mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 7,677 | T→C | 11.0% | M95V (ATG→GTG) | Y75_RS00040 ← | sodium:alanine symporter family protein |
| RA | 7,710 | T→A | 10.6% | I84F (ATT→TTT) | Y75_RS00040 ← | sodium:alanine symporter family protein |
| RA | 82,766 | A→G | 12.0% | L255P (CTC→CCC) | leuA ← | 2‑isopropylmalate synthase |
| RA | 228,688 | Δ1 bp | 100% | intergenic (+9/‑70) | Y75_RS01035 → / → rrf | 23S ribosomal RNA/5S ribosomal RNA |
| RA | 249,538 | T→G | 35.1% | H187P (CAC→CCC) | flhA ← | flagellar type III secretion system protein FlhA |
| RA | 249,540 | C→G | 14.0% | P186P (CCG→CCC) | flhA ← | flagellar type III secretion system protein FlhA |
| RA | 260,444 | T→A | 9.1% | I278N (ATC→AAC) | proB → | glutamate 5‑kinase |
| RA | 284,748 | A→G | 13.0% | I44V (ATT→GTT) | Y75_RS01395 → | MFS transporter |
| RA | 296,909 | A→C | 7.6% | V36G (GTT→GGT) | Y75_RS01460 ← | hypothetical protein |
| RA | 297,575 | A→G | 11.1% | S126P (TCG→CCG) | paoD ← | molybdenum cofactor insertion chaperone PaoD |
| RA | 303,229 | C→A | 10.3% | A60S (GCC→TCC) | Y75_RS01490 ← | YkgJ family cysteine cluster protein |
| RA | 304,460 | A→C | 10.1% | F528V (TTT→GTT) | ecpD ← | fimbrial adhesin EcpD |
| RA | 339,916 | A→C | 8.3% | A176A (GCA→GCC) | Y75_RS01670 → | carbamate kinase family protein |
| RA | 346,895 | G→C | 11.4% | A258G (GCG→GGG) | prpR ← | propionate catabolism operon regulatory protein PrpR |
| RA | 359,586 | T→G | 14.3% | V133G (GTG→GGG) | cynX → | cyanate transporter CynX |
| RA | 368,917 | T→C | 12.5% | A361A (GCT→GCC) | Y75_RS01785 → | bifunctional 3‑(3‑hydroxy‑phenyl)propionate/3‑hydroxycinnamic acid hydroxylase |
| RA | 385,021 | T→G | 12.3% | V189G (GTG→GGG) | tauA → | taurine ABC transporter substrate‑binding protein |
| RA | 386,930 | A→G | 9.0% | I246V (ATC→GTC) | tauC → | taurine ABC transporter permease TauC |
| RA | 396,785 | A→C | 6.3% | N308T (AAC→ACC) | sbmA → | peptide antibiotic transporter SbmA |
| RA | 416,826 | A→G | 8.9% | E154G (GAG→GGG) | phoB → | phosphate response regulator transcription factor PhoB |
| RA | 421,445 | G→T | 7.9% | L412L (CTG→CTT) | proY → | proline‑specific permease ProY |
| RA | 421,455 | A→T | 9.8% | I416F (ATC→TTC) | proY → | proline‑specific permease ProY |
| RA | 432,873 | T→G | 28.4% | G65G (GGT→GGG) | ribD → | bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5‑amino‑6‑(5‑phosphoribosylamino)uracil reductase RibD |
| RA | 471,229 | A→G | 10.8% | E457G (GAG→GGG) | Y75_RS02310 → | SmdB family multidrug efflux ABC transporter permease/ATP‑binding protein |
| RA | 487,626 | A→C | 8.6% | T623P (ACC→CCC) | mscK → | mechanosensitive channel MscK |
| RA | 547,694 | A→G | 100% | E38E (GAA→GAG) | Y75_RS02655 → | hypothetical protein |
| RA | 547,831:1 | +G | 100% | coding (251/261 nt) | Y75_RS02655 → | hypothetical protein |
| RA | 556,858 | A→T | 100% | L36Q (CTG→CAG) | folD ← | bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD |
| RA | 564,474 | G→T | 11.7% | S243* (TCA→TAA) | Y75_RS02750 ← | site‑specific integrase |
| RA | 594,075 | G→C | 11.4% | L198V (CTG→GTG) | cusR ← | copper response regulator transcription factor CusR |
| RA | 622,087 | A→T | 7.1% | T189S (ACC→TCC) | entS → | enterobactin transporter EntS |
| RA | 629,465 | A→G | 8.3% | M117V (ATG→GTG) | cstA → | carbon starvation protein CstA |
| MC JC | 654,214 | Δ1,199 bp | 100% | Y75_RS03225–[dcuC] | Y75_RS03225, [dcuC] | |
| RA | 659,182 | T→G | 8.4% | pseudogene (730/788 nt) | Y75_RS03250 → | deaminated glutathione amidase |
| RA | 693,319 | T→C | 7.9% | E174G (GAG→GGG) | Y75_RS03425 ← | PhoH family protein |
| RA | 747,683 | T→G | 10.7% | N170T (AAC→ACC) | Y75_RS03700 ← | AbrB family transcriptional regulator |
| RA | 795,452 | A→G | 89.4% | intergenic (+108/‑59) | Y75_RS03980 → / → modA | multidrug efflux pump accessory protein AcrZ/molybdate ABC transporter substrate‑binding protein |
| RA | 812,143 | T→G | 29.8% | V67G (GTG→GGG) | bioC → | malonyl‑ACP O‑methyltransferase BioC |
| RA | 822,425 | T→A | 7.3% | I166F (ATT→TTT) | Y75_RS04110 ← | UPF0104 family protein |
| RA | 888,454 | T→A | 10.8% | intergenic (+73/+102) | Y75_RS04405 → / ← Y75_RS04410 | DNA‑binding transcriptional regulator RcdA/aspartate:alanine antiporter |
| RA | 974,882 | A→G | 8.8% | S48G (AGT→GGT) | mukF → | chromosome partition protein MukF |
| RA | 981,675 | T→G | 14.0% | G69G (GGT→GGG) | ldtD → | L,D‑transpeptidase |
| RA | 990,367 | A→G | 14.6% | S138P (TCA→CCA) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,058,908 | T→C | 9.8% | S135P (TCG→CCG) | torC → | pentaheme c‑type cytochrome TorC |
| RA | 1,065,700 | C→T | 100% | R415C (CGT→TGT) | Y75_RS05220 → | YccE family protein |
| RA | 1,077,331 | A→C | 14.3% | G658G (GGT→GGG) | putA ← | trifunctional transcriptional regulator/proline dehydrogenase/L‑glutamate gamma‑semialdehyde dehydrogenase |
| RA | 1,081,122 | A→G | 10.9% | I466V (ATT→GTT) | putP → | sodium/proline symporter PutP |
| RA | 1,093,686 | T→C | 100% | V130A (GTA→GCA) | Y75_RS05355 → | GGDEF domain‑containing protein |
| RA | 1,158,866 | A→G | 8.9% | G171G (GGA→GGG) | Y75_RS05755 → | metal‑dependent hydrolase |
| RA | 1,239,439 | A→C | 11.0% | T98P (ACC→CCC) | Y75_RS06220 → | D‑amino acid dehydrogenase |
| RA | 1,262,461 | C→A | 8.9% | intergenic (‑81/+44) | dauA ← / ← Y75_RS06315 | C4‑dicarboxylic acid transporter DauA/ribose‑phosphate diphosphokinase |
| RA | 1,273,414 | G→T | 7.3% | Q5K (CAA→AAA) | chaA ← | sodium‑potassium/proton antiporter ChaA |
| RA | 1,303,712 | A→G | 100% | S273G (AGC→GGC) | oppA → | oligopeptide ABC transporter substrate‑binding protein OppA |
| RA | 1,306,094 | G→T | 9.6% | V183L (GTG→TTG) | oppC → | oligopeptide ABC transporter permease OppC |
| RA | 1,324,175 | C→G | 10.1% | P162P (CCG→CCC) | trpE ← | anthranilate synthase component I |
| RA | 1,327,725 | A→G | 11.3% | G422G (GGA→GGG) | Y75_RS06660 → | DUF2207 domain‑containing protein |
| RA | 1,379,311 | G→T | 8.4% | A256S (GCA→TCA) | Y75_RS06935 → | Gfo/Idh/MocA family oxidoreductase |
| RA | 1,385,434 | G→A | 12.4% | S81F (TCT→TTT) | Y75_RS06960 ← | LacI family transcriptional regulator |
| MC JC | 1,413,639 | Δ23,060 bp | 100% | [ttcA]–Y75_RS24865 | 33 genes [ttcA], Y75_RS23540, xisR, rcbA, ralR, recT, recE, Y75_RS07140, Y75_RS07145, kilR, Y75_RS07155, Y75_RS07160, racR, ydaS, Y75_RS07175, Y75_RS07180, Y75_RS07185, Y75_RS07190, rzoD, Y75_RS07200, Y75_RS07205, Y75_RS07210, Y75_RS07215, Y75_RS07220, Y75_RS07225, Y75_RS07230, Y75_RS07235, Y75_RS23570, Y75_RS07255, Y75_RS07260, ydfK, Y75_RS24860, Y75_RS24865 |
|
| RA | 1,441,997 | C→A | 7.6% | D168Y (GAT→TAT) | nifJ ← | pyruvate:ferredoxin (flavodoxin) oxidoreductase |
| RA | 1,447,718 | T→G | 13.3% | V42G (GTT→GGT) | Y75_RS07310 → | YdbL family protein |
| RA | 1,467,915 | T→C | 7.6% | pseudogene (810/2526 nt) | Y75_RS07400 → | autotransporter domain‑containing protein |
| RA | 1,468,137 | T→C | 5.4% | pseudogene (1032/2526 nt) | Y75_RS07400 → | autotransporter domain‑containing protein |
| RA | 1,478,899 | T→C | 8.5% | L681P (CTC→CCC) | Y75_RS07430 → | DUF2773 domain‑containing bactofilin |
| RA | 1,521,793 | C→G | 11.1% | intergenic (+15/‑183) | curA → / → Y75_RS07665 | NADPH‑dependent curcumin/dihydrocurcumin reductase/DNA‑binding transcriptional regulator McbR |
| RA | 1,521,798 | G→A | 11.7% | intergenic (+20/‑178) | curA → / → Y75_RS07665 | NADPH‑dependent curcumin/dihydrocurcumin reductase/DNA‑binding transcriptional regulator McbR |
| RA | 1,552,363 | C→G | 12.5% | V63V (GTC→GTG) | fdxH → | formate dehydrogenase N subunit beta |
| RA | 1,703,339 | A→G | 14.5% | G223G (GGA→GGG) | malY → | bifunctional maltose regulon transcriptional repressor/cystathionine beta‑lyase MalY |
| RA | 1,739,298 | A→G | 100% | intergenic (‑39/‑260) | ynhF ← / → purR | stress response protein YnhF/HTH‑type transcriptional repressor PurR |
| RA | 1,767,050 | G→C | 8.9% | R99R (CGC→CGG) | menI ← | 1,4‑dihydroxy‑2‑naphthoyl‑CoA hydrolase |
| RA | 1,826,878 | A→T | 6.4% | G154G (GGT→GGA) | spy ← | ATP‑independent periplasmic protein‑refolding chaperone |
| RA | 1,898,302 | T→C | 13.2% | L140P (CTC→CCC) | Y75_RS09545 → | CoA pyrophosphatase |
| RA | 1,961,858 | T→G | 14.5% | V28G (GTT→GGT) | argS → | arginine‑‑tRNA ligase |
| RA | 1,971,688 | A→C | 16.7% | G337G (GGT→GGG) | tap ← | methyl‑accepting chemotaxis protein IV |
| RA | 1,986,321 | T→C | 13.2% | S296G (AGC→GGC) | Y75_RS10005 ← | arabinose ABC transporter ATP binding protein AraG |
| RA | 1,989,132 | A→C | 13.4% | Y24S (TAC→TCC) | Y75_RS10015 → | non‑heme ferritin‑like protein |
| RA | 2,016,339 | T→C | 11.2% | I325T (ATC→ACC) | fliF → | flagellar basal body M‑ring protein FliF |
| RA | 2,072,206 | G→A | 11.6% | Q53* (CAA→TAA) | Y75_RS10480 ← | IS3‑like element IS2 family transposase |
| RA | 2,072,207 | C→T | 11.5% | R52R (CGG→CGA) | Y75_RS10480 ← | IS3‑like element IS2 family transposase |
| RA | 2,152,044 | A→C | 18.9% | V360G (GTG→GGG) | yegI ← | protein kinase YegI |
| RA | 2,173,679 | A→C | 12.6% | pseudogene (192/306 nt) | Y75_RS10955 ← | DeoR/GlpR transcriptional regulator |
| MC JC | 2,176,983 | Δ1,199 bp | 100% | Y75_RS10980–[gatA] | Y75_RS10980, [gatA] | |
| RA | 2,277,683 | T→G | 11.7% | G57G (GGT→GGG) | Y75_RS11430 → | microcin C ABC transporter permease YejB |
| RA | 2,307,856 | G→T | 5.8% | intergenic (+129/+586) | eco → / ← mqo | serine protease inhibitor ecotin/malate dehydrogenase (quinone) |
| RA | 2,307,857 | G→C | 7.5% | intergenic (+130/+585) | eco → / ← mqo | serine protease inhibitor ecotin/malate dehydrogenase (quinone) |
| RA | 2,307,871 | A→G | 8.8% | intergenic (+144/+571) | eco → / ← mqo | serine protease inhibitor ecotin/malate dehydrogenase (quinone) |
| RA | 2,308,747 | T→G | 7.9% | T448P (ACC→CCC) | mqo ← | malate dehydrogenase (quinone) |
| RA | 2,312,466 | C→T | 5.5% | T70T (ACG→ACA) | alkB ← | DNA oxidative demethylase AlkB |
| MC JC | 2,320,795 | Δ1,336 bp | 100% | Y75_RS11650–[rcsC] | Y75_RS11650, Y75_RS11650, [rcsC] | |
| RA | 2,360,200 | A→C | 10.1% | T4P (ACC→CCC) | glpC → | anaerobic glycerol‑3‑phosphate dehydrogenase subunit C |
| RA | 2,464,671 | T→C | 14.2% | G415G (GGA→GGG) | fadI ← | acetyl‑CoA C‑acyltransferase FadI |
| RA | 2,469,925 | T→C | 11.3% | T177A (ACC→GCC) | mlaA ← | phospholipid‑binding lipoprotein MlaA |
| RA | 2,573,524 | T→G | 14.1% | T46P (ACC→CCC) | eutQ ← | ethanolamine utilization acetate kinase EutQ |
| RA | 2,576,109 | T→G | 10.8% | T309P (ACC→CCC) | maeB ← | NADP‑dependent oxaloacetate‑decarboxylating malate dehydrogenase |
| RA | 2,606,884 | C→G | 14.8% | R438G (CGG→GGG) | hyfF → | hydrogenase 4 subunit F |
| RA | 2,660,496 | A→T | 100% | C98S (TGC→AGC) | iscR ← | Fe‑S cluster assembly transcriptional regulator IscR |
| RA | 2,669,181 | A→C | 8.8% | T46P (ACC→CCC) | Y75_RS13285 → | 3‑phenylpropionate/cinnamic acid dioxygenase subunit beta |
| RA | 2,825,084 | T→G | 12.8% | W13G (TGG→GGG) | srlE → | PTS glucitol/sorbitol transporter subunit IIB |
| RA | 2,827,162 | T→G | 16.0% | V257G (GTG→GGG) | srlD → | sorbitol‑6‑phosphate dehydrogenase |
| RA | 2,827,233 | T→C | 9.3% | intergenic (+61/‑44) | srlD → / → gutM | sorbitol‑6‑phosphate dehydrogenase/transcriptional regulator GutM |
| RA | 2,864,722 | T→G | 12.0% | G322G (GGT→GGG) | Y75_RS14290 → | GntP family transporter |
| RA | 2,866,109 | C→A | 100% | pseudogene (99/993 nt) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,875,251 | G→T | 12.3% | L5F (TTG→TTT) | iap → | alkaline phosphatase isozyme conversion aminopeptidase |
| RA | 2,906,975 | C→G | 100% | D450H (GAC→CAC) | pyrG ← | CTP synthase (glutamine hydrolyzing) |
| MC JC | 2,910,136 | Δ12 bp | 100% | coding (2161‑2172/2235 nt) | Y75_RS14515 ← | GTP pyrophosphokinase |
| RA | 2,939,008 | A→C | 13.9% | C298G (TGC→GGC) | rlmM ← | 23S rRNA (cytidine(2498)‑2'‑O)‑methyltransferase RlmM |
| RA | 2,948,829 | A→G | 10.0% | E311G (GAG→GGG) | argA → | amino‑acid N‑acetyltransferase |
| RA | 2,973,749 | T→G | 12.8% | T308P (ACT→CCT) | aas ← | bifunctional acyl‑ACP‑‑phospholipid O‑acyltransferase/long‑chain‑fatty‑acid‑‑ACP ligase |
| RA | 2,973,763 | A→T | 7.6% | I303N (ATC→AAC) | aas ← | bifunctional acyl‑ACP‑‑phospholipid O‑acyltransferase/long‑chain‑fatty‑acid‑‑ACP ligase |
| RA | 2,976,798 | T→C | 11.5% | E253G (GAG→GGG) | lysA ← | diaminopimelate decarboxylase |
| RA | 2,976,802 | G→C | 11.7% | R252G (CGT→GGT) | lysA ← | diaminopimelate decarboxylase |
| RA | 3,089,466 | T→G | 12.1% | V155G (GTC→GGC) | endA → | deoxyribonuclease I |
| RA | 3,137,862 | T→G | 7.7% | G160G (GGT→GGG) | yghU → | glutathione‑dependent disulfide‑bond oxidoreductase |
| RA | 3,198,591 | A→G | 11.2% | I344T (ATC→ACC) | Y75_RS15900 ← | inorganic triphosphatase |
| RA | 3,205,094 | G→A | 25.2% | intergenic (‑182/‑25) | ttdR ← / → ttdA | DNA‑binding transcriptional activator TtdR/L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,205,132 | G→A | 14.6% | S5N (AGT→AAT) ‡ | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,205,133 | T→A | 13.6% | S5R (AGT→AGA) ‡ | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,205,139 | G→A | 24.0% | K7K (AAG→AAA) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,205,140 | C→A | 12.6% | Q8K (CAA→AAA) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,205,143 | C→A | 11.5% | Q9K (CAG→AAG) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,205,162 | C→A | 8.9% | T15K (ACA→AAA) | ttdA → | L(+)‑tartrate dehydratase subunit alpha |
| RA | 3,236,547 | A→G | 13.8% | E194G (GAG→GGG) | Y75_RS16075 → | Gfo/Idh/MocA family oxidoreductase |
| MC JC | 3,261,134 | Δ1,199 bp | 100% | Y75_RS16205–[tdcD] | Y75_RS16205, [tdcD] | |
| RA | 3,308,855 | G→C | 15.3% | intergenic (‑76/+33) | nlpI ← / ← pnp | lipoprotein NlpI/polyribonucleotide nucleotidyltransferase |
| JC | 3,315,267 | (CGACGTGCTTCTTCAGCAACG)1→2 | 100% | coding (603/2673 nt) | infB ← | translation initiation factor IF‑2 |
| RA | 3,315,356 | C→T | 8.7% | E172K (GAA→AAA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,315,372 | A→T | 11.0% | T166T (ACT→ACA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,315,410 | C→T | 6.0% | E154K (GAA→AAA) | infB ← | translation initiation factor IF‑2 |
| RA | 3,370,730 | A→C | 10.8% | G54G (GGT→GGG) | Y75_RS16755 ← | N‑acetylmannosamine‑6‑phosphate 2‑epimerase |
| RA | 3,375,420 | C→A | 12.1% | Q233K (CAA→AAA) | dcuC → | anaerobic C4‑dicarboxylate transporter DcuC |
| RA | 3,411,477 | C→T | 5.8% | intergenic (+55/‑31) | fis → / → yhdJ | DNA‑binding transcriptional regulator Fis/adenine‑specific DNA‑methyltransferase |
| RA | 3,414,977 | G→T | 7.5% | L30F (TTG→TTT) | acrF → | multidrug efflux RND transporter permease subunit AcrF |
| RA | 3,477,968 | A→C | 6.8% | V75G (GTG→GGG) | oxyR ← | DNA‑binding transcriptional regulator OxyR |
| RA | 3,485,352 | A→C | 21.6% | A590A (GCA→GCC) | ppc → | phosphoenolpyruvate carboxylase |
| RA | 3,485,358 | T→C | 18.5% | A592A (GCT→GCC) | ppc → | phosphoenolpyruvate carboxylase |
| RA | 3,491,593 | C→G | 12.3% | R365P (CGC→CCC) | Y75_RS17340 ← | formate C‑acetyltransferase |
| RA | 3,538,290 | T→G | 23.1% | Y219S (TAC→TCC) | rhaS ← | HTH‑type transcriptional activator RhaS |
| RA | 3,571,090 | C→G | 8.7% | A59G (GCG→GGG) | Y75_RS17735 → | MFS transporter |
| RA | 3,609,535 | G→C | 11.9% | A207G (GCG→GGG) | fre ← | NAD(P)H‑flavin reductase |
| RA | 3,609,538 | A→C | 17.1% | M206R (ATG→AGG) | fre ← | NAD(P)H‑flavin reductase |
| RA | 3,645,110 | A→T | 100% | L140Q (CTG→CAG) | cyaA ← | class I adenylate cyclase |
| RA | 3,656,455 | C→T | 100% | V91I (GTT→ATT) | rffM ← | lipopolysaccharide N‑acetylmannosaminouronosyltransferase |
| RA | 3,661,414 | T→C | 8.7% | E41G (GAG→GGG) | rffA ← | dTDP‑4‑amino‑4,6‑dideoxygalactose transaminase |
| JC | 3,670,427 | Δ27 bp | 5.8% | [rhoL] | [rhoL] | |
| RA | 3,685,148 | A→T | 92.4% | pseudogene (974/1645 nt) | Y75_RS18285 ← | acetolactate synthase 2 catalytic subunit |
| RA | 3,732,053 | A→C | 15.2% | T324P (ACC→CCC) | bglF → | PTS beta‑glucoside transporter subunit IIABC |
| MC JC | 3,746,911 | Δ1,199 bp | 100% | Y75_RS18585–[tnaB] | Y75_RS18585, [tnaB] | |
| MC JC | 3,750,591 | Δ1,199 bp | 100% | Y75_RS18600 | Y75_RS18600 | |
| RA | 3,764,880 | G→T | 7.9% | T33N (ACC→AAC) | Y75_RS18670 ← | hypothetical protein |
| RA | 3,777,742 | C→T | 16.0% | L311L (CTG→TTG) | Y75_RS18735 → | PTS transporter subunit EIIC |
| RA | 3,777,745 | A→T | 21.4% | I312F (ATT→TTT) | Y75_RS18735 → | PTS transporter subunit EIIC |
| RA | 3,777,754 | A→C | 31.4% | T315P (ACC→CCC) | Y75_RS18735 → | PTS transporter subunit EIIC |
| RA | 3,787,552 | A→C | 10.6% | intergenic (+27/‑79) | ivbL → / → ilvB | ilvB operon leader peptide IvbL/acetolactate synthase large subunit |
| RA | 3,856,941 | T→C | 5.1% | L63P (CTC→CCC) | gpsA → | NAD(P)H‑dependent glycerol‑3‑phosphate dehydrogenase |
| RA | 3,857,507 | A→C | 19.5% | T252P (ACC→CCC) | gpsA → | NAD(P)H‑dependent glycerol‑3‑phosphate dehydrogenase |
| RA | 3,857,513 | A→C | 21.2% | T254P (ACC→CCC) | gpsA → | NAD(P)H‑dependent glycerol‑3‑phosphate dehydrogenase |
| RA | 3,890,038 | A→G | 10.2% | S98P (TCG→CCG) | Y75_RS19280 ← | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 3,890,726 | T→C | 12.7% | E153G (GAG→GGG) | Y75_RS19285 ← | L‑ribulose‑5‑phosphate 3‑epimerase |
| RA | 3,942,186 | G→T | 8.3% | Q6K (CAA→AAA) | bcsG ← | cellulose biosynthesis protein BcsG |
| RA | 3,942,675 | A→C | 17.9% | V428G (GTG→GGG) | bcsE ← | cellulose biosynthesis protein BcsE |
| RA | 3,953,876 | A→G | 7.3% | S879G (AGC→GGC) | bcsC → | cellulose biosynthesis protein BcsC |
| RA | 3,994,338 | A→G | 10.7% | D231D (GAT→GAC) | Y75_RS19765 ← | 23S rRNA (adenine(2030)‑N(6))‑methyltransferase |
| RA | 4,012,909 | A→C | 9.4% | H678P (CAC→CCC) | rbbA → | ribosome‑associated ATPase/putative transporter RbbA |
| RA | 4,017,888 | A→C | 12.1% | S1112R (AGT→AGG) | Y75_RS19860 ← | rhs element protein RhsB |
| RA | 4,021,098 | T→C | 17.2% | G42G (GGA→GGG) | Y75_RS19860 ← | rhs element protein RhsB |
| RA | 4,044,279 | A→G | 6.6% | S90G (AGT→GGT) | livH → | high‑affinity branched‑chain amino acid ABC transporter permease LivH |
| RA | 4,071,644 | C→A | 10.9% | N186K (AAC→AAA) | glgC → | glucose‑1‑phosphate adenylyltransferase |
| RA | 4,087,131 | A→C | 9.2% | G67G (GGT→GGG) | malT ← | HTH‑type transcriptional regulator MalT |
| RA | 4,091,484 | C→G | 9.6% | A380G (GCG→GGG) | malQ → | 4‑alpha‑glucanotransferase |
| RA | 4,091,507 | T→G | 15.4% | C388G (TGT→GGT) | malQ → | 4‑alpha‑glucanotransferase |
| RA | 4,091,582 | T→G | 10.2% | W413G (TGG→GGG) | malQ → | 4‑alpha‑glucanotransferase |
| RA | 4,104,271 | T→C | 12.0% | L147P (CTC→CCC) | ompR → | two‑component system response regulator OmpR |
| RA | 4,104,281 | C→G | 10.3% | R150R (CGC→CGG) | ompR → | two‑component system response regulator OmpR |
| RA | 4,108,967 | T→G | 8.5% | S331A (TCG→GCG) | Y75_RS20260 → | DUF4153 domain‑containing protein |
| RA | 4,179,667 | A→T | 11.0% | G311G (GGT→GGA) | gspF ← | type II secretion system inner membrane protein GspF |
| RA | 4,262,217 | A→C | 9.2% | T296P (ACC→CCC) | dinF → | MATE family efflux transporter DinF |
| RA | 4,273,250 | C→G | 6.6% | R83G (CGC→GGC) | Y75_RS21155 → | acid phosphatase AphA |
| RA | 4,290,120 | T→A | 11.3% | Y281F (TAT→TTT) | acs ← | acetate‑‑CoA ligase |
| RA | 4,330,626 | A→G | 5.8% | intergenic (‑207/+451) | yjdN ← / ← Y75_RS21430 | VOC family metalloprotein YjdN/phnA family protein |
| RA | 4,341,559 | T→A | 11.4% | I51F (ATC→TTC) | adiC ← | arginine/agmatine antiporter |
| RA | 4,346,346 | A→G | 5.5% | intergenic (‑40/‑243) | melR ← / → melA | transcriptional regulator MelR/alpha‑galactosidase |
| RA | 4,371,271 | Δ2 bp | 100% | pseudogene (182‑183/1304 nt) | Y75_RS21600 ← | anaerobic C4‑dicarboxylate transporter |
| RA | 4,395,445 | T→G | 14.7% | T249P (ACC→CCC) | rsgA ← | small ribosomal subunit biogenesis GTPase RsgA |
| RA | 4,399,551 | C→G | 12.5% | A269G (GCT→GGT) | nnr → | bifunctional ADP‑dependent NAD(P)H‑hydrate dehydratase/NAD(P)H‑hydrate epimerase |
| RA | 4,408,585 | T→G | 12.7% | G202G (GGT→GGG) | hflC → | protease modulator HflC |
| RA | 4,421,891 | G→A | 5.1% | S87N (AGT→AAT) | yjfP → | esterase |
| RA | 4,428,816 | T→G | 8.3% | V146G (GTG→GGG) | Y75_RS21910 → | L‑ribulose‑5‑phosphate 4‑epimerase UlaF |
| RA | 4,479,393 | A→G | 11.0% | E197G (GAG→GGG) | Y75_RS22170 → | TetR/AcrR family transcriptional regulator |
| RA | 4,527,463 | T→G | 11.5% | T438P (ACC→CCC) | Y75_RS22420 ← | xylonate dehydratase YjhG |
| RA | 4,595,559 | T→C | 11.2% | D134G (GAC→GGC) | btsT ← | pyruvate/proton symporter BtsT |
| RA | 4,611,582 | A→G | 20.2% | S267P (TCC→CCC) | rsmC ← | 16S rRNA (guanine(1207)‑N(2))‑methyltransferase RsmC |
| RA | 4,623,416 | A→C | 14.1% | T170P (ACC→CCC) | deoA → | thymidine phosphorylase |
| RA | 4,624,158 | T→G | 12.1% | V417G (GTG→GGG) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_007779 | 1301041–1302370 | 1302407 | 38–1367 | 209 [0] | [0] 166 | Y75_RS06530–Y75_RS06530 | Y75_RS06530,Y75_RS06530 |
| * | * | ÷ | NC_007779 | 1397907–1398957 | 1406267 | 7311–8361 | 65 [63] | [0] 141 | [Y75_RS07025]–[Y75_RS07065] | [Y75_RS07025],Y75_RS07030,uspE,Y75_RS07040,ogt,abgT,Y75_RS07060,[Y75_RS07065] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_007779 | 224412 = | NA (NA) | 6 (0.030) | 5/396 | NT | NA | noncoding (642/1554 nt) | Y75_RS01020 | 16S ribosomal RNA |
| ? | NC_007779 | 224936 = | NA (NA) | noncoding (1166/1554 nt) | Y75_RS01020 | 16S ribosomal RNA | |||||
| * | ? | NC_007779 | 273180 = | NA (NA) | 198 (1.110) | 116/408 | NT | 100% | intergenic (+3/+145) | Y75_RS01330/Y75_RS01335 | hypothetical protein/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 701988 = | 0 (0.000) | coding (29/1221 nt) | nagC | DNA‑binding transcriptional regulator NagC | |||||
| * | ? | NC_007779 | 314625 = | NA (NA) | 9 (0.050) | 8/384 | NT | NA | coding (111/300 nt) | Y75_RS24740 | transposase |
| ? | NC_007779 | 314851 = | NA (NA) | coding (41/867 nt) | Y75_RS01555 | IS3 family transposase | |||||
| * | ? | NC_007779 | 374146 = | 154 (0.860) | 11 (0.060) | 9/394 | NT | 5.9% | intergenic (+41/‑537) | dmpG/Y75_RS01815 | 4‑hydroxy‑2‑oxovalerate aldolase/3‑(3‑hydroxy‑phenyl)propionate transporter |
| ? | NC_007779 | 376553 = | 204 (1.190) | intergenic (+18/+206) | Y75_RS01820/Y75_RS01825 | DUF2058 domain‑containing protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_007779 | 380758 = | NA (NA) | 7 (0.040) | 6/394 | NT | NA | coding (229/361 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | 381396 = | NA (NA) | coding (507/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | = 381377 | NA (NA) | 11 (0.060) | 5/398 | NT | NA | coding (488/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 381470 | NA (NA) | coding (581/914 nt) | Y75_RS01860 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | 571584 = | 246 (1.370) | 28 (0.160) | 25/410 | NT | 10.2% | intergenic (+110/‑7) | Y75_RS02805/Y75_RS23245 | helix‑turn‑helix transcriptional regulator/hypothetical protein |
| ? | NC_007779 | = 1106952 | NA (NA) | intergenic (‑46/‑39) | Y75_RS05455/Y75_RS05465 | IS3‑like element IS2 family transposase/hypothetical protein | |||||
| * | ? | NC_007779 | = 571589 | 246 (1.370) | 26 (0.150) | 24/408 | NT | 9.6% | intergenic (+115/‑2) | Y75_RS02805/Y75_RS23245 | helix‑turn‑helix transcriptional regulator/hypothetical protein |
| ? | NC_007779 | = 1302368 | NA (NA) | intergenic (+10/‑528) | Y75_RS06530/oppA | IS3‑like element IS2 family transposase/oligopeptide ABC transporter substrate‑binding protein OppA | |||||
| * | ? | NC_007779 | 607256 = | NA (NA) | 13 (0.080) | 8/358 | NT | 8.1% | intergenic (+45/‑32) | Y75_RS03010/Y75_RS03015 | type I toxin‑antitoxin system toxin HokE/IS4‑like element IS421 family transposase |
| ? | NC_007779 | 608549 = | 170 (0.950) | intergenic (+149/+133) | Y75_RS03015/entD | IS4‑like element IS421 family transposase/enterobactin synthase subunit EntD | |||||
| * | ? | NC_007779 | = 689467 | NA (NA) | 124 (0.690) | 73/410 | NT | 100% | intergenic (‑32/+298) | Y75_RS03405/lnt | IS5‑like element IS5 family transposase/apolipoprotein N‑acyltransferase |
| ? | NC_007779 | = 701992 | 0 (0.000) | coding (25/1221 nt) | nagC | DNA‑binding transcriptional regulator NagC | |||||
| * | ? | NC_007779 | = 1051773 | 216 (1.210) | 13 (0.070) | 6/402 | NT | 5.9% | intergenic (‑176/‑110) | cspH/cspG | cold shock‑like protein CspH/cold shock protein CspG |
| ? | NC_007779 | = 1051897 | 203 (1.160) | coding (15/213 nt) | cspG | cold shock protein CspG | |||||
| * | ? | NC_007779 | 1209367 = | 74 (0.410) | 122 (0.740) | 78/378 | NT | 63.7% | coding (290/630 nt) | Y75_RS06020 | hypothetical protein |
| ? | NC_007779 | 1211196 = | 71 (0.430) | intergenic (‑6/‑66) | Y75_RS06035/pinE | tail fiber protein/site‑specific DNA recombinase | |||||
| * | ? | NC_007779 | = 1209382 | 71 (0.400) | 102 (0.620) | 63/378 | NT | 59.9% | coding (305/630 nt) | Y75_RS06020 | hypothetical protein |
| ? | NC_007779 | = 1211179 | 71 (0.430) | coding (12/495 nt) | Y75_RS06035 | tail fiber protein | |||||
| * | ? | NC_007779 | 1294701 = | 95 (0.530) | 6 (0.030) | 6/410 | NT | 5.9% | intergenic (‑202/‑403) | hns/tdk | DNA‑binding transcriptional regulator H‑NS/thymidine kinase |
| ? | NC_007779 | = 1398952 | NA (NA) | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein | |||||
| * | ? | NC_007779 | = 1294704 | 86 (0.480) | 5 (0.030) | 4/410 | NT | 5.5% | intergenic (‑205/‑400) | hns/tdk | DNA‑binding transcriptional regulator H‑NS/thymidine kinase |
| ? | NC_007779 | 2176983 = | NA (NA) | intergenic (‑3/‑32) | gatA/Y75_RS10980 | PTS galactitol transporter subunit IIA/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | 1294773 = | 2 (0.010) | 262 (1.460) | 121/410 | NT | 99.2% | intergenic (‑274/‑331) | hns/tdk | DNA‑binding transcriptional regulator H‑NS/thymidine kinase |
| ? | NC_007779 | = 1398952 | NA (NA) | intergenic (+146/‑127) | Y75_RS07025/Y75_RS07030 | IS5‑like element IS5 family transposase/DUF2534 family protein | |||||
| * | ? | NC_007779 | = 1294776 | 2 (0.010) | 199 (1.110) | 105/410 | NT | 99.0% | intergenic (‑277/‑328) | hns/tdk | DNA‑binding transcriptional regulator H‑NS/thymidine kinase |
| ? | NC_007779 | 1397758 = | NA (NA) | intergenic (‑122/‑32) | ynaI/Y75_RS07025 | low conductance mechanosensitive channel YnaI/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 1301040 | 0 (0.000) | 163 (1.050) +28 bp |
82/354 | NT | 100% | intergenic (+218/‑45) | ychE/Y75_RS06530 | NAAT family transporter YchE/IS3‑like element IS2 family transposase |
| ? | NC_007779 | = 4311564 | NA (NA) | pseudogene (914/921 nt) | alsK | allose kinase | |||||
| * | ? | NC_007779 | 1302408 = | 0 (0.000) | 159 (0.890) | 89/410 | NT | 100% | intergenic (+50/‑488) | Y75_RS06530/oppA | IS3‑like element IS2 family transposase/oligopeptide ABC transporter substrate‑binding protein OppA |
| ? | NC_007779 | 1397758 = | NA (NA) | intergenic (‑122/‑32) | ynaI/Y75_RS07025 | low conductance mechanosensitive channel YnaI/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | = 1388812 | 174 (0.970) | 19 (0.110) | 10/398 | NT | 10.1% | coding (379/1542 nt) | tyrR | transcriptional regulator TyrR |
| ? | NC_007779 | = 1388962 | 171 (0.980) | coding (529/1542 nt) | tyrR | transcriptional regulator TyrR | |||||
| * | ? | NC_007779 | 1406268 = | 0 (0.000) | 138 (0.770) | 83/410 | NT | 100% | coding (12/1311 nt) | Y75_RS07065 | p‑aminobenzoyl‑glutamate hydrolase subunit AbgA |
| ? | NC_007779 | 1980209 = | NA (NA) | intergenic (‑298/+146) | flhD/Y75_RS09980 | flagellar transcriptional regulator FlhD/IS5‑like element IS5 family transposase | |||||
| * | ? | NC_007779 | 1463803 = | 200 (1.120) | 12 (0.070) | 10/386 | NT | 5.8% | coding (1197/1206 nt) | Y75_RS07380 | 3‑oxoadipyl‑CoA thiolase |
| ? | NC_007779 | 1463937 = | 202 (1.200) | coding (99/1314 nt) | paaF | phenylacetate‑‑CoA ligase | |||||
| * | ? | NC_007779 | = 1817916 | 174 (0.970) | 12 (0.070) | 6/382 | NT | 6.4% | intergenic (+74/+184) | katE/chbG | catalase HPII/chitin disaccharide deacetylase |
| ? | NC_007779 | = 1818069 | 187 (1.120) | intergenic (+227/+31) | katE/chbG | catalase HPII/chitin disaccharide deacetylase | |||||
| * | ? | NC_007779 | = 1830395 | 91 (0.510) | 7 (0.040) | 7/392 | NT | 7.4% | coding (1054/1479 nt) | astD | succinylglutamate‑semialdehyde dehydrogenase |
| ? | NC_007779 | = 1830409 | 87 (0.510) | coding (1040/1479 nt) | astD | succinylglutamate‑semialdehyde dehydrogenase | |||||
| * | ? | NC_007779 | 1881541 = | 0 (0.000) | 5 (0.030) | 5/406 | NT | 100% | coding (122/360 nt) | yeaR | DUF1971 domain‑containing protein |
| ? | NC_007779 | 2519722 = | NA (NA) | intergenic (+32/‑55) | nupC/Y75_RS12570 | nucleoside permease NupC/IS4‑like element IS421 family transposase | |||||
| * | ? | NC_007779 | 1881541 = | 0 (0.000) | 180 (1.010) | 106/406 | NT | 100% | coding (122/360 nt) | yeaR | DUF1971 domain‑containing protein |
| ? | NC_007779 | = 2521060 | NA (NA) | intergenic (+171/+29) | Y75_RS12570/Y75_RS12575 | IS4‑like element IS421 family transposase/sensor domain‑containing phosphodiesterase | |||||
| * | ? | NC_007779 | = 1881551 | 9 (0.050) | 186 (1.050) | 94/404 | NT | 95.4% | coding (112/360 nt) | yeaR | DUF1971 domain‑containing protein |
| ? | NC_007779 | 2519723 = | NA (NA) | intergenic (+33/‑54) | nupC/Y75_RS12570 | nucleoside permease NupC/IS4‑like element IS421 family transposase | |||||
| * | ? | NC_007779 | = 1881551 | 9 (0.050) | 6 (0.030) | 5/404 | NT | 40.4% | coding (112/360 nt) | yeaR | DUF1971 domain‑containing protein |
| ? | NC_007779 | = 2521059 | NA (NA) | intergenic (+170/+30) | Y75_RS12570/Y75_RS12575 | IS4‑like element IS421 family transposase/sensor domain‑containing phosphodiesterase | |||||
| * | ? | NC_007779 | 2071829 = | NA (NA) | 33 (0.190) | 7/388 | NT | 83.3% | coding (174/914 nt) | Y75_RS10480 | IS3‑like element IS2 family transposase |
| ? | NC_007779 | 2072195 = | 7 (0.040) | coding (168/361 nt) | Y75_RS10480 | IS3‑like element IS2 family transposase | |||||
| * | ? | NC_007779 | = 2537411 | 193 (1.080) | 15 (0.090) | 6/390 | NT | 7.0% | coding (503/762 nt) | cysZ | sulfate transporter CysZ |
| ? | NC_007779 | = 2537613 | 218 (1.280) | coding (705/762 nt) | cysZ | sulfate transporter CysZ | |||||
| * | ? | NC_007779 | = 2712485 | 177 (0.990) | 12 (0.070) | 12/388 | NT | 6.9% | coding (934/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB |
| ? | NC_007779 | = 2712564 | 158 (0.930) | coding (1013/1335 nt) | srmB | ATP‑dependent RNA helicase SrmB | |||||
| * | ? | NC_007779 | = 2899085 | 166 (0.930) | 10 (0.060) | 7/396 | NT | 6.8% | intergenic (‑156/‑163) | Y75_RS14460/Y75_RS14465 | SDR family oxidoreductase/MFS transporter |
| ? | NC_007779 | = 2899239 | 112 (0.650) | intergenic (‑310/‑9) | Y75_RS14460/Y75_RS14465 | SDR family oxidoreductase/MFS transporter | |||||
| * | ? | NC_007779 | = 3742935 | 0 (0.000) | 173 (1.010) | 85/394 | NT | 100% | intergenic (‑135/+9) | Y75_RS18555/Y75_RS18560 | 4'‑phosphopantetheinyl transferase/IS3‑like element IS2 family transposase |
| ? | NC_007779 | 3744272 = | 0 (0.000) | intergenic (‑55/+21) | Y75_RS18560/yidZ | IS3‑like element IS2 family transposase/HTH‑type transcriptional regulator YidZ | |||||
| * | ? | NC_007779 | 3748316 = | 0 (0.000) | 188 (1.050) | 97/410 | NT | 100% | pseudogene (665/873 nt) | tnaB | low affinity tryptophan permease TnaB |
| ? | NC_007779 | = 4056987 | NA (NA) | coding (391/417 nt) | Y75_RS20060 | hypothetical protein | |||||
| * | ? | NC_007779 | = 3748324 | 4 (0.020) | 195 (1.090) | 95/410 | NT | 98.0% | pseudogene (657/873 nt) | tnaB | low affinity tryptophan permease TnaB |
| ? | NC_007779 | 4056220 = | NA (NA) | intergenic (‑209/+15) | Y75_RS25055/Y75_RS20055 | hypothetical protein/IS1‑like element IS1A family transposase | |||||
| * | ? | NC_007779 | 3876427 = | NA (NA) | 3 (0.020) | 3/388 | NT | 9.9% | coding (1806/4134 nt) | Y75_RS19225 | RHS element protein RhsA |
| ? | NC_007779 | 3876545 = | 29 (0.160) | coding (1688/4134 nt) | Y75_RS19225 | RHS element protein RhsA | |||||
| * | ? | NC_007779 | 3970002 = | 174 (0.970) | 10 (0.060) | 7/398 | NT | 5.5% | coding (822/1650 nt) | treF | alpha,alpha‑trehalase TreF |
| ? | NC_007779 | 3970183 = | 176 (1.010) | coding (641/1650 nt) | treF | alpha,alpha‑trehalase TreF | |||||
| * | ? | NC_007779 | 4056221 = | NA (NA) | 165 (0.930) | 87/408 | NT | 97.6% | intergenic (‑210/+14) | Y75_RS25055/Y75_RS20055 | hypothetical protein/IS1‑like element IS1A family transposase |
| ? | NC_007779 | 4370787 = | 4 (0.020) | pseudogene (667/1304 nt) | Y75_RS21600 | anaerobic C4‑dicarboxylate transporter | |||||
| * | ? | NC_007779 | = 4056987 | NA (NA) | 210 (1.170) | 108/410 | NT | 97.7% | coding (391/417 nt) | Y75_RS20060 | hypothetical protein |
| ? | NC_007779 | = 4370795 | 5 (0.030) | pseudogene (659/1304 nt) | Y75_RS21600 | anaerobic C4‑dicarboxylate transporter | |||||
| * | ? | NC_007779 | = 4310362 | 1 (0.010) | 181 (1.030) | 85/402 | NT | 99.7% | intergenic (‑286/‑33) | yjcS/Y75_RS21310 | alkyl sulfatase YjcS/IS5‑like element IS5 family transposase |
| ? | NC_007779 | 4311562 = | 0 (0.000) | pseudogene (916/921 nt) | alsK | allose kinase | |||||