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 | 67,887:1 | +G | 66.7% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 67,887:2 | +T | 66.7% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| JC | 216,143 | (C)6→3 | 3.2% | intergenic (+164/+34) | nlpE → / ← yaeF | lipoprotein involved with copper homeostasis and adhesion/putative lipoprotein |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 516,921 | Δ1 bp | 3.2% | coding (339/780 nt) | fetB → | iron export ABC transporter permease, peroxide resistance protein |
| RA | 621,529 | T→C | 4.1% | S221G (AGC→GGC) | fepD ← | ferrienterobactin ABC transporter permease |
| RA | 736,663 | C→T | 4.3% | pseudogene (219/240 nt) | ybfQ → | pseudogene, H repeat‑associated protein |
| JC | 898,433 | (CTG)2→1 | 2.8% | coding (445‑447/489 nt) | ybjO → | DUF2593 family inner membrane protein |
| RA | 912,579 | G→T | 3.2% | R412R (CGC→CGA) | hcp ← | hybrid‑cluster [4Fe‑2S‑2O] subunit of anaerobic terminal reductases |
| RA | 1,109,776 | A→G | 4.9% | I148V (ATC→GTC) | opgG → | OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase |
| JC | 1,187,885 | (CCG)3→2 | 4.0% | coding (354‑356/1122 nt) | roxA ← | 50S ribosomal protein L16 arginine hydroxylase, 2‑oxoglutarate oxygenase |
| RA | 1,232,479 | C→T | 4.5% | intergenic (+25/+21) | umuC → / ← dsbB | translesion error‑prone DNA polymerase V subunit, DNA polymerase activity/oxidoreductase that catalyzes reoxidation of DsbA protein disulfide isomerase I |
| RA | 1,269,884 | C→T | 4.3% | noncoding (27/66 nt) | rdlB → | sRNA antisense regulator affects LdrB translation, proposed addiction module in LDR‑B repeat, with toxic peptide LdrB |
| RA | 1,283,309 | C→T | 3.0% | A1149V (GCG→GTG) | narG → | nitrate reductase 1, alpha subunit |
| 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 |
| JC | 1,326,599 | Δ36 bp | 7.8% | coding (1854‑1889/1896 nt) | yciQ → | enhancer of membrane protein expression, putative inner membrane protein |
| RA | 1,594,342 | Δ1 bp | 4.2% | pseudogene (3646/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,616,910 | A→T | 4.5% | intergenic (+32/‑118) | yneK → / → ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible |
| RA | 1,616,911 | A→T | 4.4% | intergenic (+33/‑117) | yneK → / → ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible |
| RA | 1,616,914 | A→T | 4.5% | intergenic (+36/‑114) | yneK → / → ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible |
| RA | 1,675,752 | C→G | 2.8% | W203C (TGG→TGC) | pntB ← | pyridine nucleotide transhydrogenase, beta subunit |
| RA | 1,708,662 | C→G | 4.2% | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,748 | G→C | 7.3% | A610A (GCG→GCC) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,758 | G→C | 5.1% | E614Q (GAA→CAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,814 | A→G | 6.1% | A632A (GCA→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,820 | G→A | 10.5% | K634K (AAG→AAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,822 | T→G | 8.1% | L635R (CTG→CGG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,844 | C→G | 7.9% | A642A (GCC→GCG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,708,854 | C→G | 6.8% | Q646E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,975,321:1 | +C | 3.3% | coding (4/1965 nt) | cheA ← | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein |
| RA | 1,975,321:2 | +A | 3.3% | coding (4/1965 nt) | cheA ← | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC | 2,023,805 | (CTTTA)2→1 | 71.2% | intergenic (+127/‑159) | fliR → / → rcsA | flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,091,825 | T→C | 2.9% | A243A (GCT→GCC) | hisD → | bifunctional histidinal dehydrogenase/ histidinol dehydrogenase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,535 | A→G | 5.6% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,633 | T→G | 8.5% | intergenic (+242/+473) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,912 | A→G | 4.8% | intergenic (+521/+194) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,316,679 | A→G | 100% | T169A (ACC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,360,901:1 | +C | 3.2% | coding (512/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,360,901:2 | +A | 3.2% | coding (512/1206 nt) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,375,279 | C→G | 2.9% | G228R (GGC→CGC) | menC ← | O‑succinylbenzoyl‑CoA synthase |
| RA | 2,392,771 | A→T | 3.6% | M90K (ATG→AAG) | nuoM ← | NADH:ubiquinone oxidoreductase, membrane subunit M |
| RA | 2,533,664 | C→T | 5.8% | intergenic (+286/‑98) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 2,773,112 | G→A | 3.9% | pseudogene (69/117 nt) | yfjV ← | pseudogene, CP4‑57 prophage,Phage or Prophage Related, putative pump protein |
| RA | 3,383,259 | Δ1 bp | 2.8% | coding (1062/1068 nt) | degS → | serine endoprotease, periplasmic |
| RA | 3,495,036 | C→A | 8.6% | A343E (GCA→GAA) | nirB → | nitrite reductase, large subunit, NAD(P)H‑binding |
| RA | 3,517,079 | C→T | 2.9% | D76N (GAT→AAT) | damX ← | cell division protein that binds to the septal ring |
| RA | 3,527,589 | C→T | 100% | Q375* (CAG→TAG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| JC | 3,538,842 | (TAG)2→1 | 2.6% | coding (1460‑1462/2322 nt) | yhgF → | putative transcriptional accessory protein |
| RA | 3,656,582 | G→C | 4.1% | A53G (GCA→GGA) | hdeA ← | stress response protein acid‑resistance protein |
| RA | 3,805,980 | T→C | 6.4% | K363E (AAA→GAA) | waaG ← | UDP‑glucose:(heptosyl)lipopolysaccharide alpha‑1,3‑glucosyltransferase, lipopolysaccharide core biosynthesis protein, lipopolysaccharide glucosyltransferase I |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,003,663 | G→A | 3.3% | A172V (GCC→GTC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,099,210 | Δ1 bp | 3.3% | coding (566/849 nt) | rhaR → | transcriptional activator of rhaSR |
| RA | 4,149,334 | G→A | 3.0% | P311S (CCG→TCG) | eptC ← | LPS heptose I phosphoethanolamine transferase |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,278,542 | Δ1 bp | 2.9% | coding (65/1350 nt) | ghxP → | guanine/hypoxanthine permease, high affinity, guanine/hypoxanthine:H+ symporter |
| RA | 4,296,189 | A→G | 26.2% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 29.3% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,267 | T→C | 21.4% | intergenic (+474/+170) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,454,651 | T→C | 2.8% | E320E (GAA→GAG) | fbp ← | fructose‑1,6‑bisphosphatase I |
| JC | 4,596,562 | (TGG)3→2 | 2.5% | coding (572‑574/1023 nt) | lgoD → | L‑galactonate oxidoreductase, L‑gulonate oxidoreductase |
| RA | 4,614,639 | G→T | 3.0% | intergenic (+378/+42) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533732 | 2536363 | 2632 | 42 [40] | [38] 42 | ptsH–crr | ptsH, ptsI, crr |
| * | * | ÷ | NC_000913 | 3423835–3424436 | 3424436 | 1–602 | 42 [41] | [41] 42 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 110 (0.940) | 68/504 | NT | 100% | 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 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 395765 | 118 (1.010) | 3 (0.030) | 3/486 | NT | 2.5% | coding (523/1158 nt) | ampH | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase, penicillin‑binding protein, weak beta‑lactamase |
| ? | NC_000913 | = 395835 | 118 (1.040) | coding (453/1158 nt) | ampH | D‑alanyl‑D‑alanine‑ carboxypeptidase/endopeptidase, penicillin‑binding protein, weak beta‑lactamase | |||||
| * | ? | NC_000913 | 1207790 = | 52 (0.440) | 62 (0.560) | 51/472 | NT | 60.6% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 32 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 49 (0.420) | 62 (0.560) | 48/472 | NT | 61.4% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 32 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 4 (0.030) | 108 (0.920) | 74/504 | NT | 96.4% | 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 | = 1397238 | NA (NA) | 4 (0.030) | 4/504 | NT | 4.3% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | NC_000913 | = 2024158 | 88 (0.750) | coding (191/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis | |||||
| * | ? | NC_000913 | = 1616905 | 78 (0.660) | 4 (0.040) | 4/484 | NT | 5.0% | intergenic (+27/‑123) | yneK/ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible |
| ? | NC_000913 | = 1616917 | 77 (0.680) | intergenic (+39/‑111) | yneK/ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 99 (0.840) | 62/504 | 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) | 107 (0.910) | 64/504 | 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 | 2024155 = | 88 (0.750) | 11 (0.090) | 11/504 | NT | 11.1% | coding (188/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
| ? | NC_000913 | = 2102943 | NA (NA) | intergenic (‑32/+1) | insH1/wbbL | IS5 transposase and trans‑activator/pseudogene, lipopolysaccharide biosynthesis protein | |||||
| * | ? | NC_000913 | 2288918 = | NA (NA) | 111 (0.950) | 78/502 | NT | 100% | intergenic (‑6/+145) | yejO/insH1 | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system/IS5 transposase and trans‑activator |
| ? | NC_000913 | 3992703 = | 0 (0.000) | coding (1552/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 97 (0.830) | 68/502 | NT | 100% | intergenic (‑31/+2) | 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 | = 3992708 | 0 (0.000) | coding (1557/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 2818079 | 76 (0.650) | 3 (0.030) | 3/492 | NT | 2.7% | noncoding (55/77 nt) | argZ | tRNA‑Arg |
| ? | NC_000913 | = 2818567 | 143 (1.250) | noncoding (77/93 nt) | serV | tRNA‑Ser | |||||
| * | ? | NC_000913 | = 3038106 | 142 (1.210) | 4 (0.030) | 4/494 | NT | 3.0% | intergenic (‑2/+4) | recJ/dsbC | ssDNA exonuclease, 5' ‑‑> 3'‑specific/protein disulfide isomerase II |
| ? | NC_000913 | = 3038912 | 119 (1.030) | coding (830/897 nt) | xerD | site‑specific tyrosine recombinase | |||||
| * | ? | NC_000913 | = 3261456 | 118 (1.010) | 3 (0.030) | 3/482 | NT | 2.6% | coding (961/2295 nt) | tdcE | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase |
| ? | NC_000913 | = 3261639 | 116 (1.030) | coding (778/2295 nt) | tdcE | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase | |||||
| * | ? | NC_000913 | = 3636852 | 82 (0.700) | 4 (0.040) | 4/476 | NT | 5.0% | coding (558/1203 nt) | yhiN | putative oxidoreductase |
| ? | NC_000913 | = 3636838 | 76 (0.690) | coding (572/1203 nt) | yhiN | putative oxidoreductase | |||||