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 | 62,822 | Δ16 bp | coding (428‑443/2907 nt) | rapA ← | RNA polymerase remodeling/recycling factor ATPase, RNA polymerase‑associated, ATP‑dependent RNA translocase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 1,196,305 | C→T | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase, e14 prophage attachment site, tellurite reductase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,936,308 | C→T | V3I (GTA→ATA) | zwf ← | glucose‑6‑phosphate 1‑dehydrogenase |
| RA | 1,938,656 | Δ1 bp | coding (1008/1443 nt) | pykA → | pyruvate kinase II |
| 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 | 3,624,956 | G→T | A194S (GCG→TCG) | yhhI → | putative transposase |
| 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 | 365852 | 366443 | 592 | 26 [25] | [25] 26 | [lacZ]–[lacI] | [lacZ], [lacI] |
| * | * | ÷ | NC_000913 | 3423741–3424232 | 3424528–3424236 | 5–788 | 27 [25] | [24] 26 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 4233748 | 4235421 | 1674 | 26 [25] | [25] 26 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 47 (0.800) | 40/284 | 0.4 | 92.2% | 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 | 4 (0.070) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.120) | 57 (1.100) | 38/252 | 0.3 | 86.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 11 (0.210) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.100) | 61 (1.180) | 50/252 | 0.0 | 88.2% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 11 (0.210) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 3 (0.050) | 65 (1.110) | 51/284 | 0.1 | 95.6% | 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 = | 3 (0.050) | 102 (1.750) | 61/284 | 0.0 | 97.1% | 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) | 49 (0.840) | 37/284 | 0.6 | 98.0% | 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 | 2288917 = | NA (NA) | 42 (0.720) | 33/284 | 0.9 | 91.3% | 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 | 3553101 = | 4 (0.070) | coding (19/2706 nt) | malT | mal regulon transcriptional activator | |||||
| * | ? | NC_000913 | = 2290110 | NA (NA) | 85 (1.460) | 49/282 | 0.1 | 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 | = 3553105 | 4 (0.070) | coding (23/2706 nt) | malT | mal regulon transcriptional activator | |||||
| * | ? | NC_000913 | 4049902 = | 3 (0.050) | 68 (1.160) | 57/284 | 0.0 | 95.8% | noncoding (5/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | 4498182 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology,IS, phage, Tn, Phage‑related functions and prophages, KpLE2 phage‑like element, P4‑like integrase/IS2 repressor TnpA | |||||
| * | ? | NC_000913 | = 4049906 | 2 (0.030) | 71 (1.210) | 55/284 | 0.0 | 97.3% | noncoding (9/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+11/+82) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||