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 |
| JC | NZ_CP022686 | 235,909 | +AGTGAT | 6.6% | coding (923/1413 nt) | pykF → | pyruvate kinase PykF |
| RA | NZ_CP022686 | 360,227 | T→G | 18.8% | 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 | 17.7% | V1607G (GTC→GGC) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,302 | T→G | 26.0% | R1609R (CGT→CGG) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 601,337 | T→G | 16.1% | V1621G (GTT→GGT) | irp1 → | yersiniabactin polyketide synthase HMWP1 |
| RA | NZ_CP022686 | 606,995 | A→C | 7.3% | R344S (AGA→AGC) | ybtU → | yersiniabactin biosynthesis oxidoreductase YbtU |
| MC JC | NZ_CP022686 | 628,478 | Δ1,286 bp | 100% | [clbP] | [clbP] | |
| RA | NZ_CP022686 | 694,391 | C→A | 13.7% | 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 | 764,997 | T→G | 14.1% | N41T (AAC→ACC) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 765,008 | A→T | 13.2% | I37I (ATT→ATA) | wcaM ← | colanic acid biosynthesis protein WcaM |
| RA | NZ_CP022686 | 794,460 | C→T | 100% | A568V (GCG→GTG) | dgcE → | diguanylate cyclase |
| RA | NZ_CP022686 | 829,452 | G→T | 26.4% | intergenic (‑41/+186) | gatY ← / ← fbaB | tagatose‑bisphosphate aldolase subunit GatY/class I fructose‑bisphosphate aldolase |
| RA | NZ_CP022686 | 837,555 | T→G | 16.9% | intergenic (‑128/+95) | thiM ← / ← rcnR | hydroxyethylthiazole kinase/Ni(II)/Co(II)‑binding transcriptional repressor RcnR |
| 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 | 948,090 | C→A | 16.5% | intergenic (+159/‑98) | CIW80_RS04855 → / → CIW80_RS04860 | terminase small subunit/hypothetical protein |
| RA | NZ_CP022686 | 973,436 | A→C | 5.3% | D253A (GAC→GCC) | rcsD → | phosphotransferase RcsD |
| JC | NZ_CP022686 | 1,061,329 | Δ6 bp | 10.0% | coding (42‑47/945 nt) | lrhA ← | transcriptional regulator LrhA |
| RA | NZ_CP022686 | 1,150,677 | T→G | 12.2% | G140G (GGT→GGG) | lpxP → | kdo(2)‑lipid IV(A) palmitoleoyltransferase |
| RA | NZ_CP022686 | 1,209,908 | T→G | 22.5% | D396A (GAC→GCC) | eutH ← | ethanolamine utilization protein EutH |
| RA | NZ_CP022686 | 1,249,402 | G→C | 9.1% | intergenic (‑49/+37) | uraA ← / ← upp | uracil permease/uracil phosphoribosyltransferase |
| RA | NZ_CP022686 | 1,293,944 | A→C | 8.7% | N201T (AAC→ACC) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| 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 | 1,558,395 | A→C | 10.0% | K464N (AAA→AAC) | vgrG → | type VI secretion system Vgr family protein |
| RA | NZ_CP022686 | 1,674,244 | T→G | 12.6% | T182P (ACC→CCC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,674,248 | T→G | 12.0% | Q180H (CAA→CAC) | ygfB ← | UPF0149 family protein YgfB |
| RA | NZ_CP022686 | 1,706,047 | G→T | 14.6% | M1M (ATG→ATT) † | metK → | methionine adenosyltransferase |
| RA | NZ_CP022686 | 1,860,070 | C→A | 24.1% | E119* (GAA→TAA) | CIW80_RS09255 ← | YtfJ family protein |
| RA | NZ_CP022686 | 1,911,602 | T→G | 11.9% | N224T (AAC→ACC) | CIW80_RS09520 ← | MurR/RpiR family transcriptional regulator |
| RA | NZ_CP022686 | 1,925,332 | A→C | 13.9% | N151T (AAC→ACC) | ygiB → | DUF1190 family protein |
| RA | NZ_CP022686 | 1,954,923 | T→G | 20.8% | T92P (ACG→CCG) | ttdR ← | DNA‑binding transcriptional activator TtdR |
| RA | NZ_CP022686 | 1,965,147 | A→T | 8.8% | L95Q (CTA→CAA) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | NZ_CP022686 | 2,046,901 | A→C | 9.1% | G304G (GGT→GGG) | mtr ← | tryptophan permease |
| RA | NZ_CP022686 | 2,123,241 | A→C | 10.4% | F208V (TTT→GTT) | tldD ← | metalloprotease TldD |
| RA | NZ_CP022686 | 2,130,829 | A→C | 14.5% | V237G (GTT→GGT) | mreC ← | rod shape‑determining protein MreC |
| RA | NZ_CP022686 | 2,172,177 | A→C | 6.1% | G87G (GGT→GGG) | smg ← | DUF494 family protein Smg |
| RA | NZ_CP022686 | 2,214,419 | T→C | 100% | K43R (AAA→AGA) | rpsL ← | 30S ribosomal protein S12 |
| RA | NZ_CP022686 | 2,226,139 | A→C | 7.9% | D9A (GAC→GCC) | crp → | cAMP‑activated global transcriptional regulator CRP |
| 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 | 21.9% | 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 | 13.5% | K72N (AAA→AAC) | glyS ← | glycine‑‑tRNA ligase subunit beta |
| RA | NZ_CP022686 | 2,516,888 | A→T | 6.7% | T766T (ACA→ACT) | upaG → | trimeric autotransporter adhesin UpaG |
| RA | NZ_CP022686 | 2,558,864 | T→G | 8.3% | F128V (TTT→GTT) | yicG → | trimeric intracellular cation channel family protein |
| RA | NZ_CP022686 | 2,559,398 | T→G | 10.0% | N461T (AAC→ACC) | ligB ← | NAD‑dependent DNA ligase LigB |
| JC | NZ_CP022686 | 2,590,563 | +TTGG | 100% | coding (109/153 nt) | CIW80_RS26455 → | hypothetical protein |
| RA | NZ_CP022686 | 2,703,299 | A→C | 12.1% | intergenic (‑203/‑277) | yieP ← / → CIW80_RS13540 | FadR/GntR family transcriptional regulator/16S ribosomal RNA |
| RA | NZ_CP022686 | 2,736,578 | C→A | 8.3% | T180T (ACC→ACA) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,736,586 | A→C | 15.0% | Y183S (TAC→TCC) | rffA → | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| RA | NZ_CP022686 | 2,834,898 | A→C | 13.0% | K601N (AAA→AAC) | polA → | DNA polymerase I |
| RA | NZ_CP022686 | 2,868,740 | T→G | 27.4% | Q22P (CAG→CCG) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 2,868,753 | T→G | 18.2% | T18P (ACC→CCC) | fdoH ← | formate dehydrogenase O subunit beta |
| RA | NZ_CP022686 | 3,111,374 | T→G | 7.2% | F362V (TTT→GTT) | gltP → | glutamate/aspartate:proton symporter GltP |
| RA | NZ_CP022686 | 3,136,940 | T→G | 11.6% | D161A (GAC→GCC) | phnN ← | ribose 1,5‑bisphosphokinase |
| JC | NZ_CP022686 | 3,196,873 | +GCGTAATCGGTT | 100% | coding (944/1122 nt) | ampC ← | BlaEC family class C beta‑lactamase |
| RA | NZ_CP022686 | 3,200,595 | A→C | 8.9% | V199G (GTT→GGT) | frdA ← | fumarate reductase (quinol) flavoprotein subunit |
| RA | NZ_CP022686 | 3,213,819 | T→G | 5.9% | R479R (CGT→CGG) | nnr → | bifunctional ADP‑dependent NAD(P)H‑hydrate dehydratase/NAD(P)H‑hydrate epimerase |
| RA | NZ_CP022686 | 3,239,387 | T→G | 8.9% | V396G (GTC→GGC) | ulaA → | PTS ascorbate transporter subunit IIC |
| RA | NZ_CP022686 | 3,265,084 | T→G | 15.3% | N77T (AAC→ACC) | 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 | 3,444,704 | T→G | 14.4% | T530P (ACC→CCC) | btsT ← | pyruvate/proton symporter BtsT |
| MC JC | NZ_CP022686 | 3,559,837 | Δ2,343 bp | 100% | coding (10‑2352/2352 nt) | polB ← | DNA polymerase II |
| 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 | 19.8% | 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 | 3,800,981 | A→C | 10.7% | pseudogene (1257/1773 nt) | CIW80_RS19080 → | ShlB/FhaC/HecB family hemolysin secretion/activation protein |
| MC JC | NZ_CP022686 | 3,844,426 | Δ1,036 bp | 100% | coding (2‑1037/1056 nt) | dinB → | DNA polymerase IV |
| RA | NZ_CP022686 | 3,949,969 | T→G | 14.5% | D141A (GAC→GCC) | hemB ← | porphobilinogen synthase |
| RA | NZ_CP022686 | 4,014,238 | C→G | 19.1% | intergenic (+84/‑260) | bolA → / → tig | transcriptional regulator BolA/trigger factor |
| RA | NZ_CP022686 | 4,368,341 | T→G | 19.5% | D47A (GAC→GCC) | ybiY ← | glycyl‑radical enzyme activating protein |
| RA | NZ_CP022686 | 4,440,324 | C→A | 19.4% | P794Q (CCG→CAG) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,440,334 | A→T | 26.3% | Q797H (CAA→CAT) | ftsK → | DNA translocase FtsK |
| RA | NZ_CP022686 | 4,452,668 | T→G | 8.4% | intergenic (‑37/+155) | pflA ← / ← pflB | pyruvate formate lyase 1‑activating protein/formate C‑acetyltransferase |
| RA | NZ_CP022686 | 4,535,285 | A→C | 13.6% | K97T (AAG→ACG) | appA → | bifunctional acid phosphatase/4‑phytase |
| RA | NZ_CP022686 | 4,632,217 | C→A | 9.7% | T288N (ACC→AAC) | mchF → | microcin export transporter peptidase/ATP‑binding subunit MchF |
| RA | NZ_CP022686 | 4,678,079 | T→A | 15.5% | intergenic (+77/‑44) | agn43 → / → CIW80_RS23450 | autotransporter adhesin Ag43/hypothetical protein |
| RA | NZ_CP022686 | 4,764,877 | T→G | 15.0% | intergenic (‑57/‑204) | ycfT ← / → lolC | acyltransferase family protein/lipoprotein‑releasing ABC transporter permease subunit LolC |
| RA | NZ_CP022686 | 4,809,441 | T→G | 13.4% | G50G (GGT→GGG) | CIW80_RS24260 → | head‑tail joining 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 | 5,042,304 | T→C | 14.3% | N645N (AAT→AAC) | CIW80_RS25525 → | EntS/YbdA MFS transporter |
| RA | pMUT1‑hok‑empty | 4,123:1 | +T | 94.9% | 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 | 370–2618 | 3061–2957 | 340–2692 | 6518 [6413] | [6390] 6441 | [JNG15_RS00005]–mobA | [JNG15_RS00005],JNG15_RS00010,JNG15_RS00015,mobA |
| * | * | ÷ | pMUT1‑hok‑empty | 1263–1317 | 3986–1722 | 406–2724 | 4036 [3799] | [3908] 3988 | 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 | = 235452 | 90 (0.670) | 7 (0.060) | 7/230 | NT | 7.3% | coding (466/1413 nt) | pykF | pyruvate kinase PykF |
| ? | NZ_CP022686 | 235630 = | 94 (0.770) | coding (644/1413 nt) | pykF | pyruvate kinase PykF | |||||
| * | ? | NZ_CP022686 | 262466 = | 1 (0.010) | 139 (1.040) | 62/250 | NT | 99.3% | 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 (0.010) | 115 (0.860) | 56/250 | NT | 98.3% | 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 | 3899666 = | 120 (0.900) | 34 (0.290) | 22/218 | NT | 24.3% | intergenic (‑40/+290) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | 3899944 = | 107 (0.920) | intergenic (‑318/+12) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | NZ_CP022686 | = 3899681 | 115 (0.860) | 39 (0.340) | 28/218 | NT | 27.3% | intergenic (‑55/+275) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA |
| ? | NZ_CP022686 | = 3899927 | 107 (0.920) | intergenic (‑301/+29) | hyxR/ipbA | LuxR family transcriptional regulator HyxR/tyrosine‑type DNA invertase IpbA | |||||
| * | ? | pMUT1‑hok‑empty | 456 = | 3203 (0.490) | 4064 (0.620) | 206/250 | NT | 65.1% | intergenic (–/+1261) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | 4136 = | 1148 (0.170) | intergenic (‑354/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||
| * | ? | pMUT1‑hok‑empty | = 491 | 4698 (0.710) | 3373 (0.640) | 169/200 | NT | 57.9% | intergenic (–/+1226) | –/putative HTH domain protein | –/– |
| ? | pMUT1‑hok‑empty | = 4098 | 1145 (0.220) | intergenic (‑316/–) | putative rom (RNA I inhibition modulator protein)/– | –/– | |||||