mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 340,453 | A→C | 12.9% | L52V (TTG→GTG) | ydjK ← | MFS transporter |
| RA | NZ_CP022686 | 349,092 | A→C | 13.8% | N602T (AAC→ACC) | yeaG → | protein kinase YeaG |
| RA | NZ_CP022686 | 360,227 | T→G | 26.5% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | NZ_CP022686 | 372,574 | A→C | 20.1% | N275T (AAC→ACC) | sdaA → | L‑serine ammonia‑lyase |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| 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 | 21.3% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 636,727 | A→C | 12.7% | L448V (TTG→GTG) | clbM ← | precolibactin export MATE transporter ClbM |
| RA | NZ_CP022686 | 694,391 | C→A | 11.8% | intergenic (+151/‑45) | CIW80_RS03555 → / → CIW80_RS03560 | transposase/PfkB family carbohydrate kinase |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,452 | G→T | 26.2% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,467 | C→A | 21.1% | intergenic (‑56/+171) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| 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 | 1,005,085 | C→A | 19.1% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,237,918 | C→A | 10.2% | C303F (TGC→TTC) | tmcA ← | tRNA cytosine(34) acetyltransferase TmcA |
| RA | NZ_CP022686 | 1,353,558 | T→A | 5.6% | intergenic (‑111/‑96) | yfiF ← / → trxC | tRNA/rRNA methyltransferase/thioredoxin TrxC |
| RA | NZ_CP022686 | 1,373,199 | G→C | 67.3% | T205T (ACG→ACC) | pheA → | bifunctional chorismate mutase/prephenate dehydratase |
| RA | NZ_CP022686 | 1,674,248 | T→G | 16.8% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,860,077 | G→T | 13.9% | G116G (GGC→GGA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,925,332 | A→C | 12.2% | N151T (AAC→ACC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 1,954,923 | T→G | 13.9% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,016,170 | A→C | 10.3% | noncoding (104/377 nt) | rnpB ← | RNase P RNA component class A |
| RA | NZ_CP022686 | 2,070,788 | A→C | 11.0% | intergenic (‑80/‑169) | greA ← / → dacB | transcription elongation factor GreA/serine‑type D‑Ala‑D‑Ala carboxypeptidase |
| 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 | 2,380,936 | A→C | 12.9% | K186N (AAA→AAC) | pitA → | inorganic phosphate transporter PitA |
| 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 | 14.0% | M1M (ATG→ATT) † | yhjY ← | autotransporter outer membrane beta‑barrel domain‑containing protein |
| RA | NZ_CP022686 | 2,516,577 | A→G | 11.8% | T663A (ACA→GCA) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,572,705 | A→C | 14.1% | G191G (GGT→GGG) | CIW80_RS12885 ← | ROK family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,617,885 | T→G | 11.0% | K190N (AAA→AAC) | ilvB ← | acetolactate synthase large subunit |
| RA | NZ_CP022686 | 2,736,578 | C→A | 10.8% | T180T (ACC→ACA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,743,563 | T→G | 11.8% | noncoding (65/87 nt) | CIW80_RS13750 → | tRNA‑Leu |
| RA | NZ_CP022686 | 2,758,109 | A→C | 6.8% | N34T (AAC→ACC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,868,740 | T→G | 17.5% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,423,638 | A→C | 9.8% | L373V (TTG→GTG) | yjiJ ← | MFS transporter |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,634,614 | A→C | 13.8% | K267N (AAA→AAC) | acnB → | bifunctional aconitate hydratase 2/2‑methylisocitrate dehydratase |
| 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 | 19.7% | 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 |
| RA | NZ_CP022686 | 3,797,481 | T→G | 18.1% | L130V (TTA→GTA) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,925,289 | A→C | 13.2% | N156T (AAC→ACC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 4,301,920 | T→G | 9.5% | V136G (GTT→GGT) | modB → | molybdate ABC transporter permease subunit |
| RA | NZ_CP022686 | 4,440,334 | A→T | 22.7% | Q797H (CAA→CAT) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,571,439 | T→G | 13.6% | H59P (CAC→CCC) | pgaC ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine synthase |
| RA | NZ_CP022686 | 4,643,107 | T→G | 6.6% | V784G (GTT→GGT) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| RA | NZ_CP022686 | 4,839,687 | T→G | 13.2% | N144T (AAC→ACC) | minD ← | septum site‑determining protein MinD |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 188–2618 | 3086–2957 | 340–2899 | 6695 [6506] | [6494] 6982 | JNG15_RS00005–mobA | JNG15_RS00005,JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pHH‑29_RBS | 2773–2841 | 5512–3104 | 264–2740 | 3152 [3135] | [2931] 3431 | putative HTH domain protein (MarR‑like)–hypothetical protein | putative HTH domain protein (MarR‑like),putative HTH domain protein,uncharacterized protein,hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 2 (0.020) | 114 (1.040) | 58/246 | NT | 98.3% | 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 | = 262468 | 2 (0.020) | 123 (1.120) | 57/246 | NT | 98.4% | 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 | |||||
| * | ? | NZ_CP022686 | = 3844425 | 1 (0.010) | 87 (0.800) | 54/244 | NT | 97.8% | coding (1/1056 nt) | dinB | DNA polymerase IV |
| ? | NZ_CP022686 | 3845462 = | 3 (0.030) | coding (1038/1056 nt) | dinB | DNA polymerase IV | |||||