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 | 1,020,961 | A→G | intergenic (‑42/‑177) | sulA ← / → sxy | SOS cell division inhibitor/CRP‑S‑dependent promoter expression factor |
| 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 |
| RA | 2,415,464 | Δ1 bp | coding (720/2145 nt) | pta → | phosphate acetyltransferase |
| RA | 2,707,558 | Δ1 bp | coding (242/480 nt) | rseC ← | SoxR iron‑sulfur cluster reduction factor component |
| 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 | 4233712 | 4235433 | 1722 | 23 [22] | [22] 24 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 51 (0.970) | 43/284 | 0.2 | 96.2% | 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 | 2 (0.040) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 458787 = | 7 (0.130) | 56 (1.080) | 46/278 | 0.1 | 89.1% | intergenic (+87/‑101) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | 608011 = | NA (NA) | intergenic (+23/‑54) | hokE/insL1 | toxic polypeptide, small/IS186 transposase | |||||
| * | ? | NC_000913 | = 458799 | 1 (0.020) | 35 (0.680) | 32/276 | 0.6 | 97.3% | intergenic (+99/‑89) | clpX/lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| ? | NC_000913 | = 609347 | NA (NA) | intergenic (+170/+112) | insL1/entD | IS186 transposase/phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 8 (0.150) | 41 (0.880) | 35/252 | 0.3 | 85.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 7 (0.150) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.110) | 40 (0.860) | 34/252 | 0.3 | 86.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 7 (0.150) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 3 (0.060) | 54 (1.020) | 48/284 | 0.1 | 94.7% | 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 | 1589990 = | 2 (0.040) | 59 (1.120) | 49/284 | 0.1 | 96.7% | pseudogene (90/1227 nt) | ydeT | pseudogene, putative outer membrane protein |
| ? | NC_000913 | = 1651548 | NA (NA) | 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 | = 1589993 | 3 (0.060) | 67 (1.270) | 57/284 | 0.0 | 95.7% | pseudogene (87/1227 nt) | ydeT | pseudogene, putative outer membrane protein |
| ? | NC_000913 | 4498181 = | NA (NA) | intergenic (+240/‑92) | 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 | 1979486 = | 0 (0.000) | 85 (1.610) | 59/284 | 0.0 | 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 | 1 (0.020) | 74 (1.400) | 46/284 | 0.1 | 98.7% | 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 | 3652035 = | NA (NA) | 67 (1.270) | 54/284 | 0.0 | 95.7% | intergenic (+5/+146) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator |
| ? | NC_000913 | = 4049924 | 3 (0.060) | noncoding (27/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent | |||||
| * | ? | NC_000913 | = 3653229 | NA (NA) | 63 (1.190) | 51/284 | 0.0 | 94.0% | intergenic (‑32/‑1) | insH1/yhiS | IS5 transposase and trans‑activator/pseudogene |
| ? | NC_000913 | 4049921 = | 4 (0.080) | noncoding (24/109 nt) | spf | Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent | |||||