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 | 192,617 | A→C | 9.4% | E676D (GAA→GAC) | rsxC → | electron transport complex subunit RsxC |
| RA | NZ_CP022686 | 349,997 | C→A | 11.4% | A221A (GCC→GCA) | yeaH → | YeaH/YhbH family protein |
| RA | NZ_CP022686 | 360,227 | T→G | 17.6% | 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 | 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 | 25.9% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 23.2% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 651,848 | A→C | 17.8% | R238R (CGT→CGG) | clbJ ← | colibactin non‑ribosomal peptide synthetase ClbJ |
| RA | NZ_CP022686 | 692,761 | C→A | 15.8% | S34Y (TCT→TAT) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 693,001 | A→C | 11.3% | N114T (AAC→ACC) | CIW80_RS03550 → | YaiO family outer membrane beta‑barrel protein |
| RA | NZ_CP022686 | 756,115 | A→G | 100% | G181G (GGT→GGC) | galE ← | UDP‑glucose 4‑epimerase GalE |
| RA | NZ_CP022686 | 764,997 | T→G | 20.8% | 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 | 829,467 | C→A | 15.4% | 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 | 9.2% | T380T (ACC→ACA) | nrdA → | ribonucleoside‑diphosphate reductase subunit alpha |
| RA | NZ_CP022686 | 1,100,944 | T→G | 18.0% | D187A (GAC→GCC) | aroC ← | chorismate synthase |
| RA | NZ_CP022686 | 1,360,724 | G→T | 11.2% | intergenic (‑59/+265) | kgtP ← / ← rrf | alpha‑ketoglutarate permease/5S ribosomal RNA |
| RA | NZ_CP022686 | 1,371,081 | C→A | 20.8% | P32Q (CCA→CAA) | bamD → | outer membrane protein assembly factor BamD |
| RA | NZ_CP022686 | 1,447,198 | T→A | 8.4% | V35V (GTA→GTT) | hycI ← | hydrogenase maturation peptidase HycI |
| RA | NZ_CP022686 | 1,504,310 | G→T | 18.2% | M249I (ATG→ATT) | CIW80_RS07520 → | YgcG family protein |
| RA | NZ_CP022686 | 1,558,395 | A→C | 16.7% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,633,846 | T→G | 37.2% | N253T (AAC→ACC) | yqeB ← | selenium‑dependent molybdenum cofactor biosynthesis protein YqeB |
| RA | NZ_CP022686 | 1,640,888 | G→T | 14.5% | intergenic (+34/‑17) | ssnA → / → ygfM | putative aminohydrolase SsnA/molybdopterin‑dependent oxidoreductase FAD‑binding subunit |
| RA | NZ_CP022686 | 1,674,244 | T→G | 9.7% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,796,792 | A→C | 10.1% | intergenic (+5/‑90) | agn43 → / → CIW80_RS08945 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 2,037,521 | A→C | 13.3% | T508P (ACC→CCC) | lpoA → | penicillin‑binding protein activator LpoA |
| RA | NZ_CP022686 | 2,110,465 | T→G | 9.9% | T10P (ACC→CCC) | rplM ← | 50S ribosomal protein L13 |
| RA | NZ_CP022686 | 2,129,903 | A→C | 7.3% | R12R (CGT→CGG) | yhdE ← | nucleoside triphosphate pyrophosphatase YhdE |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,257,128 | A→C | 5.8% | G94G (GGT→GGG) | hofM ← | DNA utilization protein HofM |
| RA | NZ_CP022686 | 2,320,775 | C→T | 100% | G274S (GGC→AGC) | CIW80_RS11675 ← | DNA‑processing protein DprA |
| RA | NZ_CP022686 | 2,397,379 | C→A | 12.4% | S12Y (TCC→TAC) | chuT → | heme ABC transporter substrate‑binding protein ChuT |
| RA | NZ_CP022686 | 2,408,861 | Δ1 bp | 100% | pseudogene (1097/3115 nt) | mdtF → | multidrug efflux pump RND permease MdtF |
| RA | NZ_CP022686 | 2,460,548 | G→C | 13.4% | Q11E (CAG→GAG) | yhjY ← | autotransporter outer membrane beta‑barrel domain‑containing protein |
| RA | NZ_CP022686 | 2,460,576 | C→A | 11.2% | M1M (ATG→ATT) † | yhjY ← | autotransporter outer membrane beta‑barrel domain‑containing protein |
| RA | NZ_CP022686 | 2,460,581 | A→C | 19.7% | intergenic (‑3/‑155) | yhjY ← / → tag | autotransporter outer membrane beta‑barrel domain‑containing protein/DNA‑3‑methyladenine glycosylase I |
| RA | NZ_CP022686 | 2,572,705 | A→C | 11.7% | G191G (GGT→GGG) | CIW80_RS12885 ← | ROK family protein |
| RA | NZ_CP022686 | 2,574,430 | T→G | 11.7% | N230H (AAC→CAC) | 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 | 2,736,573 | G→T | 11.3% | E179* (GAA→TAA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,736,585 | T→A | 13.0% | Y183N (TAC→AAC) ‡ | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,736,586 | A→C | 18.3% | Y183S (TAC→TCC) ‡ | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,769,196 | A→C | 17.3% | F47C (TTT→TGT) | rarD ← | EamA family transporter RarD |
| RA | NZ_CP022686 | 2,834,886 | A→C | 10.3% | K597N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,834,898 | A→C | 8.9% | K601N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,868,740 | T→G | 21.2% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 13.8% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,937,030 | T→G | 9.0% | K278N (AAA→AAC) | yijO ← | AraC family transcriptional regulator |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,424,795 | A→C | 100% | intergenic (‑41/+27) | yjiJ ← / ← yjiK | MFS transporter/YjiK family protein |
| RA | NZ_CP022686 | 3,461,215 | A→T | 14.0% | intergenic (‑24/+11) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,218 | G→C | 13.6% | intergenic (‑27/+8) | CIW80_RS17335 ← / ← CIW80_RS17340 | tRNA‑Leu/tRNA‑Leu |
| RA | NZ_CP022686 | 3,461,229 | T→G | 19.2% | 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 | 3,655,540 | A→C | 8.7% | 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 | 21.9% | 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 | 3,797,493 | G→T | 11.5% | G134C (GGT→TGT) | 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 | 13.9% | T383P (ACG→CCG) | ecpC ← | fimbrial usher EcpC |
| RA | NZ_CP022686 | 3,897,762 | C→A | 15.7% | pseudogene (114/1083 nt) | hyxB ← | outer membrane autotransporter HyxB |
| RA | NZ_CP022686 | 3,925,289 | A→C | 20.1% | N156T (AAC→ACC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 3,925,318 | G→C | 8.3% | D166H (GAC→CAC) | prpC → | 2‑methylcitrate synthase |
| RA | NZ_CP022686 | 3,928,369 | T→G | 13.1% | W285G (TGG→GGG) | prpE → | propionate‑‑CoA ligase |
| RA | NZ_CP022686 | 3,940,724 | A→C | 13.5% | V308G (GTA→GGA) | frmA ← | S‑(hydroxymethyl)glutathione dehydrogenase |
| RA | NZ_CP022686 | 3,949,969 | T→G | 17.1% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 3,971,626 | T→G | 6.5% | K121N (AAA→AAC) | araJ ← | MFS transporter AraJ |
| RA | NZ_CP022686 | 3,981,933 | T→G | 13.2% | intergenic (+70/‑86) | proY → / → malZ | proline‑specific permease ProY/maltodextrin glucosidase |
| RA | NZ_CP022686 | 4,014,238 | C→G | 17.8% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,056,962 | C→A | 18.9% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | NZ_CP022686 | 4,433,082 | A→C | 9.1% | L279V (TTA→GTA) | cydC ← | cysteine/glutathione ABC transporter ATP‑binding protein/permease CydC |
| RA | NZ_CP022686 | 4,448,670 | A→C | 9.2% | K161N (AAA→AAC) | dmsB → | dimethylsulfoxide reductase subunit B |
| RA | NZ_CP022686 | 4,562,550 | T→G | 14.2% | N140H (AAC→CAC) | putA ← | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
| RA | NZ_CP022686 | 4,589,367 | T→G | 11.2% | T247P (ACC→CCC) | CIW80_RS22920 ← | PatB family C‑S lyase |
| RA | NZ_CP022686 | 4,601,518 | T→A | 6.3% | I94F (ATT→TTT) | CIW80_RS22990 ← | thioesterase family protein |
| RA | NZ_CP022686 | 4,632,182 | T→G | 10.6% | R276R (CGT→CGG) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,762,516 | T→G | 13.8% | K368N (AAA→AAC) | mfd ← | transcription‑repair coupling factor |
| RA | NZ_CP022686 | 4,764,877 | T→G | 21.1% | intergenic (‑57/‑204) | 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 |
| 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 | 4,919,017 | T→G | 18.9% | E330D (GAA→GAC) | adhE ← | bifunctional acetaldehyde‑CoA/alcohol dehydrogenase |
| RA | NZ_CP022686 | 5,041,191 | G→A | 5.2% | A274A (GCG→GCA) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | NZ_CP022686 | 5,042,304 | T→C | 8.9% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 1,376 | Δ1 bp | 100% | intergenic (–/+341) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 1,412 | G→T | 8.0% | intergenic (–/+305) | – / ← putative HTH domain protein | –/– |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 100% | 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 | 4,130:1 | +T | 93.1% | intergenic (‑348/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| JC | pMUT1‑hok‑empty | 4,132 | Δ3 bp | 94.2% | intergenic (‑350/–) | putative rom (RNA I inhibition modulator protein) ← / – | –/– |
| RA | pMUT1‑hok‑empty | 4,135 | G→A | 100% | intergenic (‑353/–) | 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 | 189–2618 | 3084–2957 | 340–2896 | 7347 [6694] | [6881] 7466 | 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 = | 0 (0.000) | 121 (0.920) | 56/248 | 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) | 115 (0.880) | 51/248 | 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 | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 2300 (0.440) | 3441 (0.660) | 211/248 | NT | 74.4% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 63 (0.010) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 3443 (0.660) | 2472 (0.590) | 162/198 | NT | 63.8% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 59 (0.010) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||