mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 182,646 | A→C | 15.7% | G68G (GGT→GGG) | malI ← | mal regulon transcriptional regulator MalI |
| RA | NZ_CP022686 | 360,227 | T→G | 16.4% | T35P (ACG→CCG) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| 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 | 13.6% | L399V (TTA→GTA) | otsA ← | alpha,alpha‑trehalose‑phosphate synthase |
| RA | NZ_CP022686 | 512,717 | T→G | 20.8% | intergenic (‑217/+13) | sdiA ← / ← yecC | transcriptional regulator SdiA/L‑cystine ABC transporter ATP‑binding protein YecC |
| 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 | 601,302 | T→G | 11.3% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| 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 | 829,441 | C→A | 23.6% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 17.8% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,467 | C→A | 25.0% | intergenic (‑56/+171) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 881,733 | A→C | 15.7% | intergenic (+248/+139) | yohP → / ← dusC | protein YohP/tRNA dihydrouridine(16) synthase DusC |
| RA | NZ_CP022686 | 881,760 | T→G | 19.3% | 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 | 948,049 | A→T | 15.6% | intergenic (+118/‑139) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 954,509 | G→C | 9.0% | A43G (GCC→GGC) | ccmF ← | cytochrome c‑type biogenesis heme lyase CcmF |
| RA | NZ_CP022686 | 1,005,085 | C→A | 12.7% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,174,272 | A→C | 14.3% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,333,577 | G→T | 8.2% | F23L (TTC→TTA) | yfhb ← | phosphatidylglycerophosphatase C |
| RA | NZ_CP022686 | 1,360,724 | G→T | 9.0% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,750 | G→T | 14.0% | intergenic (‑85/+239) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,371,086 | G→T | 20.7% | E34* (GAA→TAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,458,792 | G→T | 9.7% | E66* (GAA→TAA) | flhA → | formate hydrogenlyase transcriptional activator FlhA |
| RA | NZ_CP022686 | 1,479,607 | A→C | 13.1% | intergenic (‑16/+177) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,481,338 | A→C | 8.5% | G284G (GGT→GGG) | cysN ← | sulfate adenylyltransferase subunit CysN |
| RA | NZ_CP022686 | 1,481,343 | A→C | 12.0% | S283A (TCT→GCT) | cysN ← | sulfate adenylyltransferase subunit CysN |
| RA | NZ_CP022686 | 1,547,000 | G→C | 19.8% | intergenic (+22/‑12) | CIW80_RS07705 → / → CIW80_RS07710 | tRNA‑Met/tRNA‑Met |
| RA | NZ_CP022686 | 1,558,395 | A→C | 10.4% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,633,846 | T→G | 30.0% | N253T (AAC→ACC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,674,224 | T→G | 16.3% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,231 | A→T | 14.6% | V186E (GTA→GAA) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 14.0% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,716,167 | A→C | 16.3% | N49T (AAC→ACC) | rdgB → | XTP/dITP diphosphatase |
| RA | NZ_CP022686 | 1,833,745 | T→G | 15.8% | N468H (AAC→CAC) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,911,602 | T→G | 14.0% | N224T (AAC→ACC) | CIW80_RS09520 ← | MurR/RpiR family transcriptional regulator |
| RA | NZ_CP022686 | 1,954,923 | T→G | 20.4% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 1,979,459 | G→T | 7.6% | D538Y (GAT→TAT) | ygjK → | alpha‑glucosidase |
| RA | NZ_CP022686 | 2,049,089 | T→G | 14.2% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,049,094 | G→T | 10.7% | T254T (ACC→ACA) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,110,457 | T→G | 12.9% | K12N (AAA→AAC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,148,115 | T→G | 16.9% | L126R (CTG→CGG) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 6.9% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,185,075 | A→C | 13.7% | 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 | 2,310,451 | C→A | 7.5% | E241* (GAA→TAA) | glgP ← | glycogen phosphorylase |
| 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 | 9.8% | N26T (AAC→ACC) | dcrB → | phage sensitivity protein DcrB |
| RA | NZ_CP022686 | 2,393,050 | C→A | 7.9% | F12L (TTC→TTA) | dctR → | LuxR C‑terminal‑related transcriptional regulator |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,516,426 | T→A | 14.5% | G612G (GGT→GGA) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,572,721 | A→C | 12.6% | F186C (TTT→TGT) | CIW80_RS12885 ← | ROK family protein |
| RA | NZ_CP022686 | 2,574,451 | T→G | 13.4% | T223P (ACT→CCT) | CIW80_RS12895 ← | class II fructose‑bisphosphate aldolase family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,736,578 | C→A | 12.1% | T180T (ACC→ACA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,801,817 | T→G | 10.3% | Y32S (TAC→TCC) | CIW80_RS14030 ← | 2‑dehydro‑3‑deoxy‑6‑phosphogalactonate aldolase |
| RA | NZ_CP022686 | 2,868,740 | T→G | 20.3% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,871,422 | T→G | 13.5% | N149T (AAC→ACC) | fdnG ← | formate dehydrogenase‑N subunit alpha |
| RA | NZ_CP022686 | 2,920,428 | A→C | 13.0% | K68N (AAA→AAC) | CIW80_RS14610 → | bifunctional UDP‑sugar hydrolase/5'‑nucleotidase |
| RA | NZ_CP022686 | 2,994,693 | T→G | 13.5% | W162G (TGG→GGG) | yjaH → | DUF1481 domain‑containing protein |
| RA | NZ_CP022686 | 3,013,755 | T→G | 8.3% | V472G (GTG→GGG) | aceK → | bifunctional isocitrate dehydrogenase kinase/phosphatase |
| RA | NZ_CP022686 | 3,017,622 | A→C | 20.0% | K839N (AAA→AAC) | metH → | methionine synthase |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,265,091 | C→G | 9.8% | E75Q (GAG→CAG) | ytfJ ← | YtfJ family protein |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,451,845 | A→C | 8.9% | E278D (GAA→GAC) | lgoD → | L‑galactonate oxidoreductase |
| RA | NZ_CP022686 | 3,516,065 | C→A | 12.5% | L210M (CTG→ATG) | nhaA → | Na+/H+ antiporter NhaA |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,606,036 | G→T | 10.8% | E250* (GAA→TAA) | secA → | preprotein translocase subunit SecA |
| 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 | 19.6% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,770,509 | A→T | 11.8% | intergenic (‑245/+218) | CIW80_RS26265 ← / ← CIW80_RS18890 | ATP‑binding protein/hypothetical 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 | 21.0% | L130V (TTA→GTA) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| 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 | 12.4% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,925,289 | A→C | 14.9% | N156T (AAC→ACC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 3,940,724 | A→C | 8.7% | V308G (GTA→GGA) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 13.6% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,074,910 | G→C | 7.4% | V20V (GTC→GTG) | CIW80_RS20380 ← | hypothetical protein |
| RA | NZ_CP022686 | 4,290,599 | T→G | 8.5% | T121P (ACC→CCC) | ybgS ← | YbgS‑like family protein |
| RA | NZ_CP022686 | 4,368,380 | T→G | 13.4% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,334 | A→C | 20.7% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,485,614 | T→G | 13.0% | F139V (TTT→GTT) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | NZ_CP022686 | 4,615,712 | G→T | 52.3% | G122C (GGT→TGT) | CIW80_RS23065 → | hypothetical protein |
| RA | NZ_CP022686 | 4,632,182 | T→G | 15.1% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,642,951 | A→C | 8.1% | N732T (AAC→ACC) | sfaF → | S/F1C fimbrial usher SfaF/FocD |
| RA | NZ_CP022686 | 4,655,834 | A→C | 9.4% | R390R (CGT→CGG) | iroC ← | salmochelin/enterobactin export ABC transporter IroC |
| RA | NZ_CP022686 | 4,712,985 | A→C | 5.5% | intergenic (‑67/+67) | yceB ← / ← grxB | lipoprotein/glutaredoxin 2 |
| RA | NZ_CP022686 | 4,764,877 | T→G | 10.5% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,880 | T→G | 10.1% | intergenic (‑60/‑201) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,809,441 | T→G | 12.7% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,814,961 | T→G | 11.6% | F61C (TTT→TGT) | CIW80_RS24295 → | phage tail protein |
| RA | NZ_CP022686 | 4,814,990 | T→G | 13.7% | F71V (TTT→GTT) | CIW80_RS24295 → | phage tail protein |
| 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 | 5,041,191 | G→A | 5.5% | A274A (GCG→GCA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,558 | T→A | 8.2% | S1063R (AGT→AGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,149 | T→A | 9.5% | G1260G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 1,314:1 | +A | 100% | intergenic (–/+403) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 1,376 | Δ1 bp | 100% | intergenic (–/+341) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 94.1% | 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) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,802 | A→C | 5.1% | intergenic (‑1020/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 817–2618 | 2960–2957 | 340–2144 | 178 [143] | [154] 331 | JNG15_RS00010–[mobA] | JNG15_RS00010,JNG15_RS00015,[mobA] |
| * | * | ÷ | pMUT1‑hok‑empty | 1451–1574 | 3986–1722 | 149–2536 | 2770 [2672] | [2725] 2785 | putative HTH domain protein–putative rom (RNA I inhibition modulator protein) | putative HTH domain protein,uncharacterized protein,hypothetical protein,putative rom (RNA I inhibition modulator protein) |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 262466 = | 1 (0.010) | 162 (1.130) | 65/250 | NT | 99.4% | 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 | 1 (0.010) | 142 (0.990) | 48/250 | NT | 99.3% | 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 | 2516475 = | NA (NA) | 3 (0.020) | 3/242 | NT | 6.4% | coding (1885/5337 nt) | upaG | trimeric autotransporter adhesin UpaG |
| ? | NZ_CP022686 | = 2516495 | 45 (0.310) | coding (1905/5337 nt) | upaG | trimeric autotransporter adhesin UpaG | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 2004 (0.450) | 2925 (0.650) | 161/250 | NT | 67.6% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 800 (0.180) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 3058 (0.680) | 2186 (0.610) | 126/200 | NT | 57.4% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 797 (0.220) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||