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 | position | mutation | annotation | gene | description |
| RA | 21,427 | A→G | I7M (ATA→ATG) | ribF → | bifunctional riboflavin kinase/FMN adenylyltransferase |
| RA | 73,675 | C→T | D283N (GAT→AAT) | thiP ← | thiamine ABC transporter membrane subunit |
| RA | 111,472 | A→G | intergenic (+39/+177) | mutT → / ← yacG | 8‑oxo‑dGTP diphosphatase/DNA gyrase inhibitor YacG |
| RA | 134,887 | T→C | K232K (AAA→AAG) | speD ← | S‑adenosylmethionine decarboxylase proenzyme |
| RA | 140,015 | Δ1 bp | coding (1211/2391 nt) | gcd ← | quinoprotein glucose dehydrogenase |
| RA | 154,247 | T→G | T394P (ACG→CCG) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 154,673 | A→G | S252P (TCT→CCT) | htrE ← | putative fimbrial usher protein HtrE |
| RA | 163,921 | A→G | D606G (GAC→GGC) | hrpB → | putative ATP‑dependent RNA helicase HrpB |
| RA | 168,708 | A→G | T409A (ACC→GCC) | fhuA → | ferrichrome outer membrane transporter/phage receptor |
| RA | 210,867 | A→G | T397A (ACC→GCC) | ldcC → | lysine decarboxylase 2 |
| RA | 256,653 | A→G | T43A (ACC→GCC) | frsA → | fermentation‑respiration switch protein |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 265,136 | A→G | V24A (GTC→GCC) | yafX ← | CP4‑6 prophage; protein YafX |
| RA | 303,093 | (G)6→7 | coding (103/615 nt) | yagU → | inner membrane protein that contributes to acid resistance |
| RA | 306,891 | A→G | G814G (GGT→GGC) | ecpC ← | putative fimbrial usher protein EcpC |
| RA | 321,642 | A→G | D12G (GAC→GGC) | ykgE → | putative lactate utilization oxidoreductase YkgE |
| RA | 324,899 | T→C | T156A (ACA→GCA) | ykgH ← | uncharacterized protein YkgH |
| RA | 331,300 | A→G | Y613C (TAC→TGC) | betT → | choline:H(+) symporter |
| RA | 342,567 | Δ1 bp | intergenic (+60/‑317) | yahJ → / → yahK | putative deaminase with metallo‑dependent hydrolase domain/aldehyde reductase, NADPH‑dependent |
| RA | 343,422 | T→G | V180G (GTG→GGG) | yahK → | aldehyde reductase, NADPH‑dependent |
| RA | 345,601 | (G)5→6 | coding (198/246 nt) | yahM → | uncharacterized protein YahM |
| RA | 347,702 | T→C | T248A (ACG→GCG) | prpR ← | DNA‑binding transcriptional dual regulator PrpR |
| RA | 349,785 | A→G | intergenic (+213/‑227) | prpB → / → prpC | 2‑methylisocitrate lyase/2‑methylcitrate synthase |
| RA | 355,098 | T→C | G59G (GGT→GGC) | codB → | cytosine transporter |
| RA | 409,791 | A→G | S77P (TCT→CCT) | rdgC ← | nucleoid‑associated protein RdgC |
| RA | 417,596 | C→T | P152L (CCG→CTG) | phoB → | DNA‑binding transcriptional dual regulator PhoB |
| RA | 428,460 | A→G | I272V (ATT→GTT) | secD → | Sec translocon accessory complex subunit SecD |
| RA | 448,202 | A→G | G153G (GGT→GGC) | cyoC ← | cytochrome bo3 ubiquinol oxidase subunit 3 |
| RA | 455,861 | T→C | R243R (CGT→CGC) | tig → | trigger factor |
| RA | 503,187 | C→T | A18T (GCC→ACC) | ybaL ← | putative transporter YbaL |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 558,618 | A→G | N136S (AAT→AGT) | sfmA → | putative fimbrial protein SfmA |
| RA | 562,090 | A→G | S798S (TCA→TCG) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 587,362 | A→G | V207A (GTC→GCC) | ybcH ← | DUF4434 domain‑containing protein YbcH |
| RA | 589,388 | A→G | Y523H (TAT→CAT) | nfrA ← | bacteriophage N4 receptor, outer membrane protein |
| RA | 591,410 | T→G | D590A (GAC→GCC) | nfrB ← | bacteriophage N4 receptor, inner membrane subunit |
| RA | 601,896 | G→A | intergenic (+39/‑63) | cusA → / → pheP | copper/silver export system RND permease/phenylalanine:H(+) symporter PheP |
| RA | 605,944 | T→C | intergenic (‑58/+7) | ybdF ← / ← ybdJ | PF04237 family protein YbdF/DUF1158 domain‑containing protein YbdJ |
| RA | 609,518 | A→G | F188L (TTT→CTT) | entD ← | phosphopantetheinyl transferase EntD |
| RA | 634,722 | A→G | A379A (GCA→GCG) | ybdL → | methionine‑oxo‑acid transaminase, PLP‑dependent |
| RA | 646,209 | A→G | R124R (CGT→CGC) | citT ← | citrate:succinate antiporter |
| RA | 656,758 | A→G | T68A (ACC→GCC) | pagP → | Lipid IVA palmitoyltransferase |
| RA | 679,763 | G→A | A86T (GCA→ACA) | ybeU → | DUF1266 domain‑containing protein YbeU |
| RA | 690,049 | T→C | Q278R (CAA→CGA) | lnt ← | apolipoprotein N‑acyltransferase |
| RA | 696,592 | T→C | noncoding (25/75 nt) | glnV ← | tRNA‑Gln |
| RA | 709,870 | T→C | S27S (AGT→AGC) | chiQ → | lipoprotein ChiQ |
| RA | 731,035 | A→T | I485M (ATA→TTG) | rhsC → | rhs element protein RhsC |
| RA | 731,037 | A→G | I485M (ATA→TTG) | rhsC → | rhs element protein RhsC |
| RA | 731,455 | T→C | C625R (TGT→CGT) | rhsC → | rhs element protein RhsC |
| RA | 731,472 | T→G | G630G (GGT→GGG) | rhsC → | rhs element protein RhsC |
| RA | 743,934 | (A)5→4 | coding (342/657 nt) | pxpB → | 5‑oxoprolinase component B |
| RA | 800,419 | T→C | T53A (ACA→GCA) | ybhD ← | putative DNA‑binding transcriptional regulator YbhD |
| RA | 810,031 | A→G | T230A (ACG→GCG) | bioB → | biotin synthase |
| RA | 813,338 | A→G | intergenic (+391/‑188) | bioD → / → uvrB | dethiobiotin synthetase/excision nuclease subunit B |
| RA | 823,294 | A→G | V149A (GTA→GCA) | clsB ← | cardiolipin synthase B |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 902,309 | A→G | V227A (GTG→GCG) | artI ← | putative ABC transporter periplasmic binding protein ArtI |
| RA | 925,969 | A→G | noncoding (3/88 nt) | serW ← | tRNA‑Ser |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 961,913 | A→G | intergenic (+29/‑82) | cmk → / → rpsA | cytidylate kinase/30S ribosomal subunit protein S1 |
| RA | 991,561 | T→C | F314L (TTC→CTC) | pepN → | aminopeptidase N |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,015,783 | A→G | G23G (GGA→GGG) | rmf → | ribosome modulation factor |
| RA | 1,018,976 | (A)8→7 | intergenic (+39/+37) | matP → / ← ompA | macrodomain Ter protein/outer membrane porin A |
| RA | 1,032,104 | T→C | intergenic (‑392/‑35) | serT ← / → hyaA | tRNA‑Ser/hydrogenase 1 small subunit |
| RA | 1,074,846 | A→G | Q202R (CAG→CGG) | rutR → | DNA‑binding transcriptional dual regulator RutR |
| RA | 1,131,195 | A→G | T60A (ACC→GCC) | flgB → | flagellar basal‑body rod protein FlgB |
| RA | 1,139,597 | T→C | V407A (GTT→GCT) | flgK → | flagellar hook‑filament junction protein 1 |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,151,919 | T→C | intergenic (+68/‑20) | acpP → / → fabF | acyl carrier protein/beta‑ketoacyl‑[acyl carrier protein] synthase II |
| RA | 1,158,486 | A→G | V206V (GTA→GTG) | ptsG → | glucose‑specific PTS enzyme IIBC component |
| RA | 1,168,979 | (A)6→5 | intergenic (‑147/‑94) | comR ← / → bhsA | DNA‑binding transcriptional repressor ComR/DUF1471 domain‑containing multiple stress resistance outer membrane protein BhsA |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,282,908 | T→C | G1015G (GGT→GGC) | narG → | nitrate reductase A subunit alpha |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,324,648 | T→C | V184A (GTT→GCT) | yciO → | putative RNA‑binding protein YciO |
| RA | 1,329,681 | T→C | V117A (GTG→GCG) | sohB → | S49 peptidase family protein |
| RA | 1,336,334 | T→C | S168S (AGT→AGC) | acnA → | aconitate hydratase 1 |
| RA | 1,336,381 | A→G | N184S (AAC→AGC) | acnA → | aconitate hydratase 1 |
| RA | 1,348,051 | G→A | L288F (CTC→TTC) | rnb ← | RNase II |
| RA | 1,351,696 | T→C | K22R (AAG→AGG) | ycjD ← | DUF559 domain‑containing protein YcjD |
| RA | 1,358,269 | C→T | A307T (GCT→ACT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,370,044 | (T)9→8 | intergenic (+41/‑172) | pspE → / → ycjM | thiosulfate sulfurtransferase PspE/glucosylglycerate phosphorylase |
| RA | 1,373,029 | A→G | N374S (AAT→AGT) | ycjN → | putative ABC transporter periplasmic binding protein YcjN |
| RA | 1,376,293 | C→T | A87V (GCG→GTG) | ycjR → | putative ketohexose‑3‑epimerase YcjR |
| RA | 1,396,107 | T→C | F11S (TTC→TCC) | insH‑4 → | IS5 transposase and trans‑activator |
| RA | 1,420,357 | T→G | intergenic (‑116/‑8) | racR ← / → ydaS | Rac prophage; DNA‑binding transcriptional repressor RacR/Rac prophage; toxin YdaS |
| RA | 1,430,254 | A→G | R402R (AGA→AGG) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,445,992 | A→G | Y38C (TAC→TGC) | ydbL → | DUF1318 domain‑containing protein YdbL |
| RA | 1,449,064 | (T)7→6 | intergenic (+46/+12) | feaB → / ← tynA | phenylacetaldehyde dehydrogenase/copper‑containing amine oxidase |
| RA | 1,488,752 | T→C | V174A (GTC→GCC) | aldA → | aldehyde dehydrogenase A |
| RA | 1,519,516 | (G)5→6 | coding (490/1038 nt) | curA → | NADPH‑dependent curcumin/dihydrocurcumin reductase |
| RA | 1,526,028 | A→G | intergenic (‑48/‑219) | ansP ← / → yncG | L‑asparagine transporter/putative glutathione S‑transferase YncG |
| RA | 1,541,275 | T→G | N439T (AAT→ACT) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,542,454 | A→G | V46A (GTG→GCG) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,542,644 | A→G | intergenic (‑54/+28) | narZ ← / ← narU | nitrate reductase Z subunit alpha/nitrate/nitrite transporter NarU |
| RA | 1,546,963 | A→G | S69S (AGT→AGC) | yddG ← | aromatic amino acid exporter |
| RA | 1,599,454 | G→A | G252G (GGC→GGT) | lsrK ← | autoinducer‑2 kinase |
| RA | 1,617,606 | T→C | S193S (AGT→AGC) | ydeA → | L‑arabinose exporter |
| RA | 1,632,327 | T→C | intergenic (‑42/‑563) | ydfJ ← / → ynfT | putative transporter YdfJ/Qin prophage; protein YnfT |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,635,861 | T→C | I169M (ATA→ATG) | nohA ← | Qin prophage; putative prophage DNA‑packaging protein NohA |
| RA | 1,641,656 | A→G | intergenic (‑102/‑199) | cspB ← / → cspF | Qin prophage; cold shock‑like protein CspB/Qin prophage; cold shock protein CspF |
| RA | 1,666,097 | A→G | A261A (GCA→GCG) | clcB → | putative chloride:H(+) antiporter ClcB |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,690,148 | T→C | G99G (GGT→GGC) | ydgA → | conserved protein YdgA |
| RA | 1,708,437 | G→T | A507S (GCT→TCT) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,714,096 | T→C | V443A (GTG→GCG) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,721,339 | T→C | W26R (TGG→CGG) | ydhJ → | putative membrane fusion protein YdhJ |
| RA | 1,736,876 | T→C | T139A (ACC→GCC) | ydhP ← | putative transporter YdhP |
| RA | 1,743,648 | G→A | L64L (CTG→CTA) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,758,213 | T→C | G171G (GGA→GGG) | ldtE ← | L,D‑transpeptidase LdtE |
| RA | 1,777,538 | A→G | T115A (ACG→GCG) | ydiO → | putative acyl‑CoA dehydrogenase |
| RA | 1,830,377 | T→C | D130G (GAC→GGC) | astA ← | arginine N‑succinyltransferase |
| RA | 1,837,853 | T→C | G214G (GGT→GGC) | ynjC → | putative ABC transporter membrane subunit YnjC |
| RA | 1,841,011 | T→C | A131A (GCA→GCG) | ynjF ← | putative phosphatidyl transferase, inner membrane protein |
| RA | 1,871,832 | (G)6→7 | coding (1448/1476 nt) | cdgI → | putative c‑di‑GMP binding protein CdgI |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| RA | 1,875,056 | (C)6→7 | coding (521/822 nt) | nimR ← | DNA‑binding transcriptional repressor NimR |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,911,616 | T→C | G447G (GGT→GGC) | yebQ → | putative transporter YebQ |
| RA | 1,923,526 | T→C | T61A (ACC→GCC) | yebY ← | DUF2511 domain‑containing protein YebY |
| RA | 1,923,946 | (G)6→7 | coding (646/873 nt) | yebZ ← | putative inner membrane protein |
| RA | 1,940,521 | T→C | Q372R (CAG→CGG) | mepM ← | peptidoglycan DD‑endopeptidase MepM |
| RA | 1,948,807 | G→A | N572N (AAC→AAT) | aspS ← | aspartate‑‑tRNA ligase |
| RA | 1,949,996 | T→C | Y176C (TAC→TGC) | aspS ← | aspartate‑‑tRNA ligase |
| RA | 1,969,994 | T→C | T331A (ACA→GCA) | tap ← | methyl‑accepting chemotaxis protein Tap |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,012,563 | (G)6→7 | pseudogene (62/279 nt) | intG → | putative defective phage integrase |
| RA | 2,014,971 | A→G | Q31R (CAG→CGG) | fliG → | flagellar motor switch protein FliG |
| RA | 2,065,765 | A→G | intergenic (‑1/+540) | cobU ← / ← insH‑6 | cobinamide‑P guanylyltransferase/cobinamide kinase/CP4‑44 prophage; IS5 transposase and trans‑activator |
| RA | 2,073,659 | T→C | R707R (CGT→CGC) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,112,219 | T→C | V281V (GTA→GTG) | rfbB ← | dTDP‑glucose 4,6‑dehydratase 1 |
| RA | 2,117,585 | Δ1 bp | coding (820/1281 nt) | wcaK ← | putative colanic acid biosynthesis pyruvyl transferase |
| RA | 2,122,017 | T→C | E321E (GAA→GAG) | cpsG ← | phosphomannomutase |
| RA | 2,139,747 | T→C | intergenic (+262/+12) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,143,407 | T→C | F48L (TTC→CTC) | dgcE → | putative diguanylate cyclase DgcE |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,101 | A→G | V35A (GTA→GCA) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY |
| RA | 2,185,875 | (G)7→8 | intergenic (‑79/‑42) | rcnR ← / → rcnA | DNA‑binding transcriptional repressor RcnR/Ni(2(+))/Co(2(+)) exporter |
| RA | 2,230,404 | (A)7→6 | intergenic (‑19/‑220) | dusC ← / → yohJ | tRNA‑dihydrouridine(16) synthase/PF03788 family membrane protein YohJ |
| RA | 2,236,296 | T→C | C344C (TGT→TGC) | preA → | NAD‑dependent dihydropyrimidine dehydrogenase subunit PreA |
| RA | 2,246,731 | A→G | C13C (TGT→TGC) | cirA ← | ferric dihyroxybenzoylserine outer membrane transporter |
| RA | 2,249,929 | T→C | G71G (GGT→GGC) | yeiH → | conserved inner membrane protein YeiH |
| RA | 2,251,878 | G→A | C60Y (TGC→TAC) | yeiI → | putative sugar kinase YeiI |
| RA | 2,278,414 | G→A | intergenic (‑177/+156) | yejG ← / ← bcr | protein YejG/multidrug efflux pump Bcr |
| RA | 2,283,721 | T→C | D76G (GAC→GGC) | yejK ← | nucleoid‑associated protein YejK |
| RA | 2,284,565 | C→T | L64L (CTG→TTG) | yejM → | putative cardiolipin transport protein |
| RA | 2,305,788 | T→C | M323V (ATG→GTG) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,313,600 | T→C | V38A (GTA→GCA) | rcsD → | RcsD phosphotransferase |
| RA | 2,324,502 | T→C | S132P (TCG→CCG) | atoA → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit beta |
| RA | 2,401,970 | T→C | H28R (CAC→CGC) | nuoE ← | NADH:quinone oxidoreductase subunit E |
| RA | 2,437,591 | T→C | A87A (GCA→GCG) | pdxB ← | erythronate‑4‑phosphate dehydrogenase |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,457,031 | G→A | A710V (GCA→GTA) | fadJ ← | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,492,281 | A→G | V325A (GTG→GCG) | frc ← | formyl‑CoA transferase |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,530,088 | A→T | I30N (ATT→AAT) | ligA ← | DNA ligase |
| RA | 2,597,353 | A→G | V89A (GTT→GCT) | purC ← | phosphoribosylaminoimidazole‑succinocarboxamide synthase |
| RA | 2,612,137 | T→C | Y80H (TAT→CAT) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,649,467 | G→A | R941C (CGT→TGT) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,660,213 | T→C | N26S (AAC→AGC) | iscU ← | scaffold protein for iron‑sulfur cluster assembly |
| RA | 2,692,772 | T→C | E924E (GAA→GAG) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,698,057 | A→G | V165A (GTC→GCC) | pgpC ← | phosphatidylglycerophosphatase C |
| RA | 2,699,413 | G→A | A219T (GCC→ACC) | yfhH → | putative DNA‑binding transcriptional regulator YfhH |
| RA | 2,707,964 | T→C | N264S (AAC→AGC) | rseB ← | anti‑sigma factor stabilizing protein RseB |
| RA | 2,731,125 | T→G | noncoding (33/1542 nt) | rrsG ← | 16S ribosomal RNA |
| RA | 2,734,706 | A→G | V110A (GTG→GCG) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,750,728 | (T)7→6 | intergenic (‑20/‑103) | grpE ← / → nadK | nucleotide exchange factor GrpE/NAD kinase |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,861,516 | T→C | G29G (GGT→GGC) | ygbJ → | putative L‑threonate dehydrogenase |
| RA | 2,887,647 | T→C | E222E (GAA→GAG) | cysH ← | phosphoadenosine phosphosulfate reductase |
| RA | 2,946,652 | T→C | N176S (AAC→AGC) | mltA ← | membrane‑bound lytic murein transglycosylase A |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,958,104 | (T)6→7 | coding (781/2889 nt) | ptrA ← | protease 3 |
| RA | 2,968,268 | (C)5→6 | coding (167/2247 nt) | ptsP ← | phosphoenolpyruvate‑protein phosphotransferase PtsP |
| RA | 2,976,386 | A→T | intergenic (‑1/‑213) | omrB ← / → galR | small regulatory RNA OmrB/DNA‑binding transcriptional dual regulator GalR |
| RA | 2,999,755 | (C)6→7 | coding (137/756 nt) | ygeR ← | LysM domain‑containing putative peptidase lipoprotein YgeR |
| RA | 3,016,207 | A→G | T50A (ACC→GCC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,089,907 | G→A | W51* (TGG→TGA) | yggI → | conserved protein YggI |
| RA | 3,099,636 | T→C | intergenic (‑71/+46) | yggM ← / ← ansB | DUF1202 domain‑containing protein YggM/L‑asparaginase 2 |
| RA | 3,103,116 | T→C | L35P (CTC→CCC) | mutY → | adenine DNA glycosylase |
| RA | 3,175,815 | A→G | G64G (GGT→GGC) | yqiA ← | esterase YqiA |
| RA | 3,177,509 | (C)6→7 | coding (402/630 nt) | nudF ← | ADP‑sugar pyrophosphatase |
| RA | 3,193,431 | A→G | T190A (ACC→GCC) | yqiK → | protein YqiK |
| RA | 3,194,843 | (G)6→7 | noncoding (23/145 nt) | sibD ← | small RNA SibD |
| RA | 3,213,347 | T→C | Y101H (TAC→CAC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,227,200 | A→G | K323E (AAA→GAA) | ygjI → | putative transporter YgjI |
| RA | 3,245,619 | T→C | R132R (CGT→CGC) | exuT → | hexuronate transporter |
| RA | 3,266,897 | (T)5→4 | coding (169/939 nt) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | 3,308,976 | A→G | intergenic (‑52/+57) | nlpI ← / ← pnp | lipoprotein NlpI/polynucleotide phosphorylase |
| RA | 3,309,006 | (C)6→7 | intergenic (‑82/+27) | nlpI ← / ← pnp | lipoprotein NlpI/polynucleotide phosphorylase |
| RA | 3,350,184 | (C)7→8 | coding (276/654 nt) | elbB ← | low activity glyoxalase ElbB |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,391,146 | T→C | T295A (ACC→GCC) | tldD ← | metalloprotease TldD |
| RA | 3,410,526 | G→A | A83T (GCA→ACA) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,411,685 | T→C | G11G (GGT→GGC) | yhdJ → | DNA adenine methyltransferase |
| RA | 3,428,493 | T→C | noncoding (270/1542 nt) | rrsD ← | 16S ribosomal RNA |
| RA | 3,481,747 | C→G | G153G (GGC→GGG) | yheS → | ABC transporter ATP‑binding protein YheS |
| RA | 3,548,433 | T→C | T546T (ACA→ACG) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,611,596 | A→G | D46D (GAT→GAC) | yhhS ← | putative transporter YhhS |
| RA | 3,635,553 | T→C | V238A (GTA→GCA) | yhiM → | inner membrane protein with a role in acid resistance |
| RA | 3,713,867 | A→G | A72A (GCA→GCG) | yiaC → | putative acyltransferase with acyl‑CoA N‑acyltransferase domain |
| RA | 3,729,347 | T→C | T9A (ACC→GCC) | xylB ← | xylulokinase |
| RA | 3,745,828 | T→C | V342A (GTA→GCA) | yiaN → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ membrane subunit |
| RA | 3,751,291 | C→T | W193* (TGG→TAG) | yiaT ← | outer membrane protein YiaT |
| RA | 3,767,204 | G→T | intergenic (+25/‑17) | yibA → / → yibJ | putative lyase containing HEAT‑repeat/putative RHS domain‑containing protein YibJ |
| RA | 3,774,056 | T→C | G592G (GGT→GGC) | mtlA → | mannitol‑specific PTS enzyme IICBA component |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,834,687 | T→A | I415F (ATC→TTC) | yicJ ← | putative xyloside transporter YicJ |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,910,688 | T→C | T280A (ACC→GCC) | pstS ← | phosphate ABC transporter periplasmic binding protein |
| RA | 3,965,557 | (T)8→7 | coding (74/1266 nt) | rhlB ← | ATP‑dependent RNA helicase RhlB |
| RA | 3,992,500 | A→G | T450A (ACC→GCC) | cyaA → | adenylate cyclase |
| RA | 4,054,870 | T→G | T137P (ACG→CCG) | glnG ← | DNA‑binding transcriptional dual regulator NtrC |
| RA | 4,074,085 | T→C | L116P (CTG→CCG) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,075,345 | A→G | N226S (AAC→AGC) | yihW → | putative DNA‑binding transcriptional regulator YihW |
| RA | 4,083,951 | A→G | G624G (GGT→GGC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,198,908 | A→G | Q40R (CAG→CGG) | nfi → | endonuclease V |
| RA | 4,285,231 | T→G | intergenic (‑18/+182) | yjcH ← / ← acs | conserved inner membrane protein YjcH/acetyl‑CoA synthetase (AMP‑forming) |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,303,801 | C→T | M103I (ATG→ATA) | mdtN ← | putative multidrug efflux pump membrane fusion protein |
| RA | 4,304,953 | A→G | S549P (TCG→CCG) | yjcS ← | alkyl sulfatase |
| RA | 4,362,554 | T→C | noncoding (73/76 nt) | pheU ← | tRNA‑Phe |
| RA | 4,394,255 | C→T | L64L (CTG→TTG) | nnr → | NAD(P)HX epimerase/NAD(P)HX dehydratase |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA 2'‑O‑ribose G2251 methyltransferase/conserved protein YjfI |
| RA | 4,436,065 | (T)7→8 | coding (501/1944 nt) | cpdB ← | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase |
| RA | 4,436,745 | A→G | intergenic (‑180/‑10) | cpdB ← / → cysQ | 2'3' cyclic nucleotide phosphodiesterase/3' nucleotidase/3'(2'),5'‑bisphosphate nucleotidase |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,446,396 | A→G | D762G (GAC→GGC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,471,253 | A→G | F65F (TTT→TTC) | pyrI ← | aspartate carbamoyltransferase, PyrI subunit |
| RA | 4,507,377 | A→G | pseudogene (181/255 nt) | insO → | KpLE2 phage‑like element; IS911B regulator fragment |
| RA | 4,534,809 | T→C | intergenic (‑134/‑206) | yjhZ ← / → yjhR | KpLE2 phage‑like element; putative acetyltransferase YjhZ/KpLE2 phage‑like element; PLD‑like domain‑containing protein YjhR |
| RA | 4,563,985 | A→G | D235D (GAT→GAC) | yjiL ← | putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehdratase |
| RA | 4,590,375 | A→G | V302A (GTG→GCG) | btsT ← | pyruvate:H(+) symporter |
| RA | 4,606,094 | (G)8→9 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,606,330 | (G)8→9 | noncoding (72/87 nt) | leuQ ← | tRNA‑Leu |
| RA | 4,624,281 | A→G | L170P (CTG→CCG) | ytjB ← | protein Smp |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 731488–731564 | 733114–733095 | 1532–1627 | 11 [10] | [10] 11 | rhsC | rhs element protein RhsC |
| * | * | ÷ | NC_000913 | 1196292 | 1211423 | 15132 | 11 [9] | [10] 12 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3423777–3424233 | 3424525–3424239 | 7–749 | 11 [9] | [7] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3944156–3945567 | 3945789–3945569 | 3–1634 | 12 [10] | [10] 12 | rrlC | 23S ribosomal RNA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374921 = | NA (NA) | 54 (1.620) | 15/190 | 1.0 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 33 (0.990) | 16/190 | 0.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375064 | NA (NA) | 10 (0.300) | 8/192 | 2.2 | NA | noncoding (33/34 nt) | other | REP31c |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375118 | NA (NA) | 12 (0.320) | 9/216 | 2.3 | NA | noncoding (1/36 nt) | other | REP31d |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 11 (0.230) +T |
9/274 | 3.0 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 375183 = | NA (NA) | 30 (0.720) | 18/238 | 1.1 | NA | intergenic (+302/‑276) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377372 = | NA (NA) | noncoding (37/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 375219 | NA (NA) | 35 (0.930) | 20/216 | 0.7 | NA | noncoding (1/36 nt) | other | REP31f |
| ? | NC_000913 | = 377333 | NA (NA) | intergenic (+22/+202) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375248 = | NA (NA) | 9 (0.220) | 8/238 | 2.8 | NA | noncoding (15/34 nt) | other | REP31g |
| ? | NC_000913 | 377507 = | NA (NA) | noncoding (16/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 3363001 = | 58 (1.200) | 68 (1.410) | 42/274 | 0.1 | 70.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 54 (1.110) | 38/276 | 0.2 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 27 (0.560) | 15 (0.330) | 15/258 | 1.7 | 34.4% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 32 (0.710) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 27 (0.560) | 17 (0.380) | 15/258 | 1.7 | 37.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 32 (0.710) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||