breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | |||||
---|---|---|---|---|---|
evidence | position | mutation | annotation | gene | description |
MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
RA | 2,509,495 | C→G | intergenic (‑71/‑133) | glk ← / → yfeO | glucokinase/putative ion channel protein |
RA | 3,088,093 | T→A | intergenic (+235/‑189) | metK → / → galP | S‑adenosylmethionine synthetase/D‑galactose transporter |
MC JC | 3,815,858 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
MC JC | 4,001,644 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
RA | 4,184,542 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
Unassigned missing coverage evidence | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|
seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | NC_000913 | 2533752 | 2536357 | 2606 | 22 [21] | [21] 23 | ptsH–crr | ptsH, ptsI, crr |
* | * | ÷ | NC_000913 | 3762326–3764073 | 3765214–3764075 | 3–2889 | 22 [21] | [21] 23 | rhsA | Rhs protein with putative toxin 55 domain, putative polysaccharide synthesis/export protein, putative neighboring cell growth inhibitor |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | 257908 = | NA (NA) | 45 (0.830) | 38/282 | 0.4 | 93.8% | 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 | 3 (0.060) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
* | ? | NC_000913 | 1207790 = | 11 (0.200) | 50 (1.050) | 46/250 | 0.0 | 88.7% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
? | NC_000913 | 1209619 = | 3 (0.060) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
* | ? | NC_000913 | = 1207805 | 8 (0.150) | 37 (0.770) | 29/250 | 0.7 | 88.0% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
? | NC_000913 | = 1209602 | 3 (0.060) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
* | ? | NC_000913 | 1293032 = | 2 (0.040) | 71 (1.310) | 56/282 | 0.0 | 97.3% | 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 | 1979486 = | 2 (0.040) | 102 (1.890) | 66/282 | 0.0 | 98.1% | 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 | 1 (0.020) | 64 (1.190) | 45/282 | 0.1 | 98.5% | 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 = | 3 (0.060) | 60 (1.110) | 49/282 | 0.1 | 95.2% | coding (188/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
? | NC_000913 | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
* | ? | NC_000913 | = 2024158 | 2 (0.040) | 79 (1.460) | 55/282 | 0.0 | 97.5% | coding (191/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
? | 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 | 2288917 = | NA (NA) | 50 (0.930) | 44/282 | 0.2 | 98.0% | intergenic (‑5/+146) | 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 | 3526447 = | 1 (0.020) | intergenic (‑300/‑20) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
* | ? | NC_000913 | = 2290110 | NA (NA) | 42 (0.780) | 32/280 | 0.7 | 95.5% | 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 | = 3526451 | 2 (0.040) | intergenic (‑304/‑16) | nudE/yrfF | adenosine nucleotide hydrolase, Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein | |||||
* | ? | NC_000913 | 3845530 = | 32 (0.590) | 45 (0.900) | 40/262 | 0.2 | 56.7% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
? | NC_000913 | = 3992759 | 39 (0.780) | coding (1608/2547 nt) | cyaA | adenylate cyclase |