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 | 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 | 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 |
| 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 | 364,850 | G→A | Q486* (CAG→TAG) | lacZ ← | beta‑galactosidase |
| RA | 392,855 | G→A | S16L (TCG→TTG) | insE2 ← | IS3 element protein InsE |
| RA | 395,831 | G→A | R153C (CGT→TGT) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | 397,530 | G→A | V298I (GTA→ATA) | sbmA → | peptide antibiotic/peptide nucleic acid transporter |
| 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 | 700,038 | G→A | H97Y (CAT→TAT) | umpH ← | UMP phosphatase |
| RA | 722,928 | G→A | A496V (GCT→GTT) | kdpD ← | sensor histidine kinase KdpD |
| RA | 723,096 | G→A | A440V (GCG→GTG) | kdpD ← | sensor histidine kinase KdpD |
| RA | 809,217 | 2 bp→AG | coding (40‑41/1290 nt) | bioA ← | adenosylmethionine‑8‑amino‑7‑oxononanoate aminotransferase |
| RA | 846,382 | C→A | E28* (GAA→TAA) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| 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 | 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 | 1,276,230 | C→T | P463P (CCG→CCA) | narX ← | sensor histidine kinase NarX |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | 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 |
| RA | 1,501,192 | C→T | P207L (CCT→CTT) | tehA → | tellurite resistance protein |
| RA | 1,514,172 | C→T | R114R (CGC→CGT) | ydcU → | putative ABC transporter membrane subunit YdcU |
| RA | 1,517,461 | C→T | L25F (CTT→TTT) | ortT → | orphan toxin OrtT |
| 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 |
| 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 | 1,721,136 | C→T | L38F (CTT→TTT) | ydhI → | DUF1656 domain‑containing protein YdhI |
| RA | 1,743,057 | G→A | D62D (GAC→GAT) | ribC ← | riboflavin synthase |
| JC JC | 1,743,496 | IS5 (–) +4 bp | coding (40‑43/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,776,715 | A→T | S377C (AGT→TGT) | ydiF → | putative acetate‑CoA transferase YdiF |
| 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 | 1,987,499 | 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 | 2,270,933 | 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 | 2,484,827 | C→T | L152F (CTT→TTT) | evgS → | sensor histidine kinase EvgS |
| 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 | 2,646,753 | G→A | S191S (TCC→TCT) | pbpC ← | peptidoglycan glycosyltransferase PbpC |
| RA | 2,654,454 | G→A | T160T (ACC→ACT) | sseB ← | protein SseB |
| RA | 2,678,218 | G→A | G48G (GGC→GGT) | yphE ← | putative ABC transporter ATP‑binding protein YphE |
| RA | 2,692,949 | G→A | G865G (GGC→GGT) | purL ← | phosphoribosylformylglycinamide synthetase |
| JC JC | 2,698,402 | IS30 (+) +2 bp | coding (148‑149/636 nt) | pgpC ← | phosphatidylglycerophosphatase C |
| 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 | 2,726,219 | C→T | intergenic (‑31/+62) | rrfG ← / ← rrlG | 5S ribosomal RNA/23S ribosomal RNA |
| RA | 2,736,417 | C→T | A91V (GCC→GTC) | bamD → | outer membrane protein assembly factor BamD |
| 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 | 3,088,010 | 2 bp→TT | intergenic (+150/‑273) | metK → / → galP | methionine adenosyltransferase/galactose:H(+) symporter |
| RA | 3,105,586 | G→T | intergenic (+74/‑128) | mltC → / → nupG | membrane‑bound lytic murein transglycosylase C/nucleoside:H(+) symporter NupG |
| 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 | 3,476,285 | G→A | H52H (CAC→CAT) | yheO ← | DNA‑binding transcriptional regulator YheO |
| RA | 3,513,409 | C→T | S77N (AGC→AAC) | trpS ← | tryptophan‑‑tRNA ligase |
| 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 | 3,539,633 | 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 | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| 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 | 3,650,642 | 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 |
| JC JC | 3,766,218 | IS5 (+) +4 bp | coding (4036‑4039/4134 nt) | rhsA → | rhs element protein RhsA |
| RA | 3,771,979 | G→T | intergenic (‑235/‑302) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| 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 | 3,869,637 | C→A | L87L (CTC→CTA) | cbrA → | colicin M resistance protein |
| 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 |
| JC JC | 3,968,900 | IS5 (–) +4 bp | coding (985‑988/1104 nt) | rfe → | UDP‑N‑acetylglucosamine‑‑undecaprenyl‑phosphate N‑acetylglucosaminephosphotransferase |
| 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 | 4,011,802 | 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 | 4,143,377 | 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 | 4,185,197 | G→A | G1318D (GGC→GAC) | rpoB → | RNA polymerase subunit beta |
| 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 | 4,282,332 | (A)5→6 | coding (744/1293 nt) | yjcF ← | pentapeptide repeat‑containing protein YjcF |
| JC JC | 4,287,445 | IS5 (–) +4 bp | intergenic (‑74/‑163) | acs ← / → ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB |
| RA | 4,293,781 | 2 bp→AT | coding (239‑240/597 nt) | nrfG → | putative formate‑dependent nitrite reductase complex subunit NrfG |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| 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 | 4,439,592 | A→C | K2N (AAA→AAC) | ytfK → | stringent response modulator YtfK |
| 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 |
| JC | 4,626,183 | (GCG)3→2 | coding (272‑274/1383 nt) | radA → | DNA recombination protein |
| 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 | 1196292 | 1211460 | 15169 | 36 [34] | [30] 37 | [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 | 776 | 127 [0] | [0] 146 | insB5–insA5 | insB5,insA5 |
| * | * | ÷ | NC_000913 | 3423817–3424231 | 3424457–3424238 | 8–641 | 35 [34] | [34] 36 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 270541 = | NA (NA) | 49 (0.490) | 32/598 | 2.2 | 41.5% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 971729 | 69 (0.690) | intergenic (+131/‑23) | kdsB/ycbJ | 3‑deoxy‑manno‑octulosonate cytidylyltransferase/putative phosphotransferase YcbJ | |||||
| * | ? | NC_000913 | 381260 = | NA (NA) | 71 (0.710) | 51/598 | 0.8 | 56.4% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 750639 | 55 (0.550) | coding (1531/2448 nt) | ybgQ | putative fimbrial usher protein YbgQ | |||||
| * | ? | NC_000913 | = 382590 | NA (NA) | 61 (0.610) | 44/598 | 1.2 | 54.0% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 750635 = | 52 (0.520) | coding (1535/2448 nt) | ybgQ | putative fimbrial usher protein YbgQ | |||||
| * | ? | NC_000913 | 971728 = | 69 (0.700) | 69 (0.700) | 53/594 | 0.6 | 50.0% | intergenic (+130/‑24) | kdsB/ycbJ | 3‑deoxy‑manno‑octulosonate cytidylyltransferase/putative phosphotransferase YcbJ |
| ? | NC_000913 | = 1470516 | NA (NA) | noncoding (1221/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 1231886 = | 39 (0.390) | 63 (0.630) | 50/598 | 0.8 | 61.8% | coding (701/1269 nt) | umuC | DNA polymerase V catalytic protein |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1231890 | 39 (0.390) | 46 (0.460) | 37/598 | 1.7 | 54.1% | coding (705/1269 nt) | umuC | DNA polymerase V catalytic protein |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.010) | 116 (1.210) | 73/574 | 0.1 | 99.2% | 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) | 118 (1.230) | 78/574 | 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) | 127 (1.270) | 84/598 | 0.0 | 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 | 1481213 = | 66 (0.660) | 60 (0.600) | 45/598 | 1.1 | 47.6% | coding (305/1293 nt) | ynbD | phosphatase domain‑containing protein YnbD |
| ? | NC_000913 | = 2290113 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1481216 | 66 (0.660) | 68 (0.680) | 58/598 | 0.5 | 50.7% | coding (308/1293 nt) | ynbD | phosphatase domain‑containing protein YnbD |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 1979271 = | 0 (0.000) | 146 (1.460) | 98/598 | 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) | 61 (0.610) | 41/598 | 1.4 | 61.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4542164 | 38 (0.380) | coding (128/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 49 (0.490) | 38/598 | 1.6 | 53.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4542161 = | 42 (0.420) | coding (125/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | 3652036 = | NA (NA) | 48 (0.480) | 41/598 | 1.4 | 53.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 4542311 | 41 (0.410) | coding (275/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 36 (0.360) | 29/598 | 2.6 | 48.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 4542308 = | 38 (0.380) | coding (272/597 nt) | fimE | regulator for fimA | |||||
| * | ? | NC_000913 | 4542682 = | 43 (0.430) | 119 (1.230) | 72/580 | 0.1 | 75.6% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 35 (0.360) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 48 (0.480) | 118 (1.220) | 75/580 | 0.1 | 74.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 35 (0.360) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||