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 | 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 | |
| JC | 2,023,805 | (CTTTA)2→1 | intergenic (+127/‑159) | fliR → / → rcsA | flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,316,679 | A→G | T169A (ACC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 3,527,589 | C→T | Q375* (CAG→TAG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| MC JC | 3,815,858 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| 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 | 2066291–2066598 | 2066598 | 1–308 | 18 [17] | [17] 19 | [insH1] | [insH1] |
| * | * | ÷ | NC_000913 | 2533763 | 2536364 | 2602 | 18 [17] | [16] 18 | [ptsH]–crr | [ptsH], ptsI, crr |
| * | * | ÷ | NC_000913 | 3423739–3424527 | 3424527 | 1–789 | 18 [16] | [17] 19 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 39 (0.840) | 33/284 | 0.4 | 95.1% | 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 (0.040) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 17 (0.370) | 43 (1.050) | 39/252 | 0.1 | 78.1% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 9 (0.220) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.350) | 34 (0.830) | 28/252 | 0.4 | 74.6% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 9 (0.220) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.020) | 64 (1.380) | 51/284 | 0.0 | 98.5% | 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 = | 1 (0.020) | 76 (1.640) | 48/284 | 0.0 | 98.7% | 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 | 2 (0.040) | 35 (0.750) | 28/284 | 0.7 | 94.6% | 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 | 2288918 = | NA (NA) | 32 (0.700) | 27/282 | 0.8 | 89.0% | 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 = | 4 (0.090) | coding (1552/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 62 (1.350) | 39/282 | 0.2 | 96.9% | 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 | 2 (0.040) | coding (1557/2547 nt) | cyaA | adenylate cyclase | |||||