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 |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 292,302 | C→G | 6.4% | intergenic (+71/+20) | yagJ → / ← yagK | CP4‑6 prophage; uncharacterized protein;Phage or Prophage Related/CP4‑6 prophage; conserved protein |
| RA | 366,726 | A→G | 5.0% | L262P (CTG→CCG) | lacI ← | lactose‑inducible lac operon transcriptional repressor |
| RA | 475,971 | C→G | 9.2% | intergenic (+20/+11) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 475,972 | C→G | 9.4% | intergenic (+21/+10) | ybaY → / ← ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| RA | 483,519 | G→A | 5.1% | T295T (ACC→ACT) | acrB ← | multidrug efflux system protein |
| RA | 606,975 | C→T | 6.1% | V137I (GTC→ATC) | ybdK ← | weak gamma‑glutamyl:cysteine ligase |
| RA | 743,260 | Δ1 bp | 5.6% | coding (434/744 nt) | ybgI → | NIF3 family metal‑binding protein |
| RA | 856,695 | A→G | 5.7% | T245A (ACC→GCC) | ybiT → | ABC‑F family putative regulatory ATPase |
| RA | 875,395 | G→T | 10.0% | A21S (GCA→TCA) | yliF → | putative membrane‑anchored diguanylate cyclase |
| RA | 895,013 | C→T | 6.7% | P8L (CCG→CTG) | potG → | putrescine ABC transporter ATPase |
| RA | 895,016 | A→G | 6.3% | Q9R (CAG→CGG) | potG → | putrescine ABC transporter ATPase |
| RA | 1,000,474 | A→G | 8.4% | D420G (GAT→GGT) | elfC → | putative outer membrane fimbrial subunit export usher protein |
| RA | 1,131,401 | A→C | 5.2% | K128N (AAA→AAC) | flgB → | flagellar component of cell‑proximal portion of basal‑body rod |
| RA | 1,183,187 | A→G | 5.6% | V145A (GTG→GCG) | potC ← | spermidine/putrescine ABC transporter permease |
| RA | 1,261,474 | C→A | 100% | Q134H (CAG→CAT) | prs ← | phosphoribosylpyrophosphate synthase |
| RA | 1,274,117 | G→A | 6.0% | A112T (GCC→ACC) | ychO → | putative invasin |
| RA | 1,274,920 | T→C | 5.3% | R379R (CGT→CGC) | ychO → | putative invasin |
| RA | 1,287,215 | T→C | 6.6% | noncoding (22/171 nt) | rttR ← | rtT sRNA, processed from tyrT transcript |
| JC JC | 1,293,015 | IS1 (+) +8 bp | 75.9% | intergenic (‑93/‑505) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| RA | 1,443,246 | G→A | 5.5% | V66M (GTG→ATG) | ydbH → | putative membrane‑anchored protein, function unknown |
| RA | 1,555,157 | A→G | 5.4% | I171I (ATT→ATC) | maeA ← | malate dehydrogenase, decarboxylating, NAD‑requiring; malic enzyme |
| RA | 1,706,847 | T→C | 6.4% | V167A (GTC→GCC) | rsxB → | SoxR iron‑sulfur cluster reduction factor component; putative iron‑sulfur protein |
| RA | 1,769,224 | G→A | 5.2% | V51I (GTA→ATA) | ydiK → | UPF0118 family inner membrane protein |
| RA | 1,865,839 | T→C | 5.9% | S212G (AGT→GGT) | mipA ← | scaffolding protein for murein synthesizing machinery |
| RA | 1,886,545 | C→T | 5.5% | A234V (GCA→GTA) | yeaX → | putative YeaWX dioxygenase beta subunit, reductase component |
| RA | 1,935,337 | C→A | 8.1% | W326C (TGG→TGT) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| RA | 1,965,176 | A→T | 6.6% | V339E (GTG→GAG) | flhB ← | flagellin export apparatus, substrate specificity protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 1,992,827 | T→C | 5.9% | intergenic (‑10/+47) | pgsA ← / ← uvrC | phosphatidylglycerophosphate synthetase/excinuclease UvrABC, endonuclease subunit |
| RA | 2,019,460 | G→A | 100% | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| RA | 2,157,974 | C→T | 7.7% | G904G (GGC→GGT) | mdtB → | multidrug efflux system, subunit B |
| RA | 2,169,602 | G→A | 5.2% | L297L (CTG→CTA) | yegS → | phosphatidylglycerol kinase, metal‑dependent |
| 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 | 2,177,715 | C→T | 5.1% | A284T (GCT→ACT) | fbaB ← | fructose‑bisphosphate aldolase class I |
| RA | 2,206,822 | A→G | 5.7% | K376K (AAA→AAG) | yehM → | uncharacterized protein |
| RA | 2,246,005 | G→A | 5.5% | Y255Y (TAC→TAT) | cirA ← | colicin IA outer membrane receptor and translocator; ferric iron‑catecholate transporter |
| RA | 2,263,235 | C→T | 10.9% | W87* (TGG→TGA) ‡ | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,263,236 | C→G | 10.9% | W87S (TGG→TCG) ‡ | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,263,237 | A→G | 10.1% | W87R (TGG→CGG) ‡ | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,275,577 | C→T | 5.4% | A102V (GCT→GTT) | yejE → | microcin C ABC transporter permease |
| RA | 2,299,544 | G→A | 8.3% | A12V (GCG→GTG) | napH ← | ferredoxin‑type protein |
| RA | 2,304,649 | C→T | 14.8% | intergenic (+256/+459) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,085 | A→G | 5.2% | intergenic (+692/+23) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,086 | C→G | 5.3% | intergenic (+693/+22) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,305,087 | C→T | 5.2% | intergenic (+694/+21) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,317,667 | T→G | 100% | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,322,461 | A→T | 5.5% | K199I (AAA→ATA) | atoC → | fused response regulator of ato operon, in two‑component system with AtoS: response regulator/sigma54 interaction protein |
| RA | 2,324,626 | T→C | 5.4% | V173A (GTC→GCC) | atoA → | acetyl‑CoA:acetoacetyl‑CoA transferase, beta subunit |
| RA | 2,357,653 | A→G | 7.6% | L250L (CTA→CTG) | yfaD → | transposase_31 family protein |
| RA | 2,357,665 | G→A | 9.2% | G254G (GGG→GGA) | yfaD → | transposase_31 family protein |
| RA | 2,357,856 | T→A | 6.0% | pseudogene (53/198 nt) | ypaA → | pseudogene, C‑terminal fragment, Transposase_31 family |
| RA | 2,361,854 | A→T | 6.0% | S120T (TCA→ACA) | rhmR ← | putative DNA‑binding transcriptional regulator for the rhm operon |
| RA | 2,518,197 | C→G | 7.7% | noncoding (35/76 nt) | alaW ← | tRNA‑Ala |
| RA | 2,566,464 | A→G | 7.4% | S141P (TCT→CCT) | eutA ← | reactivating factor for ethanolamine ammonia lyase |
| RA | 2,591,413 | A→G | 5.2% | N56S (AAC→AGC) | yffB → | putative ArsC family reductase |
| RA | 2,610,971 | G→A | 5.1% | R89H (CGT→CAT) | hyfI → | hydrogenase 4, Fe‑S subunit |
| RA | 2,632,046 | G→T | 100% | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,675,495 | G→A | 7.3% | G89G (GGC→GGT) | yphC ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 2,703,102 | G→A | 5.1% | V95V (GTC→GTT) | era ← | membrane‑associated, 16S rRNA‑binding GTPase |
| RA | 2,855,412 | C→T | 5.1% | R359W (CGG→TGG) | fhlA → | formate hydrogenlyase transcriptional activator |
| RA | 3,002,530 | G→A | 100% | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,045,126 | C→A | 5.1% | intergenic (+25/+32) | bglA → / ← ygfF | 6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase |
| RA | 3,045,127 | T→G | 5.7% | intergenic (+26/+31) | bglA → / ← ygfF | 6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase |
| RA | 3,045,129 | G→A | 5.7% | intergenic (+28/+29) | bglA → / ← ygfF | 6‑phospho‑beta‑glucosidase A/putative NAD(P)‑dependent oxidoreductase |
| RA | 3,139,640 | C→A | 6.4% | intergenic (+47/+76) | yghU → / ← hybG | putative S‑transferase/hydrogenase 2 accessory protein |
| RA | 3,269,969 | A→C | 8.8% | intergenic (+367/+247) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,269,970 | A→G | 6.5% | intergenic (+368/+246) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| RA | 3,270,030 | T→C | 22.5% | intergenic (+428/+186) | yhaC → / ← rnpB | pentapetide repeats‑related protein/RNase P, M1 RNA component |
| MC JC | 3,366,751 | Δ1,271 bp | 100% | IS5‑mediated | [yhcE]–[yhcG] | [yhcE], yhcF, [yhcG] |
| JC JC | 3,463,556 | IS2 (+) +5 bp | 35.4% | coding (633‑637/984 nt) | gspK → | general secretory pathway component, cryptic |
| JC JC | 3,486,024 | IS2 (+) +5 bp | 28.6% | intergenic (‑206/‑92) | yhfA ← / → crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression |
| 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 |
| JC JC | 3,890,075 | IS5 (–) +4 bp | 100% | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 3,992,052 | T→A | 5.3% | D300E (GAT→GAA) | cyaA → | adenylate cyclase |
| RA | 4,044,385 | Δ1 bp | 100% | coding (187/1431 nt) | yihF → | DUF945 family protein |
| RA | 4,153,472 | C→A | 13.7% | intergenic (‑374/+224) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,187,232 | G→T | 8.5% | G628V (GGC→GTC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 31.5% | 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 | 4,457,648 | A→G | 5.4% | I73T (ATT→ACT) | yjgA ← | ribosome‑associated UPF0307 family protein |
| RA | 4,552,306 | A→G | 5.1% | E224G (GAA→GGA) | uxuA → | mannonate hydrolase |
| RA | 4,620,278 | C→A | 42.6% | R226S (CGT→AGT) | deoB → | phosphopentomutase |
| RA | 4,620,569:1 | +A | 9.0% | coding (967/1224 nt) | deoB → | phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423780–3424234 | 3424538–3424238 | 5–759 | 30 [28] | [28] 29 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514371 | 3515093 | 723 | 31 [28] | [27] 29 | [gph]–[dam] | [gph],rpe,[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 381669 | NA (NA) | 3 (0.040) | 3/250 | NT | NA | noncoding (410/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 381695 | NA (NA) | noncoding (436/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 475970 | 75 (0.870) | 4 (0.050) | 6/240 | NT | 5.3% | intergenic (+19/+12) | ybaY/ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL |
| ? | NC_000913 | = 475972 | 74 (0.940) | intergenic (+21/+10) | ybaY/ybaZ | outer membrane lipoprotein/excision repair protein, alkyltransferase‑like protein ATL | |||||
| * | ? | NC_000913 | = 867463 | 71 (0.820) | 4 (0.050) | 4/252 | NT | 5.5% | coding (896/966 nt) | iaaA | Isoaspartyl peptidase |
| ? | NC_000913 | = 867471 | 69 (0.830) | coding (904/966 nt) | iaaA | Isoaspartyl peptidase | |||||
| * | ? | NC_000913 | 1207790 = | 25 (0.290) | 19 (0.250) | 17/232 | NT | 43.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 28 (0.370) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 24 (0.280) | 29 (0.380) | 27/232 | NT | 54.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 28 (0.370) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 114 (1.360) | 91/256 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 1396531 = | NA (NA) | 5 (0.060) | 5/252 | NT | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1742580 | 50 (0.580) | 4 (0.050) | 4/246 | NT | 7.8% | intergenic (+19/+21) | cfa/ribC | cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit |
| ? | NC_000913 | = 1742585 | 48 (0.590) | intergenic (+24/+16) | cfa/ribC | cyclopropane fatty acyl phospholipid synthase, SAM‑dependent/riboflavin synthase, alpha subunit | |||||
| * | ? | NC_000913 | 2236520 = | NA (NA) | 3 (0.040) | 3/244 | NT | NA | intergenic (+20/+223) | preA/mglC | dihydropyrimidine dehydrogenase, NADH‑dependent, subunit C/methyl‑galactoside transporter subunit |
| ? | NC_000913 | 2236534 = | NA (NA) | noncoding (1/150 nt) | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | REP156 (repetitive extragenic palindromic) element; contains 3 REP sequences | |||||
| * | ? | NC_000913 | = 2453080 | 56 (0.650) | 3 (0.040) | 3/252 | NT | 5.5% | pseudogene (1922/2646 nt) | yfcU | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein |
| ? | NC_000913 | = 2453107 | 50 (0.600) | pseudogene (1895/2646 nt) | yfcU | pseudogene, FimD fimbrial export usher family;putative membrane; Not classified; putative outer membrane protein | |||||
| * | ? | NC_000913 | 2555191 = | NA (NA) | 4 (0.050) | 4/244 | NT | NA | intergenic (‑9/+37) | eutR/eutK | eut operon transcriptional activator, AraC family/putative ethanol utilization carboxysome structural protein |
| ? | NC_000913 | 2555217 = | NA (NA) | intergenic (‑35/+11) | eutR/eutK | eut operon transcriptional activator, AraC family/putative ethanol utilization carboxysome structural protein | |||||
| * | ? | NC_000913 | 2681503 = | 58 (0.670) | 3 (0.040) | 3/256 | NT | 5.2% | coding (1243/3282 nt) | yphG | DUF4380 domain‑containing TPR repeat protein |
| ? | NC_000913 | 2681545 = | 53 (0.630) | coding (1201/3282 nt) | yphG | DUF4380 domain‑containing TPR repeat protein | |||||
| * | ? | NC_000913 | = 2854465 | 92 (1.060) | 5 (0.060) | 4/248 | NT | 5.5% | coding (128/2079 nt) | fhlA | formate hydrogenlyase transcriptional activator |
| ? | NC_000913 | = 2854495 | 85 (1.040) | coding (158/2079 nt) | fhlA | formate hydrogenlyase transcriptional activator | |||||
| * | ? | NC_000913 | 2888334 = | NA (NA) | 3 (0.040) | 3/250 | NT | NA | noncoding (1/37 nt) | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences |
| ? | NC_000913 | 2888367 = | NA (NA) | noncoding (34/37 nt) | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences | REP200 (repetitive extragenic palindromic) element; contains 1 REP sequences | |||||
| * | ? | NC_000913 | 3621402 = | NA (NA) | 4 (0.050) | 4/252 | NT | 100% | coding (2211/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor |
| ? | NC_000913 | 3621407 = | 0 (0.000) | coding (2216/4236 nt) | rhsB | Rhs protein with DUF4329 family putative toxin domain; putative neighboring cell growth inhibitor | |||||
| * | ? | NC_000913 | 3676121 = | NA (NA) | 3 (0.040) | 3/250 | NT | NA | noncoding (1/161 nt) | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site |
| ? | NC_000913 | 3676146 = | NA (NA) | noncoding (26/161 nt) | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | RIP264 (repetitive extragenic palindromic) element; contains 3 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913 | 4542682 = | 116 (1.340) | 12 (0.150) | 11/246 | NT | 9.0% | intergenic (+49/‑433) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) |
| ? | NC_000913 | 4542996 = | 134 (1.660) | intergenic (+363/‑119) | fimE/fimA | tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin) | |||||