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 | 45,854 | C→T | H16H (CAC→CAT) | yaaU → | putative transporter YaaU |
| RA | 51,712 | C→T | G240E (GGA→GAA) | rsmA ← | 16S rRNA m(6)2A1518,m(6)2A1519 dimethyltransferase |
| RA | 52,812 | C→T | R202H (CGC→CAC) | pdxA ← | 4‑hydroxythreonine‑4‑phosphate dehydrogenase |
| JC JC | 57,276 | IS2 (+) +5 bp | intergenic (‑167/‑84) | lptD ← / → djlA | lipopolysaccharide assembly protein LptD/co‑chaperone protein DjlA |
| RA | 71,134 | G→A | G250S (GGT→AGT) | araC → | DNA‑binding transcriptional dual regulator AraC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 269,161 | C→T | intergenic (‑201/+128) | ykfA ← / ← perR | putative GTP‑binding protein YkfA/putative transcriptional regulator PerR |
| RA | 557,635 | A→T | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase |
| JC JC | 568,449 | IS2 (–) +5 bp | coding (135‑139/333 nt) | emrE → | multidrug/betaine/choline efflux transporter EmrE |
| RA | 631,633 | G→A | W580* (TGG→TGA) | cstA → | pyruvate transporter CstA |
| RA | 727,115 | C→T | A540T (GCA→ACA) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 727,117 | C→T | G539D (GGC→GAC) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 728,330 | C→T | V135M (GTG→ATG) | kdpA ← | K(+) transporting P‑type ATPase subunit KdpA |
| RA | 749,268 | C→T | G147E (GGA→GAA) | ybgP ← | putative fimbrial chaperone YbgP |
| RA | 750,845 | C→T | S442N (AGC→AAC) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 750,858 | C→T | D438N (GAT→AAT) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 759,426 | G→A | E241K (GAG→AAG) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 759,576 | G→A | G291S (GGC→AGC) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 784,462 | C→T | G121D (GGC→GAC) | zitB ← | Zn(2(+))/Cd(2(+))/Ni(2(+))/Cu(2(+)) exporter |
| RA | 787,273 | C→T | G108D (GGC→GAC) | gpmA ← | 2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| RA | 790,185 | C→T | G282D (GGC→GAC) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 793,306 | C→T | E161E (GAG→GAA) | modF ← | ABC family protein ModF |
| RA | 797,186 | C→T | G211G (GGC→GGT) | modC → | molybdate ABC transporter ATP binding subunit |
| RA | 802,526 | C→T | L214L (CTG→TTG) | ybhI → | putative tricarboxylate transporter |
| RA | 811,317 | C→T | L313F (CTT→TTT) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 812,699 | C→T | L144L (CTG→TTG) | bioD → | dethiobiotin synthetase |
| RA | 816,122 | C→T | A176T (GCG→ACG) | ybhK ← | putative transferase YbhK |
| RA | 831,431 | C→T | S187F (TCC→TTC) | rhlE → | ATP‑dependent RNA helicase RhlE |
| RA | 850,617 | C→T | D56D (GAC→GAT) | ompX → | outer membrane protein X |
| RA | 869,690 | G→A | E94K (GAA→AAA) | gsiB → | glutathione ABC transporter periplasmic binding protein |
| RA | 874,129 | C→T | A384V (GCG→GTG) | pdeI → | putative c‑di‑GMP phosphodiesterase PdeI |
| RA | 884,712 | G→A | G347D (GGT→GAT) | mdfA → | multidrug efflux pump MdfA/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 885,116 | G→A | P39S (CCT→TCT) | ybjH ← | uncharacterized protein YbjH |
| RA | 889,829 | C→T | intergenic (‑10/‑260) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 890,342 | C→T | P85L (CCG→CTG) | ybjM → | putative inner membrane protein |
| RA | 891,909 | C→T | intergenic (+3/‑58) | nfsA → / → rimK | NADPH‑dependent nitro/quinone reductase NfsA/ribosomal protein S6 modification protein |
| RA | 896,433 | C→T | L100L (CTC→CTT) | potH → | putrescine ABC transporter membrane subunit PotH |
| RA | 904,702 | C→T | A37V (GCC→GTC) | ybjQ → | putative heavy metal binding protein YbjQ |
| RA | 908,889 | C→T | E136K (GAA→AAA) | ltaE ← | low‑specificity L‑threonine aldolase |
| RA | 910,080 | C→T | E324K (GAA→AAA) | poxB ← | pyruvate oxidase |
| RA | 915,852 | C→T | V66I (GTC→ATC) | aqpZ ← | water channel AqpZ |
| RA | 917,753 | C→T | R427R (CGC→CGT) | ybjD → | DUF2813 domain‑containing protein YbjD |
| RA | 921,399 | C→T | A351A (GCC→GCT) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| RA | 921,756 | C→T | N470N (AAC→AAT) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| RA | 937,458 | C→T | S29S (AGC→AGT) | lolA → | outer membrane lipoprotein carrier protein |
| RA | 943,967 | C→T | P185L (CCC→CTC) | dmsB → | dimethyl sulfoxide reductase subunit B |
| RA | 969,683 | C→T | L99F (CTT→TTT) | ycaQ → | interstrand DNA crosslink repair glycosylase |
| RA | 972,831 | G→A | P191S (CCG→TCG) | elyC ← | envelope biogenesis factor |
| RA | 987,152 | G→T | intergenic (‑170/+433) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,041,693 | C→T | R359R (CGC→CGT) | appA → | periplasmic phosphoanhydride phosphatase/multiple inositol‑polyphosphate phosphatase |
| RA | 1,057,826 | C→T | Q43Q (CAG→CAA) | torR ← | DNA‑binding transcriptional dual regulator TorR |
| RA | 1,069,024 | C→T | G272G (GGG→GGA) | rutG ← | pyrimidine:H(+) symporter |
| RA | 1,072,484 | C→T | G127D (GGC→GAC) | rutB ← | ureidoacrylate amidohydrolase |
| RA | 1,076,800 | C→T | A695T (GCG→ACG) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,077,916 | C→T | G323R (GGG→AGG) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,078,308 | C→T | G192D (GGT→GAT) | putA ← | fused DNA‑binding transcriptional repressor/proline dehydrogenase/1‑pyrroline‑5‑carboxylate dehydrogenase PutA |
| RA | 1,086,382 | C→T | W46* (TGG→TGA) | pgaD ← | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaD |
| RA | 1,095,379 | C→T | R20H (CGC→CAC) | insE4 ← | IS3 element protein InsE |
| RA | 1,098,239 | C→T | R118R (CGC→CGT) | ghrA → | glyoxylate/hydroxypyruvate reductase A |
| JC JC | 1,105,376 | IS2 (–) +5 bp | intergenic (+83/‑34) | csgC → / → ymdA | curlin chaperone/uncharacterized protein YmdA |
| RA | 1,111,819 | C→T | R319R (CGC→CGT) | opgH → | osmoregulated periplasmic glucans biosynthesis protein H |
| RA | 1,115,639 | C→T | intergenic (‑149/+23) | mdtG ← / ← lpxL | efflux pump MdtG/lauroyl acyltransferase |
| RA | 1,116,975 | C→T | R57* (CGA→TGA) | trhO → | tRNA U34 hydroxylase TrhO |
| RA | 1,121,634 | C→T | S325N (AGC→AAC) | pyrC ← | dihydroorotase |
| RA | 1,125,203 | C→T | G42S (GGC→AGC) | mdtH ← | multidrug efflux pump MdtH |
| RA | 1,125,597 | C→T | R12R (CGC→CGT) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,128,392 | C→T | P185L (CCG→CTG) | murJ → | lipid II flippase MurJ |
| RA | 1,134,882 | C→T | P52S (CCG→TCG) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,135,255 | C→T | T176I (ACC→ATC) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,135,448 | C→T | Y240Y (TAC→TAT) | flgG → | flagellar basal‑body rod protein FlgG |
| RA | 1,164,563 | G→A | G157R (GGA→AGA) | nagZ → | beta‑N‑acetylglucosaminidase |
| RA | 1,167,940 | C→T | G114G (GGC→GGT) | ycfJ → | PF05433 family protein YcfJ |
| 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 | 1,255,644 | G→A | A103A (GCC→GCT) | ycgV ← | putative autotransporter adhesin YcgV |
| RA | 1,290,881 | C→T | L214F (CTT→TTT) | rssB → | regulator of RpoS |
| MC JC | 1,294,035 | Δ141 bp | [tdk] | [tdk] | |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| JC | 1,303,073 | Δ12 bp | coding (175‑186/921 nt) | oppB → | murein tripeptide ABC transporter/oligopeptide ABC transporter inner membrane subunit OppB |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,353,758 | T→A | D254V (GAT→GTT) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,494,388 | Δ1 bp | coding (684/924 nt) | ydcI ← | DNA‑binding transcriptional dual regulator YdcI |
| RA | 1,517,508 | G→T | V40V (GTG→GTT) | ortT → | orphan toxin OrtT |
| RA | 1,564,294 | C→T | K480K (AAG→AAA) | dosP ← | oxygen‑sensing c‑di‑GMP phosphodiesterase DosP |
| RA | 1,580,143 | C→T | T216T (ACG→ACA) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,591,418 | C→T | E253E (GAG→GAA) | hipA ← | serine/threonine‑protein kinase toxin HipA |
| RA | 1,593,422 | C→T | intergenic (‑980/+5195) | hipB ← / ← lsrK | antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase |
| RA | 1,598,229 | C→T | intergenic (‑5787/+388) | hipB ← / ← lsrK | antitoxin/DNA‑binding transcriptional repressor HipB/autoinducer‑2 kinase |
| RA | 1,605,649 | C→T | S200L (TCG→TTG) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,627,000 | C→T | G127G (GGG→GGA) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,628,875 | C→T | S175F (TCT→TTT) | rspR → | DNA‑binding transcriptional repressor RspR |
| RA | 1,637,739 | G→A | S15F (TCT→TTT) | gnsB ← | protein GnsB |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,667,887 | Δ1 bp | coding (678/1221 nt) | mlc ← | DNA‑binding transcriptional repressor Mlc |
| RA | 1,693,035 | G→A | A410V (GCC→GTC) | uidB ← | glucuronide:H(+) symporter |
| RA | 1,716,110 | G→A | S371S (TCC→TCT) | tyrS ← | tyrosine‑‑tRNA ligase |
| RA | 1,723,394 | T→C | V425A (GTG→GCG) | ydhK → | putative transporter YdhK |
| RA | 1,744,751 | Δ1 bp | coding (1295/1374 nt) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,784,535 | G→A | R520Q (CGG→CAG) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,789,888 | G→A | P453S (CCT→TCT) | selO ← | protein adenylyltransferase SelO |
| RA | 1,792,138 | G→A | intergenic (‑118/+129) | rflP ← / ← nlpC | anti‑FlhDC factor RflP/NlpC/P60 family lipoprotein NlpC |
| JC JC | 1,792,772 | IS2 (–) +5 bp | intergenic (‑41/+33) | nlpC ← / ← btuD | NlpC/P60 family lipoprotein NlpC/vitamin B12 ABC transporter ATP binding subunit |
| RA | 1,814,697 | C→T | F277F (TTC→TTT) | katE → | catalase HPII |
| RA | 1,834,800 | G→A | intergenic (+7/‑8) | ydjY → / → ydjZ | 4Fe‑4S ferredoxin‑type domain‑containing protein YdjY/DedA family protein YdjZ |
| RA | 1,841,889 | G→A | A134T (GCG→ACG) L83L (CTG→TTG) |
nudG → ynjH ← |
5‑hydroxy‑CTP diphosphatase DUF1496 domain‑containing protein YnjH |
| RA | 1,844,327 | G→A | A182V (GCC→GTC) | ynjI ← | DUF1266 domain‑containing protein YnjI |
| RA | 1,890,220 | G→A | L105L (CTG→TTG) | yeaY ← | Slp family lipoprotein YeaY |
| RA | 1,911,287 | G→A | A338T (GCT→ACT) | yebQ → | putative transporter YebQ |
| RA | 1,914,184 | G→A | F211F (TTC→TTT) | prc ← | tail‑specific protease |
| RA | 1,918,760 | G→A | Q417Q (CAG→CAA) | letB → | lipophilic envelope spanning tunnel |
| RA | 1,944,191 | G→A | A260T (GCC→ACC) | znuB → | Zn(2(+)) ABC transporter membrane subunit |
| RA | 1,953,879 | C→T | H146H (CAC→CAT) | cmoB → | tRNA U34 carboxymethyltransferase |
| RA | 1,954,628 | C→T | G794S (GGC→AGC) | torZ ← | trimethylamine N‑oxide reductase 2 |
| RA | 1,959,513 | C→T | E112K (GAA→AAA) | yecM ← | putative metal‑binding enzyme YecM |
| RA | 1,962,183 | C→T | A71V (GCT→GTT) | yecT → | protein YecT |
| RA | 1,964,451 | C→T | G200G (GGG→GGA) | flhA ← | flagellar biosynthesis protein FlhA |
| RA | 1,969,912 | C→T | G358D (GGC→GAC) | tap ← | methyl‑accepting chemotaxis protein Tap |
| RA | 1,970,990 | C→T | intergenic (‑6/+40) | tap ← / ← tar | methyl‑accepting chemotaxis protein Tap/methyl‑accepting chemotaxis protein Tar |
| RA | 1,973,377 | C→T | A650T (GCG→ACG) A650T (GCG→ACG) |
cheA ← cheA ← |
chemotaxis protein CheA chemotaxis protein CheA |
| RA | 1,978,243 | G→T | intergenic (‑46/+275) | flhD ← / ← insB5 | DNA‑binding transcriptional dual regulator FlhD/IS1 family protein InsB |
| RA | 2,003,264 | C→T | E115K (GAA→AAA) | fliC ← | flagellar filament structural protein |
| RA | 2,032,423 | G→A | V219V (GTC→GTT) | yedJ ← | putative HD superfamily phosphohydrolase YedJ |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,242,121 | A→G | S283P (TCG→CCG) | yeiB ← | DUF418 domain‑containing protein YeiB |
| JC JC | 2,269,876 | IS5 (+) +4 bp | intergenic (+309/‑100) | lpxT → / → mepS | lipid A‑core phosphotransferase/peptidoglycan endopeptidase/peptidoglycan L,D‑carboxypeptidase |
| JC JC | 2,319,850 | IS2 (+) +5 bp | coding (23‑27/2850 nt) | rcsC ← | histidine kinase RcsC |
| RA | 2,397,444 | G→A | Q908* (CAA→TAA) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| JC JC | 2,406,780 | IS1 (–) +8 bp | intergenic (‑139/‑774) | lrhA ← / → alaA | DNA‑binding transcriptional dual regulator LrhA/glutamate‑‑pyruvate aminotransferase AlaA |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| JC JC | 2,666,074 | IS1 (+) +9 bp | coding (640‑648/1281 nt) | csiE → | stationary phase‑inducible protein CsiE |
| RA | 2,713,696 | G→A | W267* (TGG→TGA) | srmB → | ATP‑dependent RNA helicase SrmB |
| RA | 2,821,231 | G→A | R261C (CGC→TGC) | alaS ← | alanine‑‑tRNA ligase/DNA‑binding transcriptional repressor |
| RA | 3,018,330 | C→T | G757G (GGC→GGT) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,021,885 | C→T | C190C (TGC→TGT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,022,725 | C→T | F470F (TTC→TTT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,022,890 | C→T | N525N (AAC→AAT) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,023,453 | C→T | S713F (TCC→TTC) | xdhD → | fused putative xanthine/hypoxanthine oxidase: molybdopterin‑binding subunit and Fe‑S binding subunit |
| RA | 3,025,706 | G→A | Q452Q (CAG→CAA) | xanQ → | xanthine:H(+) symporter XanQ |
| RA | 3,036,530 | C→T | G526D (GGC→GAC) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,037,220 | C→T | R296Q (CGA→CAA) | recJ ← | ssDNA‑specific exonuclease RecJ |
| RA | 3,045,508 | C→T | G132S (GGC→AGC) | ygfF ← | putative oxidoreductase YgfF |
| RA | 3,047,801 | C→T | S414N (AGC→AAC) | gcvP ← | glycine decarboxylase |
| RA | 3,054,549 | C→T | A98T (GCC→ACC) | pepP ← | Xaa‑Pro aminopeptidase |
| RA | 3,061,743 | C→T | S298S (AGC→AGT) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,062,669 | C→T | A607V (GCC→GTC) | scpA → | methylmalonyl‑CoA mutase |
| RA | 3,079,623 | C→T | intergenic (‑293/+21) | cmtB ← / ← tktA | mannitol‑specific PTS enzyme IIA component CmtB/transketolase 1 |
| RA | 3,083,186 | C→T | V204V (GTG→GTA) | speB ← | agmatinase |
| RA | 3,088,390 | T→C | I36T (ATT→ACT) | galP → | galactose:H(+) symporter |
| RA | 3,099,793 | G→A | G312G (GGC→GGT) | ansB ← | L‑asparaginase 2 |
| RA | 3,099,992 | G→A | S246F (TCC→TTC) | ansB ← | L‑asparaginase 2 |
| RA | 3,100,526 | G→A | A68V (GCG→GTG) | ansB ← | L‑asparaginase 2 |
| RA | 3,113,731 | C→T | D208N (GAT→AAT) | pppA ← | prepilin peptidase |
| RA | 3,115,541 | G→A | P1191L (CCG→CTG) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,115,607 | G→A | T1169I (ACC→ATC) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,116,497 | G→A | H872H (CAC→CAT) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,117,082 | G→A | I677I (ATC→ATT) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,118,246 | G→A | G289G (GGC→GGT) | yghJ ← | putative lipoprotein YghJ |
| RA | 3,120,989 | G→A | S97S (AGC→AGT) | glcA ← | glycolate/lactate:H(+) symporter GlcA |
| RA | 3,123,938 | G→A | G98G (GGC→GGT) | glcG ← | putative heme‑binding protein GlcG |
| RA | 3,124,449 | G→A | S337S (AGC→AGT) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| RA | 3,125,051 | G→A | L137L (CTG→TTG) | glcF ← | glycolate dehydrogenase, putative iron‑sulfur subunit |
| RA | 3,126,605 | G→A | P473S (CCC→TCC) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,127,230 | C→T | L264L (CTG→CTA) | glcD ← | glycolate dehydrogenase, putative FAD‑linked subunit |
| RA | 3,133,041 | G→A | L58L (CTG→TTG) | yghR ← | putative ATP‑binding protein YghR |
| RA | 3,135,565 | G→A | N269N (AAC→AAT) | pitB ← | metal phosphate:H(+) symporter PitB |
| RA | 3,173,797 | C→T | E534K (GAG→AAG) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,191,118 | C→T | L163L (CTA→TTA) | yqiI → | putative fimbrial protein YqiI |
| RA | 3,227,310 | G→A | Q359Q (CAG→CAA) | ygjI → | putative transporter YgjI |
| RA | 3,239,627 | G→A | intergenic (+82/‑317) | alx → / → sstT | putative membrane‑bound redox modulator Alx/serine/threonine:Na(+) symporter |
| RA | 3,268,970 | A→G | T186A (ACA→GCA) | yhaC → | uncharacterized protein YhaC |
| RA | 3,338,426 | G→A | I12I (ATC→ATT) | mlaD ← | intermembrane phospholipid transport system, substrate binding protein MlaD |
| RA | 3,395,215 | G→A | G348G (GGC→GGT) | yhdP ← | phospholipid transport factor YhdP |
| RA | 3,486,205 | C→A | T29K (ACG→AAG) | crp → | DNA‑binding transcriptional dual regulator CRP |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,682,261 | Δ34 bp | coding (1154‑1187/1287 nt) | dctA ← | C4 dicarboxylate/orotate:H(+) symporter |
| JC JC | 3,737,137 | IS2 (+) +5 bp | coding (37‑41/825 nt) | bax ← | putative glycoside hydrolase Bax |
| RA | 3,782,932 | C→T | A244T (GCG→ACG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase |
| RA | 3,809,561 | C→T | A341V (GCA→GTA) | waaA → | KDO transferase |
| RA | 3,849,102 | C→T | Q345Q (CAG→CAA) | uhpB ← | sensory histidine kinase UhpB |
| RA | 3,861,543 | C→T | intergenic (+367/+444) | yidL → / ← glvB | putative DNA‑binding transcriptional regulator YidL/putative PTS enzyme II component GlvB |
| RA | 3,862,227 | C→T | G82G (GGG→GGA) | glvB ← | putative PTS enzyme II component GlvB |
| RA | 3,865,439 | C→T | D279N (GAT→AAT) | yidE ← | putative transport protein YidE |
| RA | 3,884,604 | C→T | R38C (CGC→TGC) | rnpA → | RNase P protein component |
| RA | 3,884,734 | C→T | P81L (CCG→CTG) | rnpA → | RNase P protein component |
| RA | 3,892,044 | C→T | P144S (CCA→TCA) | mdtL → | efflux pump MdtL |
| RA | 3,900,687 | C→T | E512K (GAA→AAA) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,921,759 | C→T | S98N (AGC→AAC) | atpB ← | ATP synthase Fo complex subunit a |
| RA | 3,923,235 | C→T | S149N (AGC→AAC) | rsmG ← | 16S rRNA m(7)G527 methyltransferase |
| RA | 3,928,607 | C→T | G333S (GGC→AGC) | viaA ← | protein ViaA |
| RA | 3,929,881 | C→T | G405S (GGC→AGC) | ravA ← | regulatory ATPase RavA |
| RA | 3,943,846 | C→T | noncoding (143/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,950,830 | C→T | intergenic (+273/‑1371) | ilvX → / → ilvM | uncharacterized protein IlvX/acetolactate synthase II subunit IlvM |
| RA | 3,958,585 | C→T | L206L (CTG→TTG) | ilvC → | ketol‑acid reductoisomerase (NADP(+)) |
| RA | 3,985,672 | G→A | N112N (AAC→AAT) | aslA ← | putative sulfatase AslA |
| RA | 4,004,371 | C→T | L109L (CTG→CTA) | yigI ← | putative thioesterase YigI |
| RA | 4,012,224 | C→T | R198Q (CGA→CAA) | metR ← | DNA‑binding transcriptional dual regulator MetR |
| RA | 4,017,393 | C→T | L21L (CTG→TTG) | rmuC → | putative recombination limiting protein RmuC |
| RA | 4,042,505 | C→T | L31F (CTT→TTT) | srkA → | stress response kinase A |
| RA | 4,048,632 | C→T | S556F (TCT→TTT) | polA → | DNA polymerase I |
| RA | 4,060,522 | C→T | P26S (CCG→TCG) | yihL → | putative DNA‑binding transcriptional regulator YihL |
| RA | 4,078,229 | C→T | P261S (CCG→TCG) | fabY → | putative fatty acid biosynthesis enzyme FabY |
| RA | 4,099,855 | C→T | G224D (GGC→GAC) | rhaT ← | rhamnose/lyxose:H(+) symporter |
| RA | 4,100,529 | C→T | intergenic (‑4/‑281) | rhaT ← / → sodA | rhamnose/lyxose:H(+) symporter/superoxide dismutase (Mn) |
| RA | 4,102,105 | C→T | A139V (GCT→GTT) | kdgT → | 2‑dehydro‑3‑deoxy‑D‑gluconate:H(+) symporter |
| JC JC | 4,123,923 | IS2 (–) +5 bp | coding (530‑534/1026 nt) | cytR ← | DNA‑binding transcriptional repressor CytR |
| RA | 4,129,874 | C→T | L14L (CTG→TTG) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| JC JC | 4,135,180 | IS2 (–) +5 bp | coding (1346‑1350/2181 nt) | katG → | catalase/hydroperoxidase HPI |
| RA | 4,146,389 | (T)6→7 | coding (132/879 nt) | pflC → | putative pyruvate formate‑lyase 2 activating enzyme PflC |
| RA | 4,163,984 | C→T | L116F (CTT→TTT) | btuB → | cobalamin outer membrane transporter |
| RA | 4,187,918 | C→T | L857F (CTC→TTC) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,192,374 | C→T | A88T (GCG→ACG) | thiG ← | 1‑deoxy‑D‑xylulose 5‑phosphate:thiol sulfurtransferase |
| RA | 4,199,021 | C→T | L78F (CTT→TTT) | nfi → | endonuclease V |
| RA | 4,231,162 | G→A | G270D (GGC→GAC) | rluF → | 23S rRNA pseudouridine(2604) and tRNA(Tyr) pseudouridine(35) synthase |
| RA | 4,232,133 | C→T | T367T (ACG→ACA) | lysC ← | aspartate kinase III |
| RA | 4,232,947 | G→A | T96I (ACT→ATT) | lysC ← | aspartate kinase III |
| RA | 4,233,152 | G→A | L28F (CTT→TTT) | lysC ← | aspartate kinase III |
| RA | 4,245,238 | G→A | I394I (ATC→ATT) | malE ← | maltose ABC transporter periplasmic binding protein |
| RA | 4,254,504 | G→A | L655L (CTG→TTG) | plsB ← | glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,264,068 | G→A | P55L (CCA→CTA) | qorA ← | putative quinone oxidoreductase 1 |
| RA | 4,267,804 | G→A | A231T (GCC→ACC) | tyrB → | tyrosine aminotransferase |
| RA | 4,269,058 | G→A | intergenic (‑46/‑356) | yjbS ← / → aphA | uncharacterized protein YjbS/acid phosphatase/phosphotransferase |
| RA | 4,269,459 | G→A | A16T (GCT→ACT) | aphA → | acid phosphatase/phosphotransferase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,345,404 | G→A | A52V (GCC→GTC) | yjdF ← | DUF2238 domain‑containing inner membrane protein YjdF |
| RA | 4,346,287 | G→A | P347L (CCA→CTA) | fumB ← | fumarase B |
| RA | 4,349,573 | G→A | R154R (CGC→CGT) | dcuR ← | DNA‑binding transcriptional activator DcuR |
| RA | 4,356,135 | C→T | G93S (GGT→AGT) | dtpC ← | dipeptide/tripeptide:H(+) symporter DtpC |
| RA | 4,362,225 | G→A | intergenic (‑291/+326) | cadC ← / ← pheU | DNA‑binding transcriptional activator CadC/tRNA‑Phe |
| RA | 4,363,123 | G→A | V62V (GTC→GTT) | yjdC ← | putative DNA‑binding transcriptional regulator YjdC |
| RA | 4,364,860 | G→A | Y61Y (TAC→TAT) | dsbD ← | thiol‑disulfide exchange protein DsbD |
| RA | 4,365,662 | G→A | S371F (TCT→TTT) | dcuA ← | C4‑dicarboxylate transporter DcuA |
| RA | 4,367,038 | G→A | I430I (ATC→ATT) | aspA ← | aspartate ammonia‑lyase |
| RA | 4,372,336 | G→A | V438M (GTG→ATG) | groL → | chaperonin GroEL |
| RA | 4,372,474 | G→A | E484K (GAA→AAA) | groL → | chaperonin GroEL |
| RA | 4,395,899 | C→T | C105C (TGC→TGT) | tsaE → | N(6)‑L‑threonylcarbamoyladenine synthase, TsaE subunit |
| RA | 4,397,434 | C→T | P8L (CCA→CTA) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,397,478 | C→T | P23S (CCT→TCT) | mutL → | DNA mismatch repair protein MutL |
| RA | 4,405,925 | C→T | I413I (ATC→ATT) | purA → | adenylosuccinate synthetase |
| RA | 4,417,140 | C→T | P63P (CCC→CCT) | yjfP → | carboxylesterase |
| RA | 4,442,824 | C→T | S148F (TCC→TTC) | tamA → | translocation and assembly module subunit TamA |
| RA | 4,445,219 | C→T | Q370* (CAG→TAG) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,447,409 | C→T | L1100F (CTT→TTT) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,454,328 | C→T | A249V (GCC→GTC) | yjfF → | galactofuranose ABC transporter putative membrane subunit YjtF |
| RA | 4,456,542 | C→T | T253I (ACC→ATC) | mpl → | UDP‑N‑acetylmuramate‑‑L‑alanyl‑gamma‑D‑glutamyl‑ meso‑2,6‑diaminoheptanedioate ligase |
| RA | 4,472,059 | C→T | A113T (GCG→ACG) | pyrB ← | aspartate carbamoyltransferase catalytic subunit |
| RA | 4,486,822 | C→T | S202F (TCC→TTC) | lptF → | lipopolysaccharide transport system protein LptF |
| RA | 4,492,537 | C→T | intergenic (‑12/+50) | idnT ← / ← idnO | L‑idonate/5‑ketogluconate/gluconate transporter/5‑keto‑D‑gluconate 5‑reductase |
| RA | 4,493,716 | C→T | A231T (GCG→ACG) | idnD ← | L‑idonate 5‑dehydrogenase |
| RA | 4,509,072 | C→T | pseudogene (64/471 nt) | insO → | IS911B regulator fragment |
| RA | 4,510,361 | C→T | intergenic (+568/+329) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,510,711 | C→T | R249R (AGG→AGA) | fecE ← | ferric citrate ABC transporter ATP binding subunit |
| RA | 4,515,901 | C→T | E259E (GAG→GAA) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,517,868 | C→T | G123D (GGC→GAC) | fecI ← | RNA polymerase sigma factor FecI |
| RA | 4,519,033 | C→T | intergenic (+231/+305) | insA7 → / ← yjhU | IS1 family repressor protein InsA/putative DNA‑binding transcriptional regulator YjhU |
| RA | 4,521,873 | C→T | V50I (GTC→ATC) | yjhF ← | putative transporter YjhF |
| RA | 4,524,922 | G→A | A30V (GCC→GTC) | yjhH ← | putative 2‑dehydro‑3‑deoxy‑D‑pentonate aldolase |
| RA | 4,525,090 | G→A | L238L (CTC→CTT) | yjhI ← | putative DNA‑binding transcriptional regulator YjhI |
| RA | 4,529,317 | C→T | L309L (CTG→CTA) | sgcC ← | putative PTS enzyme IIC component SgcC |
| JC JC | 4,536,236 | IS5 (+) +4 bp | intergenic (‑2183/‑358) | topAI ← / → ythB | toxin of the TopAI‑YjhQ toxin‑antitoxin system, TopA inhibitor/protein YthB |
| RA | 4,542,683 | Δ1 bp | intergenic (+50/‑432) | fimE → / → fimA | regulator for fimA/type 1 fimbriae major subunit |
| MC JC | 4,549,192 | Δ39 bp | coding (385‑423/903 nt) | fimH → | type 1 fimbriae D‑mannose specific adhesin |
| RA | 4,552,055 | C→T | I140I (ATC→ATT) | uxuA → | D‑mannonate dehydratase |
| RA | 4,552,344 | C→T | P237S (CCG→TCG) | uxuA → | D‑mannonate dehydratase |
| RA | 4,560,376 | C→T | G102D (GGT→GAT) | yjiH ← | uncharacterized protein YjiH |
| RA | 4,566,967 | C→T | E94K (GAA→AAA) | yjiN ← | DUF445 domain‑containing protein YjiN |
| RA | 4,574,257 | G→A | intergenic (+326/+2655) | yjiT → / ← mcrC | putative uncharacterized protein YjiT/Type IV methyl‑directed restriction enzyme EcoKMcrBC subunit |
| RA | 4,579,530 | C→T | G104E (GGA→GAA) | symE ← | nucleoid‑associated protein SymE |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196259 | 1211514 | 15256 | 9 [8] | [8] 9 | [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 | 45 [0] | [0] 34 | insB5–insA5 | insB5,insA5 |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 381260 = | NA (NA) | 69 (1.090) | 61/484 | 0.2 | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382183 | NA (NA) | noncoding (924/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 382179 = | NA (NA) | 58 (0.920) | 51/480 | 0.3 | NA | noncoding (920/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 566774 | 58 (0.910) | 25 (0.400) | 16/480 | 2.2 | 31.0% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 54 (0.860) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | = 1397238 | NA (NA) | 45 (0.710) | 40/484 | 0.6 | 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) | 34 (0.530) | 31/484 | 1.0 | 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 | |||||