mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 51,290 | C→T | G106D (GGC→GAC) | apaG ← | DUF525 domain‑containing protein ApaG |
| RA | 93,591 | C→T | G142G (GGC→GGT) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase |
| RA | 109,960 | G→A | R561H (CGT→CAT) | secA → | protein translocation ATPase |
| RA | 135,764 | G→A | A234V (GCA→GTA) | speE ← | spermidine synthase |
| RA | 177,404 | A→T | L74Q (CTG→CAG) | yadS ← | PF03458 family protein YadS |
| RA | 186,539 | C→T | T704T (ACG→ACA) | glnD ← | protein‑PII uridylyltransferase/uridylyl‑removing enzyme |
| RA | 202,615 | C→T | S19L (TCA→TTA) | lpxA → | acyl‑[acyl‑carrier‑protein]‑‑UDP‑N‑ acetylglucosamine O‑acyltransferase |
| RA | 220,524 | C→T | V135V (GTG→GTA) | metQ ← | L‑methionine/D‑methionine ABC transporter membrane anchored binding protein |
| RA | 225,731 | G→A | intergenic (+156/‑28) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 225,736 | C→T | intergenic (+161/‑23) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 280,709 | C→T | W9* (TGG→TGA) | yagB ← | orphan antitoxin YagB |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| JC JC | 332,367 | IS2 (–) +5 bp | [pdeL] | [pdeL] | |
| RA | 339,935 | C→T | A56V (GCC→GTC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,941 | C→T | T58I (ACT→ATT) | yahH → | putative uncharacterized protein YahH |
| RA | 339,958 | G→A | D64N (GAC→AAC) | yahH → | putative uncharacterized protein YahH |
| RA | 339,986 | G→A | R73Q (CGA→CAA) | yahH → | putative uncharacterized protein YahH |
| RA | 356,036 | G→A | G372E (GGG→GAG) | codB → | cytosine transporter |
| RA | 364,850 | G→A | Q486* (CAG→TAG) | lacZ ← | beta‑galactosidase |
| MC JC | 392,967 | Δ5,466 bp | IS3‑mediated | yaiT–[yaiW] | yaiT, iprA, ampH, sbmA, [yaiW] |
| RA | 402,739 | G→A | L331L (TTG→TTA) | phoA → | alkaline phosphatase |
| RA | 431,286 | G→A | A243V (GCT→GTT) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 431,591 | G→A | R141R (CGC→CGT) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 435,874 | G→A | A81T (GCC→ACC) | thiL → | thiamine monophosphate kinase |
| RA | 437,421 | G→A | L239F (CTC→TTC) | yajO ← | 1‑deoxyxylulose‑5‑phosphate synthase YajO |
| RA | 441,092 | G→A | P4S (CCG→TCG) | ispA ← | geranyl diphosphate/farnesyl diphosphate synthase |
| RA | 441,907 | G→A | S120N (AGC→AAC) | thiI → | tRNA uridine 4‑sulfurtransferase |
| RA | 447,020 | G→A | A229V (GCT→GTT) | cyoE ← | heme O synthase |
| RA | 448,014 | G→A | S11S (TCC→TCT) | cyoD ← | cytochrome bo3 subunit 4 |
| RA | 451,013 | G→A | P200S (CCC→TCC) | cyoA ← | cytochrome bo3 subunit 2 |
| RA | 459,694 | G→A | E269E (GAG→GAA) | lon → | Lon protease |
| RA | 460,576 | G→A | K563K (AAG→AAA) | lon → | Lon protease |
| RA | 464,112 | G→A | G59D (GGC→GAC) | ybaV → | helix‑hairpin‑helix 3 family protein |
| RA | 466,723 | G→A | A197V (GCA→GTA) | ybaE ← | uncharacterized protein YbaE |
| RA | 467,244 | G→A | T23T (ACC→ACT) | ybaE ← | uncharacterized protein YbaE |
| RA | 478,694 | G→A | intergenic (‑77/+87) | pdeB ← / ← ylaC | c‑di‑GMP phosphodiesterase PdeB/putative inner membrane protein |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 509,517 | C→T | E621E (GAG→GAA) | copA ← | Cu(+) exporting P‑type ATPase |
| RA | 631,537 | G→A | W548* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 690,948 | G→A | V279V (GTC→GTT) | ybeX ← | CorC‑HlyC family protein YbeX |
| RA | 698,679 | G→A | P167S (CCA→TCA) | asnB ← | asparagine synthetase B |
| RA | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 869,418 | G→A | R3K (AGA→AAA) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| RA | 871,045 | G→A | V27I (GTC→ATC) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| RA | 873,115 | G→A | R46H (CGC→CAC) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| RA | 884,344 | G→A | G224G (GGG→GGA) | mdfA → | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 897,642 | G→A | V187I (GTC→ATC) | potI → | putrescine ABC transporter membrane subunit PotI |
| RA | 909,012 | G→A | L95L (CTG→TTG) | ltaE ← | low‑specificity L‑threonine aldolase |
| RA | 914,713 | C→T | A49T (GCG→ACG) | lysO ← | L‑lysine/thialysine exporter |
| RA | 924,350 | C→T | P363S (CCG→TCG) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 968,837 | G→A | D158N (GAT→AAT) | lpxK → | tetraacyldisaccharide 4'‑kinase |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 987,159 | T→A | intergenic (‑177/+426) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,040,126 | G→T | L277L (CTG→CTT) | appB → | cytochrome bd‑II subunit 2 |
| RA | 1,061,935 | G→A | S46N (AGC→AAC) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,070,014 | A→G | L114P (CTG→CCG) | rutF ← | FMN reductase RutF |
| RA | 1,106,559 | G→A | A69T (GCA→ACA) | clsC → | cardiolipin synthase C |
| RA | 1,109,816 | G→A | G161D (GGT→GAT) | opgG → | osmoregulated periplasmic glucans biosynthesis protein G |
| RA | 1,111,727 | 2 bp→TT | coding (865‑866/2544 nt) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,111,867 | G→A | W335* (TGG→TGA) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,113,805 | G→A | *76* (TGA→TAA) | yceK → | DUF1375 domain‑containing lipoprotein YceK |
| RA | 1,115,668 | G→A | R305R (CGC→CGT) | lpxL ← | lauroyl acyltransferase |
| RA | 1,125,322 | G→A | S2F (TCC→TTC) | mdtH ← | multidrug efflux pump MdtH |
| RA | 1,127,608 | G→A | G268D (GGC→GAC) | yceM → | putative oxidoreductase YceM |
| RA | 1,132,149 | G→A | G99D (GGC→GAC) | flgD → | flagellar biosynthesis, initiation of hook assembly |
| RA | 1,132,865 | G→A | G98R (GGA→AGA) | flgE → | flagellar hook protein FlgE |
| RA | 1,135,235 | G→A | Q169Q (CAG→CAA) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,136,053 | G→A | V164M (GTG→ATG) | flgH → | flagellar L‑ring protein |
| RA | 1,140,714 | G→A | A228T (GCG→ACG) | flgL → | flagellar hook‑filament junction protein 2 |
| RA | 1,150,616 | C→T | L297L (CTG→TTG) | fabD → | [acyl‑carrier‑protein] S‑malonyltransferase |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| 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 | 1,196,292 | C→T | T390T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,304 | G→A | E394E (GAG→GAA) | icd → | isocitrate dehydrogenase |
| RA | 1,220,797 | G→A | intergenic (+1596/+1508) | ymgF → / ← ymgD | inner membrane protein YmgF/PF16456 family protein YmgD |
| RA | 1,276,230 | C→T | P463P (CCG→CCA) | narX ← | sensor histidine kinase NarX |
| RA | 1,300,882 | G→A | intergenic (+335/‑300) | insH21 → / → oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| MC JC | 1,302,147 | Δ5 bp | coding (966‑970/1632 nt) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,310,770 | A→G | H32H (CAT→CAC) | yciI ← | protein YciI |
| RA | 1,315,384 | G→A | Y129Y (TAC→TAT) | yciF ← | DUF892 domain‑containing protein YciF |
| RA | 1,317,129 | G→A | Q32* (CAG→TAG) | trpA ← | tryptophan synthase subunit alpha |
| RA | 1,322,325 | G→A | L208F (CTC→TTC) | trpE ← | anthranilate synthase subunit TrpE |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,356,932 | G→A | T60I (ACC→ATC) | sapA ← | putative periplasmic binding protein SapA |
| RA | 1,357,202 | C→T | intergenic (‑92/+221) | sapA ← / ← ymjA | putative periplasmic binding protein SapA/DUF2543 domain‑containing protein YmjA |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,366,433 | G→A | G295D (GGC→GAC) | puuE → | 4‑aminobutyrate aminotransferase PuuE |
| RA | 1,400,978 | C→T | G266S (GGT→AGT) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| MC JC | 1,428,795 | Δ115,337 bp | IS5‑mediated | lomR–narU | 104 genes lomR, stfR, tfaR, pinR, ynaE, ynaM, uspF, ompN, micC, ydbK, ydbJ, hslJ, ldhA, ydbH, ynbE, ydbL, feaR, feaB, tynA, paaZ, paaA, paaB, paaC, paaD, paaE, paaF, paaG, paaH, paaI, paaJ, paaK, paaX, paaY, ynbG, ydbA, insD2, insC2, ydbA, insI2, ydbA, pdxI, ydbD, ynbA, ynbB, ynbC, ynbD, azoR, hrpA, ydcF, aldA, cybB, rydC, ydcA, yncP, hokB, mokB, sokB, trg, ydcI, ydcJ, opgD, ydcH, rimL, ydcK, tehA, tehB, ydcL, insQ, ydcO, sutR, rlhA, yncJ, hicA, hicB, ydcR, ydcS, ydcT, ydcU, ydcV, patD, yncL, ortT, ydcY, ydcZ, mnaT, curA, mcbR, yncD, yncE, ansP, yncG, yncH, ydcD, yncO, ydcC, pptA, yddH, nhoA, yddE, narV, narW, narY, narZ, narU |
| RA | 1,603,321 | C→T | L101L (CTC→CTT) | lsrC → | Autoinducer‑2 ABC transporter membrane subunit LsrC |
| RA | 1,604,223 | C→T | G59G (GGC→GGT) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,604,840 | C→T | S265F (TCC→TTC) | lsrD → | Autoinducer‑2 ABC transporter membrane subunit LsrD |
| RA | 1,605,533 | C→T | S161S (AGC→AGT) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,606,464 | C→T | A122V (GCC→GTC) | lsrF → | 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase |
| RA | 1,608,089 | C→T | A248A (GCC→GCT) | tam → | trans‑aconitate 2‑methyltransferase |
| JC JC | 1,633,913 | IS5 (–) +4 bp | coding (292‑295/591 nt) | pinQ → | putative recombinase PinQ |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,712,661 | A→T | intergenic (+503/‑108) | nth → / → dtpA | endonuclease III/dipeptide/tripeptide:H(+) symporter DtpA |
| RA | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,743,057 | G→A | D62D (GAC→GAT) | ribC ← | riboflavin synthase |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| RA | 1,888,498 | C→T | G417S (GGT→AGT) | fadD ← | long‑chain‑fatty‑acid‑‑CoA ligase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| JC JC | 1,907,451 | IS2 (+) +5 bp | coding (137‑141/144 nt) | yobF ← | DUF2527 domain‑containing protein YobF |
| RA | 1,919,728 | C→T | T740I (ACT→ATT) | letB → | lipophilic envelope spanning tunnel |
| RA | 1,978,245 | A→C | intergenic (‑48/+273) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 1,983,190 | G→A | G117G (GGC→GGT) | araH ← | arabinose ABC transporter membrane subunit |
| RA | 1,986,333 | A→G | intergenic (‑205/‑592) | araF ← / → ftnB | arabinose ABC transporter periplasmic binding protein/putative ferritin‑like protein |
| RA | 1,987,499 | C→A | intergenic (+71/+8) | ftnB → / ← yecJ | putative ferritin‑like protein/DUF2766 domain‑containing protein YecJ |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| JC JC | 2,174,817 | IS1 (+) +9 bp | coding (225‑233/453 nt) | gatA ← | galactitol‑specific PTS enzyme IIA component |
| RA | 2,188,087 | T→C | T110A (ACG→GCG) | yehA ← | putative fimbrial adhesin YehA |
| RA | 2,195,035 | G→A | A246T (GCG→ACG) | metG → | methionine‑‑tRNA ligase |
| RA | 2,223,182 | G→A | G333D (GGC→GAC) | dld → | quinone‑dependent D‑lactate dehydrogenase |
| RA | 2,223,909 | G→A | intergenic (+9/+29) | dld → / ← pbpG | quinone‑dependent D‑lactate dehydrogenase/peptidoglycan DD‑endopeptidase PbpG |
| RA | 2,225,926 | G→A | P42P (CCG→CCA) | yohD → | DedA family protein YohD |
| RA | 2,248,732 | G→A | intergenic (‑200/+5) | lysP ← / ← yeiE | lysine:H(+) symporter/DNA‑binding transcriptional regulator YeiE |
| RA | 2,249,800 | G→A | G28G (GGG→GGA) | yeiH → | PF03601 family inner membrane protein YeiH |
| RA | 2,251,644 | G→A | A269T (GCA→ACA) | nfo → | endonuclease IV |
| RA | 2,270,933 | C→T | P70S (CCG→TCG) | pdeN → | putative c‑di‑GMP phosphodiesterase PdeN |
| RA | 2,286,554 | C→T | pseudogene (2361/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,384,808 | C→T | K305K (AAG→AAA) | yfbK ← | IPR002035/DUF3520 domain‑containing protein YfbK |
| RA | 2,410,419 | G→A | L312L (CTG→TTG) | yfbS ← | putative transporter YfbS |
| RA | 2,415,485 | G→A | G247S (GGC→AGC) | pta → | phosphate acetyltransferase |
| RA | 2,435,922 | C→T | G243D (GGT→GAT) | usg ← | putative semialdehyde dehydrogenase Usg |
| RA | 2,454,553 | G→A | intergenic (‑2217/+530) | yfcS ← / ← yfcV | putative fimbrial chaperone YfcS/putative fimbrial protein YfcV |
| RA | 2,473,881 | G→A | R93H (CGC→CAC) | yfdP → | uncharacterized protein YfdP |
| RA | 2,474,474 | G→A | G148D (GGC→GAC) | yfdQ → | DUF2303 domain‑containing protein YfdQ |
| RA | 2,474,924 | G→A | intergenic (+68/‑60) | yfdQ → / → yfdR | DUF2303 domain‑containing protein YfdQ/5'‑deoxynucleotidase |
| RA | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| RA | 2,486,855 | G→A | A828T (GCG→ACG) | evgS → | sensor histidine kinase EvgS |
| RA | 2,535,852 | C→T | L7L (CTG→TTG) | crr → | Enzyme IIA(Glc) |
| RA | 2,536,118 | C→T | D95D (GAC→GAT) | crr → | Enzyme IIA(Glc) |
| RA | 2,552,984 | G→A | K211K (AAG→AAA) | amiA → | N‑acetylmuramoyl‑L‑alanine amidase A |
| RA | 2,555,841 | G→A | A187V (GCA→GTA) | eutL ← | putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,557,071 | G→A | A76V (GCC→GTC) | eutC ← | ethanolamine ammonia‑lyase subunit beta |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,600,716 | G→A | R80H (CGT→CAT) | bcp → | thiol peroxidase |
| RA | 2,602,942 | G→A | G375G (GGG→GGA) | hyfB → | hydrogenase 4 component B |
| RA | 2,603,828 | G→A | A671T (GCC→ACC) | hyfB → | hydrogenase 4 component B |
| RA | 2,609,438 | G→A | E318K (GAA→AAA) | hyfG → | hydrogenase 4 catalytic subunit HyfG |
| RA | 2,622,358 | G→A | G42D (GGC→GAC) | purN → | phosphoribosylglycinamide formyltransferase 1 |
| RA | 2,638,495 | C→T | G53D (GGT→GAT) | bamB ← | outer membrane protein assembly factor BamB |
| RA | 2,639,290 | C→T | intergenic (‑7/+11) | yfgM ← / ← hisS | ancillary SecYEG translocon subunit/histidine‑‑tRNA ligase |
| RA | 2,644,140 | C→T | W48* (TGG→TGA) | rlmN ← | 23S rRNA m(2)A2503 methyltransferase/tRNA m(2)A37 methyltransferase |
| RA | 2,644,810 | C→T | V19I (GTC→ATC) | ndk ← | nucleoside diphosphate kinase |
| RA | 2,646,753 | G→A | S191S (TCC→TCT) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,647,248 | C→T | W26* (TGG→TGA) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,647,438 | C→T | R1617Q (CGG→CAG) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,649,752 | C→T | G846S (GGT→AGT) | yfhM ← | alpha2‑macroglobulin |
| RA | 2,653,730 | C→T | intergenic (‑275/‑125) | timR ← / → ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA |
| RA | 2,654,454 | G→A | T160T (ACC→ACT) | sseB ← | protein SseB |
| RA | 2,656,285 | C→T | S25N (AGC→AAC) | pepB ← | aminopeptidase B |
| RA | 2,661,953 | C→T | G60E (GGA→GAA) | iscR ← | DNA‑binding transcriptional dual regulator IscR |
| RA | 2,663,356 | C→T | intergenic (‑33/‑86) | trmJ ← / → suhB | tRNA Cm32/Um32 methyltransferase/Nus factor SuhB |
| RA | 2,666,527 | C→T | L365L (CTG→TTG) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 2,670,240 | C→T | R403R (CGC→CGT) | hcaE → | putative 3‑phenylpropionate/cinnamate dioxygenase subunit alpha |
| RA | 2,674,066 | C→T | G208D (GGT→GAT) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,675,846 | C→T | S327N (AGC→AAC) | yphD ← | putative ABC transporter membrane subunit YphD |
| RA | 2,676,664 | C→T | M54I (ATG→ATA) | yphD ← | putative ABC transporter membrane subunit YphD |
| RA | 2,678,218 | G→A | G48G (GGC→GGT) | yphE ← | putative ABC transporter ATP‑binding protein YphE |
| RA | 2,685,310 | G→A | G66G (GGC→GGT) | glyA ← | serine hydroxymethyltransferase |
| RA | 2,692,949 | G→A | G865G (GGC→GGT) | purL ← | phosphoribosylformylglycinamide synthetase |
| RA | 2,698,650 | G→A | intergenic (‑100/‑109) | pgpC ← / → yfhH | phosphatidylglycerophosphatase C/putative DNA‑binding transcriptional regulator YfhH |
| RA | 2,713,679 | C→T | H262Y (CAT→TAT) | srmB → | ATP‑dependent RNA helicase SrmB |
| RA | 2,718,545 | G→A | intergenic (‑17/‑190) | yfiF ← / → trxC | putative methyltransferase YfiF/reduced thioredoxin 2 |
| RA | 2,722,605 | G→A | E885K (GAA→AAA) | patZ → | peptidyl‑lysine N‑acetyltransferase |
| RA | 2,725,233 | C→T | G172R (GGA→AGA) | kgtP ← | alpha‑ketoglutarate:H(+) symporter |
| RA | 2,726,177 | G→T | noncoding (12/120 nt) | rrfG ← | 5S ribosomal RNA |
| RA | 2,736,417 | C→T | A91V (GCC→GTC) | bamD → | outer membrane protein assembly factor BamD |
| RA | 2,777,980 | Δ2 bp | intergenic (+198/+165) | ypjF → / ← ypjA | toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,777,984 | Δ1 bp | intergenic (+202/+162) | ypjF → / ← ypjA | toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA |
| RA | 2,796,259 | G→A | A196T (GCG→ACG) | glaR → | DNA‑binding transcriptional repressor GlaR |
| RA | 2,912,293 | G→A | Y453Y (TAC→TAT) | relA ← | GDP/GTP pyrophosphokinase |
| JC JC | 2,913,392 | IS2 (–) +5 bp | coding (256‑260/2235 nt) | relA ← | GDP/GTP pyrophosphokinase |
| RA | 2,928,781 | C→T | P185S (CCG→TCG) | sdaC → | L‑serine:H(+) symporter SdaC |
| RA | 3,053,212 | C→T | G103R (GGA→AGA) | ubiH ← | 2‑octaprenyl‑6‑methoxyphenol 4‑hydroxylase |
| RA | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,241,019 | T→A | F359Y (TTC→TAC) | sstT → | serine/threonine:Na(+) symporter |
| RA | 3,279,461 | A→G | H183R (CAT→CGT) | kbaZ → | putative tagatose‑1,6‑bisphosphate aldolase 1 chaperone |
| RA | 3,336,411 | 2 bp→AT | coding (83‑84/1260 nt) | murA ← | UDP‑N‑acetylglucosamine 1‑carboxyvinyltransferase |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,413,728 | G→A | intergenic (‑263/‑136) | envR ← / → acrE | DNA‑binding transcriptional repressor EnvR/multidrug efflux pump membrane fusion lipoprotein AcrE |
| RA | 3,436,697 | G→A | E60E (GAG→GAA) | trkA → | NAD‑binding component of Trk potassium transporters |
| RA | 3,441,060 | T→C | K206E (AAG→GAG) | rpsD ← | 30S ribosomal subunit protein S4 |
| RA | 3,476,285 | G→A | H52H (CAC→CAT) | yheO ← | DNA‑binding transcriptional regulator YheO |
| RA | 3,510,832 | C→T | A49T (GCG→ACG) | yhfX ← | putative PLP‑binding protein YhfX |
| RA | 3,513,409 | C→T | S77N (AGC→AAC) | trpS ← | tryptophan‑‑tRNA ligase |
| RA | 3,513,818 | C→T | G191D (GGC→GAC) | gph ← | phosphoglycolate phosphatase |
| RA | 3,515,325 | G→A | H197Y (CAC→TAC) | dam ← | DNA adenine methyltransferase |
| RA | 3,518,683 | G→A | P128S (CCG→TCG) | aroK ← | shikimate kinase 1 |
| RA | 3,523,302 | C→T | V144V (GTC→GTT) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,525,188 | C→T | A773V (GCC→GTC) | mrcA → | peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA |
| RA | 3,531,645 | C→T | M265I (ATG→ATA) | yhgE ← | putative transport protein YhgE |
| RA | 3,539,633 | G→A | G750D (GGT→GAT) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,539,686 | G→A | A768T (GCA→ACA) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,540,703 | G→A | E99E (GAG→GAA) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,541,225 | G→A | A273A (GCG→GCA) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,542,695 | C→T | C763C (TGC→TGT) | feoB → | Fe(2(+)) transporter FeoB |
| RA | 3,546,362 | C→T | intergenic (+163/‑197) | nfuA → / → gntT | iron‑sulfur cluster carrier protein NfuA/high‑affinity gluconate transporter |
| RA | 3,553,272 | C→T | S63L (TCG→TTG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,557,528 | C→T | L184L (CTG→CTA) | rtcB ← | RNA‑splicing ligase |
| RA | 3,559,945 | C→T | intergenic (+79/+677) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,566,536 | C→T | A16T (GCT→ACT) | glgP ← | glycogen phosphorylase |
| RA | 3,571,615 | C→T | V630M (GTG→ATG) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,586,056 | C→T | Q256Q (CAG→CAA) | ggt ← | glutathione hydrolase proenzyme |
| RA | 3,611,604 | C→T | V44I (GTC→ATC) | yhhS ← | putative transporter YhhS |
| RA | 3,639,771 | C→T | intergenic (‑51/‑340) | uspB ← / → uspA | universal stress protein B/universal stress protein A |
| RA | 3,640,380 | C→T | D90D (GAC→GAT) | uspA → | universal stress protein A |
| RA | 3,642,547 | G→A | P196S (CCG→TCG) | rsmJ ← | 16S rRNA m(2)G1516 methyltransferase |
| RA | 3,643,308 | G→A | F625F (TTC→TTT) | prlC ← | oligopeptidase A |
| RA | 3,649,441 | C→T | G169G (GGC→GGT) | arsB → | arsenite/antimonite:H(+) antiporter |
| RA | 3,650,642 | G→A | A136T (GCG→ACG) | arsC → | arsenate reductase |
| MC JC | 3,653,231 | Δ52,001 bp | IS5‑mediated | yhiS–[dppB] | 43 genes yhiS, slp, dctR, yhiD, hdeB, hdeA, hdeD, arrS, gadE, gadF, mdtE, mdtF, gadW, gadY, gadX, gadA, ccp, treF, yhjB, rcdB, yhjD, yhjE, yhjG, pdeH, kdgK, yhjJ, dctA, pdeK, bcsC, bcsZ, bcsB, bcsA, yhjR, bcsE, bcsF, bcsG, ldrD, rdlD, yhjV, dppF, dppD, dppC, [dppB] |
| RA | 3,705,623 | G→A | L56L (CTC→CTT) | dppB ← | dipeptide ABC transporter membrane subunit DppB |
| RA | 3,706,152 | G→A | G518G (GGC→GGT) | dppA ← | dipeptide ABC transporter periplasmic binding protein |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| MC JC | 3,708,467 | Δ168 bp | [proK] | [proK] | |
| RA | 3,708,813 | G→A | P555S (CCG→TCG) | eptB ← | phosphoethanolamine transferase EptB |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,771,979 | G→T | intergenic (‑235/‑302) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,775,395 | G→A | L324L (CTG→CTA) | mtlD → | mannitol‑1‑phosphate 5‑dehydrogenase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| JC | 3,822,651 | (CAGGAT)1→2 | coding (252/2109 nt) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,823,162 | C→T | H255Y (CAC→TAC) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,824,443 | G→A | A682T (GCG→ACG) | spoT → | bifunctional (p)ppGpp synthase/hydrolase SpoT |
| RA | 3,831,443 | C→T | S329S (AGC→AGT) | yicH → | AsmA family protein YicH |
| RA | 3,858,618 | G→A | P500L (CCG→CTG) | yidK ← | putative transporter YidK |
| RA | 3,869,637 | C→A | L87L (CTC→CTA) | cbrA → | colicin M resistance protein |
| RA | 3,878,124 | C→T | V666M (GTG→ATG) | gyrB ← | DNA gyrase subunit B |
| RA | 3,878,536 | G→A | Y528Y (TAC→TAT) | gyrB ← | DNA gyrase subunit B |
| RA | 3,938,295 | +T | coding (69/993 nt) | rbsR → | DNA‑binding transcriptional dual regulator RbsR |
| RA | 3,966,690 | C→T | R92C (CGC→TGC) | rho → | transcription termination factor Rho |
| RA | 3,991,149 | C→T | intergenic (‑383/‑4) | hemC ← / → cyaA | hydroxymethylbilane synthase/adenylate cyclase |
| JC | 3,991,164 | +CTAT | coding (12/2547 nt) | cyaA → | adenylate cyclase |
| RA | 3,993,531 | T→C | R793R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 3,996,049 | T→A | L156* (TTG→TAG) | yigA → | DUF484 domain‑containing protein YigA |
| RA | 4,005,873 | G→A | A4T (GCG→ACG) | recQ → | ATP‑dependent DNA helicase RecQ |
| RA | 4,011,802 | C→T | P243S (CCG→TCG) | bioP → | biotin transporter |
| RA | 4,046,937 | C→T | intergenic (‑335/‑29) | yihG ← / → polA | 1‑acylglycerol‑3‑phosphate O‑acyltransferase YihG/DNA polymerase I |
| RA | 4,084,903 | T→G | N307T (AAC→ACC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,092,703 | A→G | F41L (TTC→CTC) | frvA ← | putative PTS enzyme IIA component FrvA |
| RA | 4,113,851 | G→A | H208Y (CAT→TAT) | fpr ← | flavodoxin/ferredoxin‑NADP(+) reductase |
| RA | 4,124,168 | C→A | G97* (GGA→TGA) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,143,377 | C→T | S283L (TCA→TTA) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,159,493 | C→T | G433D (GGC→GAC) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,161,248 | G→T | G61V (GGC→GTC) | fabR → | DNA‑binding transcriptional repressor FabR |
| RA | 4,164,123 | C→G | A162G (GCA→GGA) | btuB → | cobalamin outer membrane transporter |
| RA | 4,207,546 | G→A | intergenic (‑14/‑601) | purH ← / → rrsE | bifunctional AICAR transformylase/IMP cyclohydrolase/16S ribosomal RNA |
| RA | 4,215,347 | T→A | intergenic (+138/‑131) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,226,518 | G→A | K897K (AAG→AAA) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,240,006 | G→A | A17V (GCT→GTT) | yjbT ← | PF17089 family protein YjbT |
| RA | 4,282,332 | (A)5→6 | coding (744/1293 nt) | yjcF ← | pentapeptide repeat‑containing protein YjcF |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,341,309 | G→A | P107L (CCG→CTG) | melR ← | DNA‑binding transcriptional dual regulator MelR |
| RA | 4,392,997 | G→A | V357V (GTC→GTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,393,552 | G→A | F172F (TTC→TTT) | queG ← | epoxyqueuosine reductase |
| RA | 4,396,373 | C→T | T103T (ACC→ACT) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,396,772 | T→C | F236F (TTT→TTC) | amiB → | N‑acetylmuramoyl‑L‑alanine amidase B |
| RA | 4,425,688 | C→A | H57N (CAC→AAC) | priB → | primosomal replication protein N |
| RA | 4,425,696 | C→A | N59K (AAC→AAA) | priB → | primosomal replication protein N |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,532,409 | T→G | intergenic (‑758/+28) | sgcX ← / ← yjhP | putative endoglucanase with Zn‑dependent exopeptidase domain/putative methyltransferase YjhP |
| RA | 4,546,601 | C→T | I502I (ATC→ATT) | fimD → | type I fimbriae usher protein |
| RA | 4,610,304 | +C | coding (891/1590 nt) | prfC → | peptide chain release factor RF3 |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| JC JC | 4,640,418 | IS30 (–) +2 bp | coding (17‑18/141 nt) | yjjY → | uncharacterized protein YjjY |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196316 | 1211460 | 15145 | 32 [30] | [30] 33 | [icd]–mcrA | [icd],C0293,ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,ymfN,ymfR,beeE,ymfQ,ycfK,tfaP,tfaE,pinE,mcrA |
| * | * | ÷ | NC_000913 | 1978495 | 1979270–1978503 | 9–776 | 111 [0] | [0] 125 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 2726239–2729245 | 2730813–2729577 | 333–4575 | 32 [31] | [30] 32 | rrlG–[rrsG] | rrlG,gltW,[rrsG] |
| * | * | ÷ | NC_000913 | 3423811–3424233 | 3424457–3424239 | 7–647 | 32 [31] | [30] 33 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4035358–4035733 | 4036902–4035735 | 3–1545 | 33 [31] | [31] 32 | [rrsA] | [rrsA] |
| * | * | ÷ | NC_000913 | 4287449 | 4312942 | 25494 | 108 [0] | [0] 87 | ytcB–[alsR] | ytcB,nrfA,nrfB,nrfC,nrfD,nrfE,nrfF,nrfG,gltP,yjcO,fdhF,mdtP,mdtO,mdtN,ytcA,yjcS,alsK,alsE,alsC,alsA,alsB,[alsR] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 104 (1.200) | 66/574 | 0.1 | 99.1% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | = 1300693 | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1299499 = | NA (NA) | 98 (1.140) | 68/574 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1300694 = | 0 (0.000) | intergenic (+147/‑488) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 110 (1.220) | 74/598 | 0.1 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1978494 | 0 (0.000) | intergenic (‑297/+24) | flhD/insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 124 (1.380) | 83/598 | 0.0 | 100% | intergenic (‑56/‑482) | insA5/uspC | IS1 family protein InsA/universal stress protein C |
| ? | NC_000913 | = 2102947 | NA (NA) | pseudogene (443/446 nt) | wbbL | interrupted rhamnosyltransferase WbbL | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 108 (1.200) | 80/598 | 0.0 | 100% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4287448 | 0 (0.000) | intergenic (‑77/‑163) | acs/ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 85 (0.950) | 51/598 | 0.5 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4312943 = | 0 (0.000) | coding (49/891 nt) | alsR | DNA‑binding transcriptional repressor AlsR | |||||