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] | |
| 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 |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 |
| RA | 4,186,085 | C→A | P246Q (CCG→CAG) | rpoC → | RNA polymerase, beta prime subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423714–3424544 | 3424544 | 1–831 | 18 [17] | [17] 18 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 4233757 | 4235424 | 1668 | 18 [17] | [16] 18 | [pgi] | [pgi] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 45 (1.010) | 36/284 | 0.2 | 91.8% | 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 | 4 (0.090) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 7 (0.160) | 38 (0.960) | 31/252 | 0.2 | 86.2% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 6 (0.150) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 7 (0.160) | 46 (1.160) | 38/252 | 0.1 | 88.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 6 (0.150) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 3 (0.070) | 51 (1.140) | 43/284 | 0.1 | 94.4% | 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 | = 1651548 | NA (NA) | 50 (1.120) | 43/284 | 0.1 | 96.2% | intergenic (+11/‑3) | insD1/intQ | IS2 transposase TnpB,IS, phage, Tn, Transposon‑related functions, extrachromosomal, transposon related/pseudogene, Qin prophage, phage integrase family,Phage or Prophage Related |
| ? | NC_000913 | = 1937140 | 2 (0.040) | coding (489/870 nt) | yebK | putative DNA‑binding transcriptional regulator | |||||
| * | ? | NC_000913 | 1937136 = | 3 (0.070) | 63 (1.410) | 52/284 | 0.0 | 95.5% | coding (485/870 nt) | yebK | putative DNA‑binding transcriptional regulator |
| ? | NC_000913 | = 2070271 | NA (NA) | intergenic (‑91/‑6) | insC1/yoeA | IS2 repressor TnpA/CP4‑44 prophage, putative disrupted hemin or colicin receptor,Phage or Prophage Related, interrupted by IS2 and C‑terminal deletion | |||||
| * | ? | NC_000913 | 1979486 = | 1 (0.020) | 64 (1.430) | 42/284 | 0.1 | 98.5% | 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) | 53 (1.190) | 35/284 | 0.2 | 96.4% | 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 | 4049912 = | 0 (0.000) | 43 (0.960) | 35/284 | 0.2 | 100% | noncoding (15/109 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 | = 4049918 | 2 (0.040) | 53 (1.200) | 46/280 | 0.0 | 96.4% | noncoding (21/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent |
| ? | NC_000913 | = 4499510 | NA (NA) | intergenic (+9/+84) | insD1/yjgX | IS2 transposase TnpB/pseudogene fragment | |||||