686 457,894 Δ1 bp 100% pseudogene (288/997 nt) CIW80_RS02445 ← DUF968 domain‑containing protein
RA NZ_CP022686 496,086 A→C 9.4% L399V (TTA→GTA)  otsA ← alpha,alpha‑trehalose‑phosphate synthase
RA NZ_CP022686 498,662 A→C 6.4% C183G (TGT→GGT)  araH ← arabinose ABC transporter permease AraH
RA NZ_CP022686 556,948 A→T 19.4% intergenic (+132/‑716) zinT → / → CIW80_RS03080 metal‑binding protein ZinT/site‑specific integrase
RA NZ_CP022686 556,949 G→T 18.3% intergenic (+133/‑715) zinT → / → CIW80_RS03080 metal‑binding protein ZinT/site‑specific integrase
RA NZ_CP022686 560,880 C→T 100% intergenic (+62/+53) CIW80_RS03085 → / ← pilV hypothetical protein/shufflon system plasmid conjugative transfer pilus tip adhesin PilV
RA NZ_CP022686 601,295 T→G 19.7% V1607G (GTC→GGC)  irp1 → yersiniabactin polyketide synthase HMWP1
MC JC NZ_CP022686 628,478 Δ1,286 bp 100% [clbP] [clbP]
RA NZ_CP022686 651,833 A→C 14.4% P243P (CCT→CCG)  clbJ ← colibactin non‑ribosomal peptide synthetase ClbJ
RA NZ_CP022686 756,115 A→G 100% G181G (GGT→GGC)  galE ← UDP‑glucose 4‑epimerase GalE
RA NZ_CP022686 764,997 T→G 14.6% N41T (AAC→ACC)  wcaM ← colanic acid biosynthesis protein WcaM
RA NZ_CP022686 765,001 A→T 13.6% Y40N (TAC→AAC)  wcaM ← colanic acid biosynthesis protein WcaM
RA NZ_CP022686 766,756 C→G 13.4% D291H (GAC→CAC)  wcaK ← colanic acid biosynthesis pyruvyl transferase WcaK
RA NZ_CP022686 794,460 C→T 100% A568V (GCG→GTG)  dgcE → diguanylate cyclase
RA NZ_CP022686 829,452 G→T 21.6% intergenic (‑41/+186) gatY ← / ← fbaB tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase
RA NZ_CP022686 881,742 A→C 21.9% intergenic (+257/+130) yohP → / ← dusC protein YohP/tRNA dihydrouridine(16) synthase DusC
RA NZ_CP022686 881,760 T→G 19.8% intergenic (+275/+112) yohP → / ← dusC protein YohP/tRNA dihydrouridine(16) synthase DusC
RA NZ_CP022686 917,427:1 +TT 100% intergenic (+130/‑91) yeiP → / → yeiQ elongation factor P‑like protein YeiP/mannitol dehydrogenase family protein
RA NZ_CP022686 1,100,944 T→G 16.9% D187A (GAC→GCC)  aroC ← chorismate synthase
RA NZ_CP022686 1,209,908 T→G 15.9% D396A (GAC→GCC)  eutH ← ethanolamine utilization protein EutH
RA NZ_CP022686 1,213,479 T→G 18.1% G420G (GGA→GGC)  eutE ← aldehyde dehydrogenase EutE
RA NZ_CP022686 1,213,483 T→G 16.8% N419T (AAC→ACC)  eutE ← aldehyde dehydrogenase EutE
RA NZ_CP022686 1,360,724 G→T 11.4% intergenic (‑59/+265) kgtP ← / ← rrf alpha‑ketoglutarate permease/5S ribosomal RNA
RA NZ_CP022686 1,360,750 G→T 10.0% intergenic (‑85/+239) kgtP ← / ← rrf alpha‑ketoglutarate permease/5S ribosomal RNA
RA NZ_CP022686 1,360,783 G→T 9.1% intergenic (‑118/+206) kgtP ← / ← rrf alpha‑ketoglutarate permease/5S ribosomal RNA
RA NZ_CP022686 1,447,199 A→C 11.4% V35G (GTA→GGA)  hycI ← hydrogenase maturation peptidase HycI
RA NZ_CP022686 1,479,634 G→C 18.4% intergenic (‑43/+150) ftsB ← / ← ygbE cell division protein FtsB/DUF3561 family protein
RA NZ_CP022686 1,482,223 T→C 100% M293V (ATG→GTG)  cysD ← sulfate adenylyltransferase subunit CysD
RA NZ_CP022686 1,504,353 G→C 11.7% A264P (GCT→CCT)  CIW80_RS07520 → YgcG family protein
RA NZ_CP022686 1,535,353 G→T 25.3% M31I (ATG→ATT)  fucI → L‑fucose isomerase
RA NZ_CP022686 1,564,569 A→C 8.6% K190N (AAA→AAC)  CIW80_RS07780 → ImcF‑related family protein
RA NZ_CP022686 1,571,260 A→C 8.7% T188P (ACG→CCG)  tssG → type VI secretion system baseplate subunit TssG
RA NZ_CP022686 1,674,244 T→G 12.9% T182P (ACC→CCC)  ygfB ← UPF0149 family protein YgfB
RA NZ_CP022686 1,674,248 T→G 10.3% Q180H (CAA→CAC)  ygfB ← UPF0149 family protein YgfB
RA NZ_CP022686 1,716,145 A→C 12.8% T42P (ACC→CCC)  rdgB → XTP/dITP diphosphatase
RA NZ_CP022686 1,735,941 A→C 13.3% pseudogene (328/569 nt) papA ← P fimbria major subunit PapA
RA NZ_CP022686 1,828,122 A→C 8.8% A81A (GCT→GCG)  gspK ← type II secretion system minor pseudopilin GspK
RA NZ_CP022686 2,016,225 T→G 9.0% noncoding (49/377 nt) rnpB ← RNase P RNA component class A
RA NZ_CP022686 2,076,554 T→G 14.1% intergenic (+24/‑209) ispB → / → sfsB octaprenyl diphosphate synthase/DNA‑binding transcriptional regulator SfsB
RA NZ_CP022686 2,148,109 T→G 16.1% V124G (GTG→GGG)  panF → sodium/pantothenate symporter
RA NZ_CP022686 2,148,115 T→G 18.4% L126R (CTG→CGG)  panF → sodium/pantothenate symporter
RA NZ_CP022686 2,148,141 T→G 18.2% F135V (TTC→GTC)  panF → sodium/pantothenate symporter
RA NZ_CP022686 2,148,176 T→G 9.3% G146G (GGT→GGG)  panF → sodium/pantothenate symporter
RA NZ_CP022686 2,185,075 A→C 8.1% V46G (GTT→GGT)  rpsE ← 30S ribosomal protein S5
RA NZ_CP022686 2,214,419 T→C 100% K43R (AAA→AGA)  rpsL ← 30S ribosomal protein S12
RA NZ_CP022686 2,320,775 C→T 100% G274S (GGC→AGC)  CIW80_RS11675 ← DNA‑processing protein DprA
RA NZ_CP022686 2,357,291 A→C 19.2% N26T (AAC→ACC)  dcrB → phage sensitivity protein DcrB
RA NZ_CP022686 2,408,861 Δ1 bp 100% pseudogene (1097/3115 nt) mdtF → multidrug efflux pump RND permease MdtF
RA NZ_CP022686 2,460,576 C→A 15.6% M1M (ATG→ATT) † yhjY ← autotransporter outer membrane beta‑barrel domain‑containing protein
RA NZ_CP022686 2,521,024 T→G 7.5% V229G (GTT→GGT)  lldP → L‑lactate permease
RA NZ_CP022686 2,546,394 A→C 18.7% V95G (GTT→GGT)  waaG ← glycosyltransferase family 4 protein
RA NZ_CP022686 2,558,864 T→G 7.1% F128V (TTT→GTT)  yicG → trimeric intracellular cation channel family protein
JC NZ_CP022686 2,590,563 +TTGG 100% coding (109/153 nt) CIW80_RS26455 → hypothetical protein
RA NZ_CP022686 2,617,890 C→A 7.9% E189* (GAA→TAA)  ilvB ← acetolactate synthase large subunit
RA NZ_CP022686 2,643,712 A→C 11.6% L413R (CTG→CGG)  dnaA ← chromosomal replication initiator protein DnaA
RA NZ_CP022686 2,717,400 T→G 9.6% L101V (TTA→GTA)  ilvA → threonine ammonia‑lyase, biosynthetic
RA NZ_CP022686 2,736,586 A→C 7.5% Y183S (TAC→TCC)  rffA → dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase
RA NZ_CP022686 2,769,196 A→C 13.2% F47C (TTT→TGT)  rarD ← EamA family transporter RarD
RA NZ_CP022686 2,801,852 T→G 6.9% K20N (AAA→AAC)  CIW80_RS14030 ← 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase
RA NZ_CP022686 2,810,040 A→C 9.4% N242T (AAC→ACC)  tatC → Sec‑independent protein translocase subunit TatC
RA NZ_CP022686 2,868,740 T→G 28.9% Q22P (CAG→CCG)  fdoH ← formate dehydrogenase O subunit beta
RA NZ_CP022686 2,904,852 T→G 11.7% T239P (ACG→CCG)  ftsN ← cell division protein FtsN
RA NZ_CP022686 2,981,612 A→C 13.1% T567P (ACC→CCC)  rpoC → DNA‑directed RNA polymerase subunit beta'
RA NZ_CP022686 3,136,940 T→G 11.5% D161A (GAC→GCC)  phnN ← ribose 1,5‑bisphosphokinase
JC NZ_CP022686 3,196,873 +GCGTAATCGGTT 100% coding (944/1122 nt) ampC ← BlaEC family class C beta‑lactamase
RA NZ_CP022686 3,200,595 A→C 8.8% V199G (GTT→GGT)  frdA ← fumarate reductase (quinol) flavoprotein subunit
RA NZ_CP022686 3,334,271 C→A 10.5% M256I (ATG→ATT)  fecD ← Fe(3+) dicitrate ABC transporter permease subunit FecD
RA NZ_CP022686 3,424,795 A→C 100% intergenic (‑41/+27) yjiJ ← / ← yjiK MFS transporter/YjiK family protein
RA NZ_CP022686 3,444,704 T→G 15.7% T530P (ACC→CCC)  btsT ← pyruvate/proton symporter BtsT
RA NZ_CP022686 3,461,229 T→G 16.0% noncoding (84/87 nt) CIW80_RS17340 ← tRNA‑Leu
MC JC NZ_CP022686 3,559,837 Δ2,343 bp 100% coding (10‑2352/2352 nt) polB ← DNA polymerase II
RA NZ_CP022686 3,652,079 T→G 10.1% intergenic (‑88/+24) panB ← / ← CIW80_RS18255 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin
RA NZ_CP022686 3,652,090 T→G 11.8% intergenic (‑99/+13) panB ← / ← CIW80_RS18255 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin
RA NZ_CP022686 3,655,540 A→C 9.9% F765V (TTT→GTT)  htrE ← outer membrane usher protein
RA NZ_CP022686 3,656,188 A→G 100% S549P (TCC→CCC)  htrE ← outer membrane usher protein
RA NZ_CP022686 3,734,367 T→G 18.7% F225V (TTT→GTT)  yafD → endonuclease/exonuclease/phosphatase family protein
RA NZ_CP022686 3,792,805 A→G 100% Y421C (TAC→TGC)  fucP → L‑fucose:H+ symporter permease
MC JC NZ_CP022686 3,844,426 Δ1,036 bp 100% coding (2‑1037/1056 nt) dinB → DNA polymerase IV
RA NZ_CP022686 3,868,846 T→G 9.5% T383P (ACG→CCG)  ecpC ← fimbrial usher EcpC
RA NZ_CP022686 3,885,457 A→C 13.6% N1404T (AAC→ACC)  fdeC → inverse autotransporter adhesin FdeC
RA NZ_CP022686 3,925,289 A→C 14.5% N156T (AAC→ACC)  prpC → 2‑methylcitrate synthase
RA NZ_CP022686 3,928,376 T→G 8.8% V287G (GTA→GGA)  prpE → propionate‑‑CoA ligase
RA NZ_CP022686 3,940,724 A→C 16.0% V308G (GTA→GGA)  frmA ← S‑(hydroxymethyl)glutathione dehydrogenase
RA NZ_CP022686 4,286,467 T→G 9.1% V42G (GTC→GGC)  cpoB → cell division protein CpoB
RA NZ_CP022686 4,287,508 A→T 9.6% noncoding (21/76 nt) CIW80_RS21480 → tRNA‑Lys
RA NZ_CP022686 4,368,372 T→G 13.4% S37R (AGC→CGC)  ybiY ← glycyl‑radical enzyme activating protein
RA NZ_CP022686 4,571,354 C→A 12.3% E87D (GAG→GAT)  pgaC ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase
RA NZ_CP022686 4,571,439 T→G 10.4% H59P (CAC→CCC)  pgaC ← poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase
RA NZ_CP022686 4,587,091 T→G 10.4% N609T (AAC→ACC)  CIW80_RS22915 ← enterotoxin
RA NZ_CP022686 4,642,951 A→C 8.7% N732T (AAC→ACC)  sfaF → S/F1C fimbrial usher SfaF/FocD
RA NZ_CP022686 4,678,047 A→C 33.8% intergenic (+45/‑76) agn43 → / → CIW80_RS23450 autotransporter adhesin Ag43/hypothetical protein
RA NZ_CP022686 4,764,883 A→T 17.3% intergenic (‑63/‑198) ycfT ← / → lolC acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC
RA NZ_CP022686 4,764,904 G→T 14.7% intergenic (‑84/‑177) ycfT ← / → lolC acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC
RA NZ_CP022686 4,815,879 T→G 13.6% F23V (TTC→GTC)  CIW80_RS24305 → C40 family peptidase
MC JC NZ_CP022686 4,844,868 Δ1,662 bp 100% [umuD]–[umuC] [umuD], [umuC]
RA NZ_CP022686 4,870,912 Δ1 bp 100% intergenic (‑108/‑120) dhaK ← / → dhaR dihydroxyacetone kinase subunit DhaK/dihydroxyacetone kinase operon transcriptional regulator DhaR
RA NZ_CP022686 4,951,521 A→C 7.7% T39P (ACC→CCC)  topA → type I DNA topoisomerase
RA NZ_CP022686 5,042,289 T→C 11.5% N640N (AAT→AAC)  CIW80_RS25525 → EntS/YbdA MFS transporter
RA NZ_CP022686 5,043,855 T→A 15.2% G1162G (GGT→GGA)  CIW80_RS25525 → EntS/YbdA MFS transporter
RA NZ_CP022686 5,044,137 G→T 10.3% V1256V (GTG→GTT)  CIW80_RS25525 → EntS/YbdA MFS transporter
RA pMUT1‑hok‑empty 1,317:1 +C 11.4% intergenic (–/+400) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,349 G→T 14.4% intergenic (–/+368) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,375 Δ1 bp 6.6% intergenic (–/+342) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,376 Δ1 bp 91.5% intergenic (–/+341) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,403 C→A 5.2% intergenic (–/+314) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,407 G→T 8.5% intergenic (–/+310) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,411 C→A 8.5% intergenic (–/+306) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,423 G→T 7.6% intergenic (–/+294) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,430 G→T 12.6% intergenic (–/+287) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 1,437 A→T 6.8% intergenic (–/+280) – / ← putative HTH domain protein –/–
RA pMUT1‑hok‑empty 4,123:1 +T 94.5% intergenic (‑341/–) putative rom (RNA I inhibition modulator protein) ← / – –/–
RA pMUT1‑hok‑empty 4,127 C→A 100% intergenic (‑345/–) putative rom (RNA I inhibition modulator protein) ← / – –/–
RA pMUT1‑hok‑empty 4,132 4 bp→TA 100% intergenic (‑350/–) putative rom (RNA I inhibition modulator protein) ← / – –/–

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_MW240712 189–2618 3084–2957 340–2896 16367 [15251] [15762] 16602 JNG15_RS00005–mobA JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP022686 262466 =1 (0.010)182 (1.260) 72/248 NT 99.5% coding (320/1647 nt) fadK medium‑chain fatty‑acid‑‑CoA ligase
?NZ_CP022686 = 1524130 NA (NA)intergenic (+8/+232) CIW80_RS07590/syd IS3‑like element ISEc52 family transposase/SecY‑interacting protein
* ? NZ_CP022686 = 2624681 (0.010)164 (1.140) 65/248 NT 99.4% coding (322/1647 nt) fadK medium‑chain fatty‑acid‑‑CoA ligase
?NZ_CP022686 = 1761697 NA (NA)intergenic (‑72/‑70) CIW80_RS08710/CIW80_RS08720 IS3‑like element ISEc52 family transposase/IS3‑like element IS600 family transposase
* ? pMUT1‑hok‑empty 456 =5492 (0.440)8085 (0.650) 233/248 NT 67.6% intergenic (–/+1261) –/putative HTH domain protein –/–
?pMUT1‑hok‑empty 4136 = 2270 (0.180)intergenic (‑354/–) putative rom (RNA I inhibition modulator protein)/– –/–
* ? pMUT1‑hok‑empty = 4918139 (0.660)6386 (0.650) 186/198 NT 59.3% intergenic (–/+1226) –/putative HTH domain protein –/–
?pMUT1‑hok‑empty = 4098 2267 (0.230)intergenic (‑316/–) putative rom (RNA I inhibition modulator protein)/– –/–