mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 65,670 | T→G | 11.0% | A37A (GCA→GCC) | polB ← | DNA polymerase II |
| RA | 73,581 | A→C | 8.7% | V314G (GTA→GGA) | thiP ← | thiamine/thiamine pyrophosphate ABC transporter permease |
| RA | 76,585 | A→G | 4.8% | L239L (TTA→CTA) | sgrR ← | transcriptional DNA‑binding transcriptional activator of sgrS sRNA |
| RA | 79,989 | G→T | 3.3% | T292T (ACC→ACA) | leuC ← | 3‑isopropylmalate dehydratase large subunit |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 345,296 | G→C | 11.2% | intergenic (+305/‑108) | yahL → / → yahM | uncharacterized protein/uncharacterized protein |
| RA | 360,362 | T→G | 12.9% | V124G (GTG→GGG) | cynX → | putative cyanate transporter |
| RA | 375,168 | G→A | 6.8% | intergenic (+287/‑291) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,247 | A→G | 4.2% | intergenic (+366/‑212) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 388,244 | T→G | 20.6% | R150R (CGT→CGG) | tauD → | taurine dioxygenase, 2‑oxoglutarate‑dependent |
| RA | 433,649 | T→G | 27.6% | G65G (GGT→GGG) | ribD → | fused diaminohydroxyphosphoribosylaminopyrimidine deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase |
| RA | 445,570 | T→C | 23.7% | D366G (GAC→GGC) | yajR ← | putative transporter |
| JC | 626,694 | (TAC)3→2 | 2.7% | coding (625‑627/1611 nt) | entE → | 2,3‑dihydroxybenzoate‑AMP ligase component of enterobactin synthase multienzyme complex |
| RA | 971,304 | Δ1 bp | 3.7% | coding (453/747 nt) | kdsB → | 3‑deoxy‑manno‑octulosonate cytidylyltransferase |
| RA | 1,017,164:1 | +A | 3.0% | coding (1136/1761 nt) | ycbZ ← | putative peptidase |
| RA | 1,196,131 | G→A | 20.7% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,196,305 | C→T | 46.0% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| RA | 1,288,961:1 | +C | 3.5% | coding (172/459 nt) | ychJ ← | UPF0225 family protein |
| 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 | 1,313,327 | Δ1 bp | 4.4% | coding (337/744 nt) | yciC ← | UPF0259 family inner membrane protein |
| RA | 1,313,328 | Δ1 bp | 4.4% | coding (336/744 nt) | yciC ← | UPF0259 family inner membrane protein |
| RA | 1,383,710 | C→A | 26.2% | L84F (TTG→TTT) | ycjW ← | LacI family putative transcriptional repressor |
| RA | 1,567,818 | T→A | 8.2% | I336F (ATT→TTT) | yddW ← | liprotein, glycosyl hydrolase homolog |
| RA | 1,576,077 | C→A | 14.7% | D515Y (GAT→TAT) | yddB ← | putative TonB‑dependent outer membrane receptor |
| RA | 1,596,176 | Δ1 bp | 5.6% | pseudogene (1812/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,708,709 | T→C | 10.3% | R597R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 8.0% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,805 | T→C | 13.8% | R629R (CGT→CGC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,736,242:1 | +G | 3.5% | coding (1049/1170 nt) | ydhP ← | putative MFS transporter, inner membrane protein |
| RA | 1,803,853 | C→T | 5.2% | pseudogene (336/1476 nt) | arpB → | pseudogene, ankyrin repeats |
| RA | 1,840,223 | Δ1 bp | 2.6% | coding (757/1308 nt) | ynjE → | molybdopterin synthase sulfurtransferase |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,336,601 | A→C | 12.3% | G14G (GGT→GGG) | yfaA ← | DUF2138 family protein, putative host defense protein |
| JC | 2,397,715 | (GGT)2→1 | 3.2% | coding (2447‑2449/2727 nt) | nuoG ← | NADH:ubiquinone oxidoreductase, chain G |
| RA | 2,418,396:1 | +C | 3.7% | coding (1318/1521 nt) | yfcC → | putative inner membrane transporter, C4‑dicarboxylate anaerobic carrier family protein |
| RA | 2,553,864 | A→T | 13.5% | L214F (TTA→TTT) | hemF → | coproporphyrinogen III oxidase |
| RA | 2,598,265 | T→C | 13.0% | E200G (GAG→GGG) | bamC ← | BamABCDE complex OM biogenesis lipoprotein |
| RA | 2,671,782:1 | +G | 2.9% | coding (560/813 nt) | hcaB → | 2,3‑dihydroxy‑2,3‑dihydrophenylpropionate dehydrogenase |
| RA | 2,738,752:1 | +C | 2.9% | coding (1010/1161 nt) | pheA → | chorismate mutase and prephenate dehydratase, P‑protein |
| RA | 3,106,332:1 | +C | 2.7% | coding (621/1257 nt) | nupG → | nucleoside transporter |
| RA | 3,203,327 | A→C | 14.4% | V268G (GTG→GGG) | bacA ← | undecaprenyl pyrophosphate phosphatase |
| RA | 3,206,436 | G→A | 11.6% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,475 | T→A | 16.3% | S5R (AGT→AGA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,482 | C→A | 21.7% | Q8K (CAA→AAA) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,492 | T→G | 13.7% | V11G (GTG→GGG) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,206,516 | C→T | 10.7% | A19V (GCT→GTT) | ttdA → | L‑tartrate dehydratase, alpha subunit |
| RA | 3,293,765 | C→G | 7.8% | A123G (GCG→GGG) | lpoA → | OM lipoprotein stimulator of MrcA transpeptidase |
| RA | 3,308,962 | T→C | 12.2% | intergenic (‑40/+69) | nlpI ← / ← pnp | lipoprotein involved in osmotic sensitivity and filamentation/polynucleotide phosphorylase/polyadenylase |
| JC | 3,382,371 | (GGT)2→1 | 3.6% | coding (174‑176/1068 nt) | degS → | serine endoprotease, periplasmic |
| JC | 3,484,549 | (CCA)4→3 | 6.3% | coding (62‑64/870 nt) | prkB → | putative phosphoribulokinase |
| RA | 3,560,493 | G→A | 5.5% | pseudogene (111/149 nt) | glpR ← | pseudogene, DNA‑binding transcriptional repressor,regulator, Energy metabolism, carbon: Anaerobic respiration, repressor of the glp operon |
| RA | 3,716,988 | T→G | 14.8% | V148G (GTG→GGG) | yiaD → | multicopy suppressor of bamB, outer membrane lipoprotein |
| RA | 3,751,536 | A→C | 16.6% | V111G (GTT→GGT) | yiaT ← | putative outer membrane protein |
| RA | 3,760,383 | A→C | 20.5% | V289G (GTG→GGG) | selA ← | selenocysteine synthase |
| RA | 3,781,896 | T→C | 16.6% | A222A (GCA→GCG) | cysE ← | serine acetyltransferase |
| RA | 3,782,912 | A→C | 19.9% | V250G (GTG→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase (NAD+) |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,842,502 | Δ1 bp | 3.3% | coding (1287/1335 nt) | adeQ ← | adenine permease, high affinity, adenine:H+ symporter |
| RA | 3,842,503 | Δ1 bp | 3.2% | coding (1286/1335 nt) | adeQ ← | adenine permease, high affinity, adenine:H+ symporter |
| RA | 3,862,660 | T→G | 34.3% | pseudogene (943/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| RA | 3,862,672 | G→A | 19.5% | pseudogene (931/1617 nt) | glvC ← | pseudogene, arbutin specific enzyme IIC component of PTS,enzyme, Transport of small molecules: Carbohydrates, organic acids, alcohols, PTS system, arbutin‑like IIB component, PTS system, arbutin‑like IIC component |
| RA | 3,895,551 | A→C | 12.9% | V353G (GTG→GGG) | adeP ← | adenine permease, high affinity, adenine:H+ symporter |
| RA | 3,978,861 | A→C | 10.5% | T88P (ACC→CCC) | wzyE → | putative ECA polysaccharide chain elongation protein |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,094,488 | G→A | 4.9% | intergenic (‑217/+234) | rhaD ← / ← rhaA | rhamnulose‑1‑phosphate aldolase/L‑rhamnose isomerase |
| RA | 4,098,390 | A→C | 18.9% | Y219S (TAC→TCC) | rhaS → | transcriptional activator of rhaBAD and rhaT |
| RA | 4,145,064 | A→C | 12.7% | L357F (TTA→TTC) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,151,322 | A→G | 15.9% | A592A (GCT→GCC) | ppc ← | phosphoenolpyruvate carboxylase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,214,301 | A→G | 2.7% | E8G (GAG→GGG) | metA → | homoserine O‑transsuccinylase |
| RA | 4,219,538 | C→T | 8.0% | A315V (GCG→GTG) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,256,052 | G→C | 8.4% | G138G (GGC→GGG) | plsB ← | glycerol‑3‑phosphate O‑acyltransferase |
| RA | 4,296,267 | T→C | 10.8% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,392,454 | C→T | 5.7% | intergenic (+18/‑19) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
| RA | 4,392,457 | A→G | 6.0% | intergenic (+21/‑16) | glyV → / → glyX | tRNA‑Gly/tRNA‑Gly |
| RA | 4,462,089 | C→T | 6.8% | G191G (GGG→GGA) | nrdD ← | anaerobic ribonucleoside‑triphosphate reductase |
| RA | 4,492,816 | G→T | 11.9% | H179Q (CAC→CAA) | idnO ← | 5‑keto‑D‑gluconate‑5‑reductase |
| RA | 4,538,110 | A→C | 19.2% | G219G (GGT→GGG) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,630,341 | A→C | 20.2% | G61G (GGT→GGG) | ettA ← | energy‑dependent translational throttle A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 300023 | 300231 | 209 | 37 [35] | [35] 37 | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| * | * | ÷ | NC_000913 | 583216 | 583771 | 556 | 36 [33] | [35] 36 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 720873 | 721154 | 282 | 36 [35] | [34] 36 | [kdpE] | [kdpE] |
| * | * | ÷ | NC_000913 | 3798979 | 3799583 | 605 | 36 [35] | [35] 36 | [waaU]–[waaZ] | [waaU], [waaZ] |
| * | * | ÷ | NC_000913 | 3804696 | 3805188 | 493 | 39 [35] | [29] 37 | [waaS]–[waaP] | [waaS], [waaP] |
| * | * | ÷ | NC_000913 | 4233707 | 4235424 | 1718 | 36 [35] | [35] 36 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 104 (0.980) | 65/430 | NT | 98.1% | intergenic (+9/‑768) | crl/crl | pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers/pseudogene, sigma factor‑binding protein, RNA polymerase holoenzyme formation stimulator,regulator, Surface structures, transcriptional regulator of cryptic csgA gene for curli surface fibers |
| ? | NC_000913 | = 1293039 | 2 (0.020) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 274254 | NA (NA) | 3 (0.030) | 3/428 | NT | NA | coding (864/1017 nt) | insH1 | IS5 transposase and trans‑activator |
| ? | NC_000913 | 274258 = | NA (NA) | coding (860/1017 nt) | insH1 | IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | 458787 = | 59 (0.550) | 34 (0.320) | 26/424 | NT | 36.9% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | 458787 = | 59 (0.550) | 3 (0.030) | 3/424 | NT | 4.9% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | = 458799 | 55 (0.520) | 52 (0.500) | 44/422 | NT | 49.1% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 22 (0.210) | 73 (0.740) | 52/398 | NT | 78.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 20 (0.200) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.220) | 83 (0.840) | 62/398 | NT | 80.1% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 20 (0.200) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1269636 | 88 (0.830) | 3 (0.030) | 3/412 | NT | 3.0% | intergenic (+247/+67) | rdlA/ldrB | sRNA antisense regulator affects LdrA translation, proposed addiction module in LDR‑A repeat, with toxic peptide LdrA/toxic polypeptide, small |
| ? | NC_000913 | = 1270179 | 110 (1.080) | intergenic (+256/+59) | rdlB/ldrC | sRNA antisense regulator affects LdrB translation, proposed addiction module in LDR‑B repeat, with toxic peptide LdrB/toxic polypeptide, small | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 96 (0.900) | 62/430 | NT | 99.0% | intergenic (‑110/‑495) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| ? | NC_000913 | = 1979270 | NA (NA) | intergenic (‑55/‑483) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | = 1877275 | 73 (0.680) | 4 (0.040) | 4/414 | NT | 5.3% | intergenic (+19/+3) | yeaO/yoaF | DUF488 family protein/DUF333 family outer membrane lipoprotein |
| ? | NC_000913 | = 1877290 | 73 (0.710) | coding (243/255 nt) | yoaF | DUF333 family outer membrane lipoprotein | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 42 (0.390) | 33/430 | NT | 100% | intergenic (‑271/‑267) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913 | = 1979489 | 0 (0.000) | 88 (0.830) | 57/430 | NT | 100% | intergenic (‑274/‑264) | insA/uspC | IS1 repressor TnpA/universal stress protein |
| ? | NC_000913 | = 2290111 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913 | = 2515612 | NA (NA) | 3 (0.030) | 3/426 | NT | 2.9% | intergenic (+171/+29) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase |
| ? | NC_000913 | 2536308 = | 103 (0.970) | coding (477/510 nt) | crr | glucose‑specific enzyme IIA component of PTS | |||||
| * | ? | NC_000913 | = 2592986 | 129 (1.210) | 5 (0.050) | 4/416 | NT | 3.8% | noncoding (11/83 nt) | REP180 (repetitive extragenic palindromic) element, contains 2 REP sequences | REP180 (repetitive extragenic palindromic) element, contains 2 REP sequences |
| ? | NC_000913 | = 2593002 | 127 (1.230) | noncoding (27/83 nt) | REP180 (repetitive extragenic palindromic) element, contains 2 REP sequences | REP180 (repetitive extragenic palindromic) element, contains 2 REP sequences | |||||
| * | ? | NC_000913 | 2596861 = | 76 (0.710) | 4 (0.040) | 4/408 | NT | 5.2% | intergenic (‑126/+42) | ypfJ/purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase |
| ? | NC_000913 | 2596888 = | 73 (0.720) | intergenic (‑153/+15) | ypfJ/purC | putative neutral zinc metallopeptidase/phosphoribosylaminoimidazole‑succinocarboxamide synthetase | |||||
| * | ? | NC_000913 | 2771953 = | 51 (0.480) | 7 (0.070) | 6/428 | NT | 12.1% | intergenic (+340/+47) | yfjT/yfjU | CP4‑57 prophage, putative periplasmic protein/CP4‑57 prophage, conserved protein,Phage or Prophage Related |
| ? | NC_000913 | = 2997688 | NA (NA) | intergenic (‑90/+2) | insC1/ygeQ | IS2 repressor TnpA/pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant | |||||
| * | ? | NC_000913 | = 3427063 | NA (NA) | 5 (0.050) | 4/412 | NT | NA | intergenic (‑32/+11) | alaU/ileU | tRNA‑Ala/tRNA‑Ile |
| ? | NC_000913 | = 3427066 | NA (NA) | intergenic (‑35/+8) | alaU/ileU | tRNA‑Ala/tRNA‑Ile | |||||
| * | ? | NC_000913 | 3515980 = | 145 (1.360) | 6 (0.060) | 6/412 | NT | 4.4% | intergenic (‑69/+38) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring |
| ? | NC_000913 | 3516008 = | 119 (1.170) | intergenic (‑97/+10) | dam/damX | DNA adenine methyltransferase/cell division protein that binds to the septal ring | |||||
| * | ? | NC_000913 | = 3640590 | 114 (1.070) | 3 (0.030) | 3/386 | NT | 2.8% | intergenic (+46/‑271) | uspA/dtpB | universal stress global response regulator/dipeptide and tripeptide permease B |
| ? | NC_000913 | = 3640568 | 108 (1.130) | intergenic (+24/‑293) | uspA/dtpB | universal stress global response regulator/dipeptide and tripeptide permease B | |||||