mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 27,887 | G→T | 5.9% | D199Y (GAC→TAC) | rihC → | ribonucleoside hydrolase 3 |
| RA | 57,081 | G→T | 6.0% | A10D (GCC→GAC) | lptD ← | LPS assembly OM complex LptDE, beta‑barrel component |
| RA | 66,840 | G→T | 5.1% | R500S (CGC→AGC) | araA ← | L‑arabinose isomerase |
| RA | 222,958 | Δ1 bp | 100% | coding (126/576 nt) | gmhB → | D,D‑heptose 1,7‑bisphosphate phosphatase |
| RA | 248,221 | T→C | 5.7% | intergenic (+87/+137) | rayT → / ← lfhA | RAYT REP element‑mobilizing transposase; TnpA(REP)/pseudogene, flagellar system protein, promoterless fragment; flagellar biosynthesis |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 423,539 | T→G | 13.0% | L341R (CTG→CGG) | malZ → | maltodextrin glucosidase |
| RA | 566,173 | C→G | 18.4% | pseudogene (204/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 566,205 | T→C | 14.6% | pseudogene (172/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 566,245 | G→A | 16.2% | pseudogene (132/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 566,323 | C→T | 8.2% | pseudogene (54/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 566,326 | T→C | 7.3% | pseudogene (51/279 nt) | exoD ← | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| RA | 663,703 | C→A | 12.5% | M87I (ATG→ATT) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5) |
| RA | 737,043 | T→C | 5.5% | pseudogene (219/1137 nt) | ybfL → | pseudogene, DDE domain transposase family;putative factor; Not classified; putative receptor protein |
| RA | 919,889 | G→T | 5.4% | D219Y (GAT→TAT) | macA → | macrolide transporter membrane fusion protein (MFP) component |
| RA | 957,931 | C→T | 12.5% | T93T (ACC→ACT) | serC → | 3‑phosphoserine/phosphohydroxythreonine aminotransferase |
| RA | 992,071 | C→A | 6.0% | P484T (CCG→ACG) | pepN → | aminopeptidase N |
| RA | 1,023,018 | G→T | 6.1% | S289* (TCA→TAA) | yccS ← | putative transporter, FUSC superfamily inner membrane protein |
| RA | 1,028,117 | C→A | 5.5% | Q58K (CAG→AAG) | yccU → | putative CoA‑binding protein |
| RA | 1,048,338 | G→T | 5.2% | V118V (GTC→GTA) | gfcC ← | putative O‑antigen capsule production periplasmic protein |
| RA | 1,049,827 | T→G | 7.5% | intergenic (‑83/‑6) | gfcA ← / → insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| RA | 1,061,284 | G→T | 7.4% | E677* (GAA→TAA) | torA → | trimethylamine N‑oxide (TMAO) reductase I, catalytic subunit |
| RA | 1,196,220 | C→T | 11.4% | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | 10.8% | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,206,494 | G→T | 5.2% | pseudogene (352/780 nt) | jayE → | pseudogene, e14 prophage;Phage or Prophage Related |
| RA | 1,227,332 | G→A | 12.0% | Y47Y (TAC→TAT) | pliG ← | periplasmic inhibitor of g‑type lysozyme |
| RA | 1,252,805 | C→T | 5.9% | T580T (ACC→ACT) | dhaR → | dhaKLM operon transcription activator |
| RA | 1,269,897 | T→G | 8.9% | noncoding (40/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,270,543 | T→A | 5.8% | intergenic (+83/+206) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| RA | 1,270,545 | G→T | 6.5% | intergenic (+85/+204) | rdlC → / ← chaA | sRNA antisense regulator affects LdrC translation; proposed addiction module in LDR‑C repeat, with toxic peptide LdrC/calcium/sodium:proton antiporter |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,331,561 | G→A | 5.4% | D172N (GAC→AAC) | topA → | DNA topoisomerase I, omega subunit |
| RA | 1,346,888 | G→T | 14.2% | T31T (ACG→ACT) | ymiB → | uncharacterized protein |
| RA | 1,466,201 | T→C | 6.3% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,466,504 | A→G | 8.0% | pseudogene (1113/2513 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,481,249 | G→T | 6.8% | G114V (GGA→GTA) | ynbD → | putative phosphatase inner membrane protein |
| RA | 1,513,266 | G→T | 6.5% | V150V (GTG→GTT) | ydcT → | putative ABC transporter ATPase |
| RA | 1,579,861 | C→A | 7.1% | R310R (CGG→CGT) | ydeM ← | putative YdeN‑specific sulfatase‑maturating enzyme |
| RA | 1,590,848 | C→A | 6.0% | intergenic (‑312/+6) | yneL ← / ← hipA | pseudogene, AraC family/inactivating GltX kinase facilitating persister formation; toxin of HipAB TA pair; autokinase |
| RA | 1,681,446 | G→T | 6.3% | A157A (GCG→GCT) | folM → | dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme |
| RA | 1,748,497 | C→A | 7.7% | P456H (CCT→CAT) | ydhS → | putative oxidoreductase |
| JC JC | 1,757,082 | IS5 (–) +4 bp | 17.2% | coding (1385‑1388/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,759,478 | C→T | 5.9% | S349N (AGT→AAT) | sufS ← | cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent |
| RA | 1,763,608 | C→A | 10.4% | V134V (GTG→GTT) | sufB ← | component of SufBCD Fe‑S cluster assembly scaffold |
| RA | 1,873,568 | C→A | 7.5% | intergenic (+37/‑6) | yeaJ → / → yeaK | putative diguanylate cyclase/aminoacyl‑tRNA editing domain protein |
| RA | 1,888,058 | C→T | 7.2% | intergenic (‑67/+3) | rnd ← / ← fadD | ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) |
| RA | 1,905,012 | C→T | 7.5% | T71I (ACA→ATA) | yobD → | UPF0266 family inner membrane protein |
| RA | 1,931,602 | C→A | 5.2% | P241Q (CCG→CAG) | purT → | phosphoribosylglycinamide formyltransferase 2 |
| RA | 1,939,460 | A→G | 9.1% | V245A (GTA→GCA) | lpxM ← | myristoyl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 1,976,145 | C→A | 5.0% | M37I (ATG→ATT) | motB ← | protein that enables flagellar motor rotation |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,061,801 | G→T | 11.5% | Q45K (CAA→AAA) | nac ← | nitrogen assimilation regulon transcriptional regulator; autorepressor |
| RA | 2,075,388 | G→T | 5.1% | E204* (GAA→TAA) | yeeR → | CP4‑44 prophage; putative membrane protein |
| RA | 2,121,340 | C→A | 7.7% | W72L (TGG→TTG) | wcaJ ← | colanic biosynthesis UDP‑glucose lipid carrier transferase |
| RA | 2,172,555 | C→A | 6.6% | D107Y (GAT→TAT) | gatD ← | galactitol‑1‑phosphate dehydrogenase, Zn‑dependent and NAD(P)‑binding |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,205,701 | G→T | 7.7% | E3* (GAG→TAG) | yehM → | uncharacterized protein |
| RA | 2,304,649 | C→T | 5.8% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| JC JC | 2,375,828 | IS186 (+) +4 bp | 100% | coding (132‑135/963 nt) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,452,436 | C→A | 9.1% | pseudogene (2566/2646 nt) | yfcU ← | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| RA | 2,525,571 | C→A | 6.7% | P149T (CCG→ACG) | yfeN → | putative outer membrane protein |
| RA | 2,642,597 | A→G | 6.0% | L83P (CTG→CCG) | rodZ ← | MreB assembly cytoskeletal protein |
| RA | 2,746,790 | C→A | 5.6% | E336* (GAG→TAG) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,904,212 | G→A | 100% | intergenic (+838/+535) | ygcE → / ← queE | putative kinase/7‑carboxy‑7‑deazaguanine synthase; queosine biosynthesis |
| RA | 2,928,373 | G→T | 5.1% | G49C (GGT→TGT) | sdaC → | putative serine transporter |
| RA | 3,010,147 | G→A | 5.5% | P40P (CCG→CCA) | hyuA → | D‑stereospecific phenylhydantoinase |
| RA | 3,076,880 | C→A | 5.2% | D193Y (GAT→TAT) | yggP ← | putative Zn‑binding dehydrogenase |
| RA | 3,116,990 | T→C | 5.8% | Q708R (CAG→CGG) | sslE ← | putative secreted and surface‑associated lipoprotein mucinase |
| RA | 3,241,102 | C→T | 5.5% | L387L (CTG→TTG) | sstT → | sodium:serine/threonine symporter |
| JC | 3,277,257 | +CATTCAA | 45.3% | coding (256/336 nt) | prlF → | antitoxin of the SohA(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,279,147 | G→T | 5.1% | L78F (TTG→TTT) | kbaZ → | tagatose 6‑phosphate aldolase 1, kbaZ subunit |
| RA | 3,279,160 | G→T | 5.2% | D83Y (GAT→TAT) | kbaZ → | tagatose 6‑phosphate aldolase 1, kbaZ subunit |
| RA | 3,298,414 | G→T | 5.0% | R145S (CGC→AGC) | yraR ← | putative nucleoside‑diphosphate‑sugar epimerase |
| RA | 3,349,137 | G→A | 6.7% | R225W (CGG→TGG) | mtgA ← | biosynthetic peptidoglycan transglycosylase |
| RA | 3,392,880 | G→A | 5.1% | R1127C (CGC→TGC) | yhdP ← | DUF3971‑AsmA2 domains protein |
| RA | 3,437,445 | G→A | 14.3% | A310T (GCC→ACC) | trkA → | NAD‑binding component of TrK potassium transporter |
| RA | 3,453,100 | G→T | 7.7% | V57V (GTC→GTA) | rpsJ ← | 30S ribosomal subunit protein S10 |
| RA | 3,543,101 | C→A | 5.3% | intergenic (+137/‑66) | feoC → / → yhgA | putative DNA‑binding transcriptional regulator/transposase_31 family protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,648,319 | C→T | 5.5% | noncoding (26/84 nt) | agrB → | antisense sRNA antitoxin for the DinQ toxin |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,892,094 | C→A | 7.6% | F160L (TTC→TTA) | mdtL → | multidrug efflux system protein |
| RA | 3,930,193 | A→G | 6.3% | L301L (TTG→CTG) | ravA ← | hexameric AAA+ MoxR family ATPase, putative molecular chaperone |
| RA | 3,971,442 | C→A | 10.1% | A61A (GCC→GCA) | wecC → | UDP‑N‑acetyl‑D‑mannosaminuronic acid dehydrogenase |
| RA | 3,994,877 | G→T | 5.6% | G39V (GGG→GTG) | dapF → | diaminopimelate epimerase |
| RA | 4,164,154 | T→C | 7.9% | Y172Y (TAT→TAC) | btuB → | vitamin B12/cobalamin outer membrane transporter |
| RA | 4,189,448 | C→T | 78.7% | Q1367* (CAG→TAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,217,252 | G→T | 5.9% | L48L (CTG→CTT) | aceA → | isocitrate lyase |
| RA | 4,233,642 | G→A | 13.6% | intergenic (‑409/‑116) | lysC ← / → pgi | lysine‑sensitive aspartokinase 3/glucosephosphate isomerase |
| RA | 4,244,074 | C→A | 7.5% | L334F (TTG→TTT) | malF ← | maltose transporter subunit |
| RA | 4,296,060 | C→T | 18.1% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,348,756 | C→A | 5.5% | intergenic (‑12/+559) | dcuB ← / ← dcuR | C4‑dicarboxylate transporter, anaerobic; DcuS co‑sensor/response regulator in two‑component regulatory system with DcuS |
| RA | 4,362,578 | G→T | 27.8% | noncoding (49/76 nt) | pheU ← | tRNA‑Phe |
| RA | 4,397,505 | G→A | 6.4% | E32K (GAA→AAA) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,406,129 | T→C | 100% | intergenic (+144/‑61) | purA → / → nsrR | adenylosuccinate synthetase/nitric oxide‑sensitive repressor for NO regulon |
| RA | 4,473,847 | G→T | 5.7% | V69V (GTC→GTA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,477,913 | G→T | 5.6% | F133L (TTC→TTA) | argI ← | ornithine carbamoyltransferase 1 |
| RA | 4,562,459 | C→A | 5.1% | G73C (GGC→TGC) | yjiJ ← | DUF1228 family putative inner membrane MFS superfamily transporter |
| RA | 4,567,347 | C→A | 6.6% | L391L (CTG→CTT) | mdtM ← | multidrug efflux system protein |
| RA | 4,632,533 | G→A | 5.1% | A601T (GCA→ACA) | slt → | lytic murein transglycosylase, soluble |
| RA | 4,633,634 | C→T | 24.0% | E38K (GAG→AAG) | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
| RA | 4,633,657 | C→T | 59.4% | C30Y (TGC→TAC) | yjjX ← | non‑canonical purine NTP phosphatase, ITPase/XTPase |
| JC JC | 4,640,551 | IS1 (–) +9 bp | 90.9% | intergenic (+9/‑383) | yjjY → / → yjtD | uncharacterized protein/putative methyltransferase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 773026 | 774175 | 1150 | 20 [19] | [17] 20 | [cydA]–[cydB] | [cydA],[cydB] |
| * | * | ÷ | NC_000913 | 1037724 | 1039282 | 1559 | 20 [13] | [19] 20 | [cbdA] | [cbdA] |
| * | * | ÷ | NC_000913 | 1166045 | 1167376 | 1332 | 20 [18] | [15] 20 | [ndh] | [ndh] |
| * | * | ÷ | NC_000913 | 3423769–3424233 | 3424526–3424238 | 6–758 | 20 [18] | [17] 21 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 5 (0.060) | 3/240 | NT | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 374930 = | NA (NA) | 9 (0.150) | 3/170 | NT | 13.6% | noncoding (1/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | 377522 = | 63 (0.960) | intergenic (+211/+13) | yaiL/frmB | DUF2058 family protein/S‑formylglutathione hydrolase | |||||
| * | ? | NC_000913 | 375248 = | 80 (0.890) | 16 (0.210) | 5/218 | NT | 18.8% | noncoding (319/436 nt) | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences | REP31 (repetitive extragenic palindromic) element; contains 9 REP sequences |
| ? | NC_000913 | 377507 = | 70 (0.920) | noncoding (173/187 nt) | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | REP32 (repetitive extragenic palindromic) element; contains 4 REP sequences | |||||
| * | ? | NC_000913 | 566098 = | 75 (0.840) | 10 (0.130) +GAGAGGAGGATTACAAA |
5/222 | NT | 9.4% | pseudogene (279/279 nt) | exoD | pseudogene, DLP12 prophage; phage‑type exonuclease family;Phage or Prophage Related |
| ? | NC_000913 | 4397412 = | 147 (1.640) | coding (1/1848 nt) | mutL | methyl‑directed mismatch repair protein | |||||
| * | ? | NC_000913 | 925857 = | 109 (1.220) | 14 (0.240) | 5/164 | NT | 20.2% | intergenic (+317/+27) | clpA/serW | ATPase and specificity subunit of ClpA‑ClpP ATP‑dependent serine protease, chaperone activity/tRNA‑Ser |
| ? | NC_000913 | = 1096994 | 41 (0.720) | intergenic (+165/+571) | ycdU/serX | putative inner membrane protein/tRNA‑Ser | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.250) | 34 (0.430) | 20/224 | NT | 66.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.190) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.260) | 27 (0.340) | 14/224 | NT | 60.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 15 (0.190) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||