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 | 119,184 | T→G | 11.3% | F47V (TTT→GTT) | marB → | multiple antibiotic resistance protein MarB |
| RA | NZ_CP022686 | 177,514 | T→G | 5.2% | T138P (ACC→CCC) | uidB ← | glucuronide transporter |
| RA | NZ_CP022686 | 379,600 | T→G | 8.4% | intergenic (+35/‑20) | manZ → / → yobD | PTS mannose transporter subunit IID/DUF986 family protein |
| RA | NZ_CP022686 | 457,894 | Δ1 bp | 100% | pseudogene (288/997 nt) | CIW80_RS02445 ← | DUF968 domain‑containing protein |
| RA | NZ_CP022686 | 498,662 | A→C | 9.5% | C183G (TGT→GGT) | araH ← | arabinose ABC transporter permease AraH |
| RA | NZ_CP022686 | 513,980 | A→C | 9.8% | R56R (CGT→CGG) | tcyL ← | cystine ABC transporter permease |
| RA | NZ_CP022686 | 556,940 | A→T | 14.3% | intergenic (+124/‑724) | 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 | 18.9% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 24.6% | 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 | 27.0% | intergenic (‑30/+197) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 829,452 | G→T | 22.7% | intergenic (‑41/+186) | 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 | 957,112 | T→G | 14.7% | T89P (ACC→CCC) | ccmA ← | cytochrome c biogenesis heme‑transporting ATPase CcmA |
| RA | NZ_CP022686 | 1,005,073 | A→C | 8.3% | E376D (GAA→GAC) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,005,085 | C→A | 11.9% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,174,272 | A→C | 9.2% | intergenic (+1/‑43) | CIW80_RS05855 → / → CIW80_RS05860 | tRNA‑Val/tRNA‑Val |
| RA | NZ_CP022686 | 1,263,001 | T→G | 7.2% | K88N (AAA→AAC) | guaB ← | IMP dehydrogenase |
| RA | NZ_CP022686 | 1,280,117 | T→G | 11.6% | N8H (AAC→CAC) | yfgM ← | ancillary SecYEG translocon subunit YfgM |
| RA | NZ_CP022686 | 1,479,607 | A→C | 11.2% | intergenic (‑16/+177) | ftsB ← / ← ygbE | cell division protein FtsB/DUF3561 family protein |
| RA | NZ_CP022686 | 1,504,361 | G→T | 20.9% | V266V (GTG→GTT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,535,319 | T→G | 13.6% | M20R (ATG→AGG) | fucI → | L‑fucose isomerase |
| RA | NZ_CP022686 | 1,640,925 | A→C | 15.4% | R7S (AGA→AGC) | ygfM → | molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,244 | T→G | 9.9% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 14.1% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,705,974 | T→G | 8.3% | intergenic (‑584/‑71) | yqgB ← / → metK | acid stress response protein YqgB/methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,734,237 | A→G | 100% | W156R (TGG→CGG) | papX ← | HTH‑type transcriptional regulator PapX |
| RA | NZ_CP022686 | 1,775,845 | T→G | 9.1% | N198T (AAC→ACC) | CIW80_RS08815 ← | N‑acetylneuraminate epimerase |
| RA | NZ_CP022686 | 1,833,745 | T→G | 18.4% | N468H (AAC→CAC) | gspD ← | type II secretion system secretin GspD |
| RA | NZ_CP022686 | 1,841,961 | T→G | 8.5% | N55T (AAC→ACC) | sslE ← | lipoprotein metalloprotease SslE |
| RA | NZ_CP022686 | 1,845,397 | T→G | 5.7% | N474T (AAC→ACC) | glcB ← | malate synthase G |
| RA | NZ_CP022686 | 1,860,077 | G→T | 15.6% | G116G (GGC→GGA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,875,760 | A→C | 5.5% | G241G (GGT→GGG) | hybO ← | hydrogenase 2 small subunit |
| RA | NZ_CP022686 | 1,925,365 | A→C | 13.2% | D162A (GAC→GCC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 1,964,332 | A→C | 8.7% | G27G (GGT→GGG) | mug ← | G/U mismatch‑specific DNA glycosylase |
| RA | NZ_CP022686 | 2,148,136 | T→G | 12.5% | V133G (GTT→GGT) | panF → | sodium/pantothenate symporter |
| RA | NZ_CP022686 | 2,184,330 | G→T | 12.1% | F64L (TTC→TTA) | rplO ← | 50S ribosomal protein L15 |
| RA | NZ_CP022686 | 2,185,071 | A→C | 7.0% | G47G (GGT→GGG) | rpsE ← | 30S ribosomal protein S5 |
| RA | NZ_CP022686 | 2,185,075 | A→C | 8.3% | 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 | 2,268,329 | A→C | 8.1% | D260A (GAC→GCC) | pckA → | phosphoenolpyruvate carboxykinase (ATP) |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,361,489 | T→G | 14.4% | V188G (GTT→GGT) | nikA → | nickel ABC transporter substrate‑binding protein |
| RA | NZ_CP022686 | 2,362,954 | T→G | 6.2% | F152V (TTT→GTT) | nikB → | nickel ABC transporter permease subunit NikB |
| RA | NZ_CP022686 | 2,394,287 | T→G | 16.3% | N115T (AAC→ACC) | chuS ← | hematinate‑forming heme oxygenase ChuS |
| 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 | 13.5% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,516,873 | A→C | 10.7% | K761N (AAA→AAC) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,572,721 | A→C | 16.6% | F186C (TTT→TGT) | CIW80_RS12885 ← | ROK family protein |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,634,140 | A→C | 9.4% | V27G (GTC→GGC) | dgoD ← | galactonate dehydratase |
| RA | NZ_CP022686 | 2,717,385 | T→G | 10.2% | F96V (TTT→GTT) | ilvA → | threonine ammonia‑lyase, biosynthetic |
| RA | NZ_CP022686 | 2,758,109 | A→C | 14.2% | N34T (AAC→ACC) | yifL → | lipoprotein |
| RA | NZ_CP022686 | 2,769,196 | A→C | 17.8% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,780,110 | T→G | 8.3% | F677C (TTT→TGT) | metE → | 5‑methyltetrahydropteroyltriglutamate‑‑ homocysteine S‑methyltransferase |
| RA | NZ_CP022686 | 2,868,740 | T→G | 20.1% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,989,627 | T→G | 7.8% | Q39H (CAA→CAC) | thiC ← | phosphomethylpyrimidine synthase ThiC |
| RA | NZ_CP022686 | 2,994,693 | T→G | 10.9% | W162G (TGG→GGG) | yjaH → | DUF1481 domain‑containing protein |
| RA | NZ_CP022686 | 3,020,229 | T→G | 11.5% | V133G (GTC→GGC) | yjbB → | Na/Pi cotransporter family protein |
| RA | NZ_CP022686 | 3,066,354 | T→G | 10.7% | K134N (AAA→AAC) | CIW80_RS15265 ← | hypothetical protein |
| RA | NZ_CP022686 | 3,090,101 | A→C | 10.6% | V9G (GTT→GGT) | yjcB ← | YjcB family protein |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,265,096 | G→T | 14.9% | A73E (GCA→GAA) | ytfJ ← | YtfJ family protein |
| RA | NZ_CP022686 | 3,281,052 | T→G | 11.3% | F91V (TTT→GTT) | yjfF → | sugar ABC transporter permease YjfF |
| RA | NZ_CP022686 | 3,357,439 | G→T | 9.1% | G8C (GGT→TGT) | CIW80_RS16765 → | DUF932 domain‑containing protein |
| 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 | 17.2% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | NZ_CP022686 | 3,461,247 | A→C | 12.6% | noncoding (66/87 nt) | CIW80_RS17340 ← | tRNA‑Leu |
| RA | NZ_CP022686 | 3,652,079 | T→G | 8.7% | intergenic (‑88/+24) | panB ← / ← CIW80_RS18255 | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase/fimbrial‑like adhesin |
| RA | NZ_CP022686 | 3,656,188 | A→G | 100% | S549P (TCC→CCC) | htrE ← | outer membrane usher protein |
| RA | NZ_CP022686 | 3,731,470 | C→T | 58.4% | intergenic (+24/‑31) | rrf → / → CIW80_RS18620 | 5S ribosomal RNA/tRNA‑Asp |
| RA | NZ_CP022686 | 3,734,367 | T→G | 23.9% | F225V (TTT→GTT) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,734,380 | T→G | 18.6% | L229R (CTC→CGC) | yafD → | endonuclease/exonuclease/phosphatase family protein |
| RA | NZ_CP022686 | 3,770,508 | T→G | 9.7% | intergenic (‑244/+219) | CIW80_RS26265 ← / ← CIW80_RS18890 | ATP‑binding protein/hypothetical protein |
| RA | NZ_CP022686 | 3,770,509 | A→T | 9.7% | 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 | 11.8% | L130V (TTA→GTA) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,797,493 | G→T | 15.6% | G134C (GGT→TGT) | CIW80_RS19065 → | LacI family DNA‑binding transcriptional regulator |
| RA | NZ_CP022686 | 3,800,979 | A→C | 10.4% | pseudogene (1255/1773 nt) | CIW80_RS19080 → | ShlB/FhaC/HecB family hemolysin secretion/activation protein |
| RA | NZ_CP022686 | 3,852,459 | T→G | 9.3% | N178T (AAC→ACC) | phoE ← | phosphoporin PhoE |
| RA | NZ_CP022686 | 3,852,554 | T→G | 8.2% | K146N (AAA→AAC) | phoE ← | phosphoporin PhoE |
| RA | NZ_CP022686 | 3,868,846 | T→G | 13.6% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,981,933 | T→G | 8.9% | intergenic (+70/‑86) | proY → / → malZ | proline‑specific permease ProY/maltodextrin glucosidase |
| RA | NZ_CP022686 | 4,014,242 | A→T | 16.2% | intergenic (+88/‑256) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,014,266 | C→A | 11.2% | intergenic (+112/‑232) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,056,393 | T→G | 9.1% | intergenic (+22/‑159) | htpG → / → adk | molecular chaperone HtpG/adenylate kinase |
| RA | NZ_CP022686 | 4,056,962 | C→A | 19.0% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,152,582 | A→C | 7.9% | T301P (ACC→CCC) | entC → | isochorismate synthase EntC |
| RA | NZ_CP022686 | 4,213,260 | T→G | 10.6% | C188W (TGT→TGG) | ubiF → | 3‑demethoxyubiquinol 3‑hydroxylase |
| RA | NZ_CP022686 | 4,331,940 | A→C | 18.8% | F289V (TTT→GTT) | ybhR ← | ABC transporter permease |
| RA | NZ_CP022686 | 4,440,334 | A→C | 20.4% | Q797H (CAA→CAC) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,562,550 | T→G | 13.1% | N140H (AAC→CAC) | putA ← | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
| RA | NZ_CP022686 | 4,764,877 | T→G | 24.0% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,809,437 | T→G | 6.0% | L49R (CTG→CGG) | CIW80_RS24260 → | head‑tail joining protein |
| RA | NZ_CP022686 | 4,839,687 | T→G | 9.7% | N144T (AAC→ACC) | minD ← | septum site‑determining protein MinD |
| 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 | 4,905,221 | T→G | 11.2% | L116R (CTT→CGT) | CIW80_RS24815 → | coenzyme F390 synthetase |
| RA | NZ_CP022686 | 5,001,130 | T→G | 9.8% | W152G (TGG→GGG) | ompG → | monomeric porin OmpG |
| RA | NZ_CP022686 | 5,001,151 | G→C | 14.2% | A159P (GCC→CCC) | ompG → | monomeric porin OmpG |
| RA | NZ_CP022686 | 5,041,113 | T→C | 10.2% | N248N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,289 | T→C | 9.1% | N640N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 10.7% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,043,855 | T→A | 15.5% | G1162G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,149 | T→A | 8.5% | G1260G (GGT→GGA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,044,641 | C→T | 5.4% | N1424N (AAC→AAT) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 2,031 | G→A | 100% | intergenic (‑235/‑1500) | putative rom (RNA I inhibition modulator protein) ← / → ompA | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 2,815 | A→C | 5.2% | intergenic (‑1019/‑716) | putative rom (RNA I inhibition modulator protein) ← / → ompA | –/– |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 3,595 | Δ15 bp | 100% | [IL2wt no signal] | [IL2wt no signal] | |
| JC | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,019 | +CAT | 8.0% | intergenic (+12/+37) | IL2wt no signal → / ← annotated as hok_sok locus | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,868 | Δ1 bp | 91.4% | intergenic (‑233/+341) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| RA | pMut‑Ompa‑D5‑IL2wt‑His6 | 4,935 | G→T | 12.5% | intergenic (‑300/+274) | annotated as hok_sok locus ← / ← putative HTH domain protein | –/– |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_MW240712 | 684–2618 | 3045–2957 | 340–2362 | 3807 [3530] | [3706] 3773 | JNG15_RS00010–mobA | JNG15_RS00010,JNG15_RS00015,mobA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP022686 | 3743172 = | 212 (1.270) | 16 (0.100) | 11/248 | NT | 7.1% | intergenic (+1/+253) | CIW80_RS18695/CIW80_RS18700 | IS66 family transposase/IS110‑like element ISEc45 family transposase |
| ? | NZ_CP022686 | = 3744618 | 211 (1.280) | intergenic (‑60/‑4) | CIW80_RS18700/CIW80_RS18705 | IS110‑like element ISEc45 family transposase/transposase | |||||
| * | ? | NZ_MW240712 | 3 = | 0 (0.000) | 14 (0.000) +TC |
13/246 | NT | 100% | intergenic (–/+204) | –/JNG15_RS00005 | –/helix‑turn‑helix domain‑containing protein |
| ? | NZ_MW240712 | = 3173 | 0 (0.000) | intergenic (+182/–) | mobA/– | plasmid mobilization protein MobA/– | |||||