mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 48,340 | C→G | 14.8% | A191G (GCG→GGG) | kefC → | potassium:proton antiporter |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 490,442 | T→C | 10.1% | E124G (GAG→GGG) | priC ← | primosomal replication protein N'' |
| RA | 520,561 | A→G | 14.3% | E49G (GAG→GGG) | ybbP → | putative ABC transporter permease |
| RA | 783,885 | Δ1 bp | 4.3% | coding (720/720 nt);coding (939/942 nt) | pnuC → zitB ← |
nicotinamide riboside transporter zinc efflux system |
| RA | 944,918 | C→T | 3.7% | intergenic (+22/+13) | dmsC → / ← ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/putative isochorismatase family hydrolase |
| RA | 1,033,892 | G→C | 3.7% | Q213H (CAG→CAC) | hyaB → | hydrogenase 1, large subunit |
| RA | 1,357,812 | C→T | 5.2% | S459N (AGT→AAT) | puuP ← | putrescine importer |
| RA | 1,395,091 | A→T | 4.0% | F278I (TTC→ATC) | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,395,092 | A→T | 4.0% | Y277* (TAT→TAA) ‡ | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,395,094 | A→C | 3.9% | Y277D (TAT→GAT) ‡ | ynaI ← | mechanosensitive channel protein, very small conductance |
| RA | 1,466,201 | T→C | 7.8% | pseudogene (810/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,258 | G→C | 6.9% | pseudogene (867/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,270 | C→T | 5.3% | pseudogene (879/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,276 | T→C | 8.0% | pseudogene (885/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,280 | A→C | 5.7% | pseudogene (889/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,579 | G→C | 10.8% | pseudogene (1188/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,533,261 | A→C | 13.5% | K70N (AAA→AAC) | pptA → | 4‑oxalocrotonate tautomerase |
| RA | 1,708,751 | A→G | 9.6% | E611E (GAA→GAG) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| 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 | 2,665,661 | G→A | 5.0% | E77K (GAA→AAA) | csiE → | stationary phase inducible protein |
| JC | 2,765,454 | (TATGGCAC)6→5 | 8.8% | intergenic (‑303/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage, uncharacterized protein |
| RA | 2,802,426 | T→A | 3.7% | S361T (TCC→ACC) | nrdE → | ribonucleoside‑diphosphate reductase 2, alpha subunit |
| RA | 2,929,617 | C→T | 3.6% | S15F (TCC→TTC) | sdaB → | L‑serine dehydratase 2 |
| RA | 2,954,067 | G→C | 5.5% | F645L (TTC→TTG) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 3,248,792 | T→C | 4.5% | L119S (TTA→TCA) | mzrA → | modulator of EnvZ/OmpR regulon |
| RA | 3,593,824 | T→C | 7.1% | S128G (AGC→GGC) | livG ← | branched‑chain amino acid ABC transporter ATPase |
| RA | 3,688,286 | A→C | 11.3% | V296G (GTG→GGG) | bcsC ← | cellulose synthase subunit |
| RA | 3,746,201 | A→T | 3.7% | T37S (ACC→TCC) | yiaO → | 2,3‑diketo‑L‑gulonate‑binding periplasmic protein |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,945,935 | T→A | 5.1% | noncoding (2233/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,979,142 | G→C | 3.7% | A181A (GCG→GCC) | 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 | 4,056,768 | Δ1 bp | 2.9% | coding (1266/1410 nt) | glnA ← | glutamine synthetase |
| RA | 4,073,312 | Δ1 bp | 2.8% | coding (259/897 nt) | yihU ← | 3‑sulpholactaldehyde (SLA) reductase, NADH‑dependent, gamma‑hydroxybutyrate dehydrogenase, NADH‑dependent |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,228,163 | A→G | 10.1% | E145G (GAG→GGG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,271,832 | T→C | 7.1% | E680G (GAG→GGG) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 4,295,833 | T→C | 8.5% | intergenic (+40/+604) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,059 | C→T | 9.8% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,189 | A→G | 17.5% | intergenic (+396/+248) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→C | 22.5% | intergenic (+397/+247) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4110638 | 4111536 | 899 | 37 [35] | [35] 37 | [cdh]–tpiA | [cdh], tpiA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 63 (0.680) | 53/500 | 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 | 1207790 = | 16 (0.170) | 59 (0.680) | 47/468 | NT | 75.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 23 (0.270) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.160) | 75 (0.870) | 50/468 | NT | 80.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 23 (0.270) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.010) | 111 (1.200) | 75/500 | NT | 99.1% | 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 | = 1299498 | 0 (0.000) | 59 (0.650) | 45/492 | 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 | = 1395088 | 94 (1.020) | 4 (0.040) | 4/486 | NT | 4.2% | coding (835/1032 nt) | ynaI | mechanosensitive channel protein, very small conductance |
| ? | NC_000913 | = 1395094 | 93 (1.040) | coding (829/1032 nt) | ynaI | mechanosensitive channel protein, very small conductance | |||||
| * | ? | NC_000913 | 1979486 = | 0 (0.000) | 49 (0.530) | 32/500 | 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) | 84 (0.910) | 51/500 | 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 | 4295831 = | NA (NA) | 12 (0.150) | 4/422 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||