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 | 160,899 | T→G | 7.9% | D283A (GAC→GCC) | pntA ← | Re/Si‑specific NAD(P)(+) transhydrogenase subunit alpha |
| RA | NZ_CP022686 | 235,363 | Δ1 bp | 8.5% | coding (377/1413 nt) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 235,398:1 | +A | 7.0% | coding (412/1413 nt) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 235,398:2 | +A | 7.0% | coding (412/1413 nt) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 360,227 | T→G | 10.9% | 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 | 531,409 | G→C | 13.4% | A45P (GCC→CCC) | fliF → | flagellar basal‑body MS‑ring/collar protein FliF |
| 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 | 15.2% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 12.9% | 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 | 764,997 | T→G | 15.5% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,441 | C→A | 20.5% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 837,573 | C→A | 14.8% | intergenic (‑146/+77) | thiM ← / ← rcnR | hydroxyethylthiazole kinase/Ni(II)/Co(II)‑binding transcriptional repressor RcnR |
| RA | NZ_CP022686 | 857,274 | T→G | 7.8% | G78G (GGT→GGG) | yehL → | MoxR family ATPase |
| 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 | 948,046 | G→T | 12.4% | intergenic (+115/‑142) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 948,090 | C→A | 19.3% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 1,005,085 | C→A | 11.0% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,040,909 | A→C | 12.4% | E232D (GAA→GAC) | rbn → | ribonuclease BN |
| RA | NZ_CP022686 | 1,100,944 | T→G | 11.4% | D187A (GAC→GCC) | aroC ← | chorismate synthase |
| RA | NZ_CP022686 | 1,174,272 | A→C | 14.2% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,209,908 | T→G | 21.5% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,213,479 | T→G | 17.5% | G420G (GGA→GGC) | eutE ← | aldehyde dehydrogenase EutE |
| RA | NZ_CP022686 | 1,360,709 | T→G | 8.8% | intergenic (‑44/+280) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,742 | C→A | 9.9% | intergenic (‑77/+247) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,360,750 | G→T | 13.2% | intergenic (‑85/+239) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,371,081 | C→A | 19.5% | P32Q (CCA→CAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,479,619 | T→A | 12.8% | intergenic (‑28/+165) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,633,846 | T→G | 31.6% | N253T (AAC→ACC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,674,224 | T→G | 13.5% | K188N (AAA→AAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,244 | T→G | 14.0% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 8.6% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,758,771 | T→G | 8.7% | intergenic (+18/‑254) | sat → / → CIW80_RS08700 | serine protease autotransporter toxin Sat/transposase |
| RA | NZ_CP022686 | 1,954,923 | T→G | 10.3% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 2,049,089 | T→G | 19.5% | N256T (AAC→ACC) | deaD ← | ATP‑dependent RNA helicase DeaD |
| RA | NZ_CP022686 | 2,148,103 | T→G | 18.2% | L122R (CTT→CGT) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,172,177 | A→C | 6.8% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,185,075 | A→C | 9.6% | 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 | 2,357,324 | A→C | 18.6% | N37T (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 | 2,470,422 | T→G | 15.1% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,558,864 | T→G | 5.7% | 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 | 2,612,255 | A→C | 7.4% | V217G (GTT→GGT) | uhpC ← | MFS transporter family glucose‑6‑phosphate receptor UhpC |
| RA | NZ_CP022686 | 2,736,586 | A→C | 15.7% | Y183S (TAC→TCC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,743,563 | T→G | 11.9% | noncoding (65/87 nt) | CIW80_RS13750 → | tRNA‑Leu |
| RA | NZ_CP022686 | 2,769,196 | A→C | 26.2% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,834,886 | A→C | 11.1% | K597N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,868,740 | T→G | 17.3% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,933,191 | A→C | 6.9% | T8P (ACC→CCC) | frwB → | PTS fructose‑like transporter subunit IIB |
| RA | NZ_CP022686 | 2,933,234 | A→C | 11.6% | E22A (GAG→GCG) | frwB → | PTS fructose‑like transporter subunit IIB |
| RA | NZ_CP022686 | 2,981,612 | A→C | 8.7% | T567P (ACC→CCC) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | NZ_CP022686 | 2,989,627 | T→G | 8.0% | Q39H (CAA→CAC) | thiC ← | phosphomethylpyrimidine synthase ThiC |
| RA | NZ_CP022686 | 3,020,229 | T→G | 16.9% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,213,199 | A→C | 7.7% | T273P (ACG→CCG) | nnr → | bifunctional ADP‑dependent NAD(P)H‑hydrate dehydratase/NAD(P)H‑hydrate epimerase |
| 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 | 13.3% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,461,218 | G→C | 11.7% | intergenic (‑27/+8) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,493,165 | G→T | 8.9% | R447L (CGT→CTT) | creD → | cell envelope integrity protein CreD |
| RA | NZ_CP022686 | 3,516,069 | T→G | 6.0% | V211G (GTT→GGT) | nhaA → | Na+/H+ antiporter NhaA |
| RA | NZ_CP022686 | 3,528,214 | A→C | 6.5% | T56P (ACC→CCC) | carB → | carbamoyl‑phosphate synthase large subunit |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| RA | NZ_CP022686 | 3,570,234 | T→G | 9.3% | L217V (TTG→GTG) | yabI → | DedA family protein |
| RA | NZ_CP022686 | 3,634,614 | A→C | 8.5% | 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 | 3,792,805 | A→G | 100% | Y421C (TAC→TGC) | fucP → | L‑fucose:H+ symporter permease |
| RA | NZ_CP022686 | 3,806,256 | G→T | 11.4% | E1583* (GAA→TAA) | cdiA → | contact‑dependent inhibition effector tRNA nuclease |
| 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 | 12.1% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,925,282 | A→C | 12.0% | S154R (AGC→CGC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 3,925,289 | A→C | 16.3% | N156T (AAC→ACC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 3,935,324 | T→G | 18.6% | N705T (AAC→ACC) | lacZ ← | beta‑galactosidase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 12.8% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 3,977,631 | A→C | 15.7% | H80P (CAC→CCC) | phoR → | phosphate regulon sensor histidine kinase PhoR |
| RA | NZ_CP022686 | 3,977,656 | A→C | 12.9% | K88N (AAA→AAC) | phoR → | phosphate regulon sensor histidine kinase PhoR |
| RA | NZ_CP022686 | 4,014,238 | C→G | 9.1% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,074,434 | T→G | 6.2% | E179A (GAG→GCG) | CIW80_RS20380 ← | hypothetical protein |
| RA | NZ_CP022686 | 4,287,491 | T→G | 8.4% | noncoding (4/76 nt) | CIW80_RS21480 → | tRNA‑Lys |
| RA | NZ_CP022686 | 4,287,507 | T→G | 8.1% | noncoding (20/76 nt) | CIW80_RS21480 → | tRNA‑Lys |
| RA | NZ_CP022686 | 4,368,380 | T→G | 17.2% | N34T (AAC→ACC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,334 | A→C | 23.7% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,445,534 | T→G | 9.0% | intergenic (+40/‑199) | serS → / → dmsA | serine‑‑tRNA ligase/dimethylsulfoxide reductase subunit A |
| RA | NZ_CP022686 | 4,485,614 | T→G | 10.1% | F139V (TTT→GTT) | gloC → | hydroxyacylglutathione hydrolase GloC |
| RA | NZ_CP022686 | 4,587,091 | T→G | 16.8% | N609T (AAC→ACC) | CIW80_RS22915 ← | enterotoxin |
| RA | NZ_CP022686 | 4,632,182 | T→G | 11.0% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,764,877 | T→G | 19.3% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,764,880 | T→G | 11.0% | intergenic (‑60/‑201) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,809,441 | T→G | 9.4% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,814,990 | T→G | 15.2% | 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 | 4,905,170 | T→G | 13.1% | V99G (GTT→GGT) | CIW80_RS24815 → | coenzyme F390 synthetase |
| RA | NZ_CP022686 | 4,905,221 | T→G | 13.8% | L116R (CTT→CGT) | CIW80_RS24815 → | coenzyme F390 synthetase |
| RA | NZ_CP022686 | 4,951,536 | G→C | 16.0% | A44P (GCC→CCC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 4,952,020 | T→G | 9.5% | V205G (GTC→GGC) | topA → | type I DNA topoisomerase |
| RA | NZ_CP022686 | 5,041,191 | G→A | 6.5% | A274A (GCG→GCA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,289 | T→C | 9.2% | N640N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→G | 13.6% | N645K (AAT→AAG) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,014 | T→A | 11.6% | V1215V (GTT→GTA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| 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 | 798–2618 | 2975–2957 | 340–2178 | 1199 [1184] | [1066] 1335 | JNG15_RS00010–[mobA] | JNG15_RS00010,JNG15_RS00015,[mobA] |
| * | * | ÷ | pMUT1‑hok‑empty | 1263–1574 | 3983–1582 | 9–2721 | 4696 [4388] | [4395] 4430 | 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 = | 0 (0.000) | 147 (0.900) | 59/250 | NT | 100% | 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 | 0 (0.000) | 159 (0.970) | 64/250 | NT | 100% | 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 | = 2864066 | NA (NA) | 18 (0.110) | 4/246 | NT | 25.7% | intergenic (+28/‑209) | CIW80_RS14325/CIW80_RS14330 | ISL3‑like element ISEc53 family transposase/hypothetical protein |
| ? | NZ_CP022686 | 4844809 = | 53 (0.320) | intergenic (‑230/‑33) | hlyE/umuD | hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit | |||||
| * | ? | NZ_CP022686 | = 3403347 | NA (NA) | 32 (0.200) | 4/250 | NT | 43.8% | intergenic (‑99/‑1) | CIW80_RS17025/fimB | ClbS/DfsB family four‑helix bundle protein/type 1 fimbria switch DNA invertase FimB |
| ? | NZ_CP022686 | = 4844816 | 41 (0.250) | intergenic (‑237/‑26) | hlyE/umuD | hemolysin HlyE/translesion error‑prone DNA polymerase V autoproteolytic subunit | |||||
| * | ? | NZ_CP022686 | 3899666 = | 165 (1.010) | 22 (0.150) | 16/218 | NT | 13.3% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 143 (1.010) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 155 (0.950) | 24 (0.170) | 14/218 | NT | 14.7% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 143 (1.010) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 3532 (0.450) | 4888 (0.620) | 214/250 | NT | 66.3% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 1432 (0.180) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 5175 (0.660) | 3919 (0.620) | 171/200 | NT | 58.5% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 1426 (0.230) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||