mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0 revision 6ff6de7d1b87
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 375,075 | G→A | 8.0% | intergenic (+194/‑384) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 470,035 | A→G | 7.7% | S389G (AGC→GGC) | mdlA → | putative multidrug ABC transporter ATPase |
| RA | 659,993 | T→G | 17.0% | N75T (AAC→ACC) | lipA ← | lipoate synthase |
| RA | 1,240,873 | G→A | 7.2% | P400L (CCG→CTG) | cvrA ← | putative cation/proton antiporter |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,367,473 | G→C | 7.0% | A147G (GCG→GGG) | pspF ← | psp operon transcriptional activator |
| RA | 1,408,129 | A→G | 6.4% | K27R (AAA→AGA) | ydaN → | putative Zn(II) transporter |
| RA | 1,466,432 | A→G | 17.8% | pseudogene (1041/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,466,438 | T→G | 20.4% | pseudogene (1047/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| RA | 2,044,728 | A→G | 6.3% | intergenic (+104/‑210) | asnT → / → yeeJ | tRNA‑Asn/putative adhesin |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,304,873 | C→T | 10.1% | intergenic (+482/+233) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| MC JC | 3,815,858 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 4,001,644 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,542 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,059 | C→T | 13.1% | intergenic (+266/+378) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,554,966 | A→G | 6.3% | Q130Q (CAA→CAG) | uxuR → | fructuronate‑inducible hexuronate regulon transcriptional repressor, autorepressor |
| RA | 4,556,097 | Δ1 bp | 2.9% | coding (225/831 nt) | yjiC ← | uncharacterized protein |
| RA | 4,557,266 | C→T | 5.3% | Y91Y (TAC→TAT) | iraD → | RpoS stabilzer after DNA damage, anti‑RssB factor |
| RA | 4,614,497 | C→T | 9.3% | intergenic (+236/+184) | yjjV → / ← yjjW | putative DNase/putative pyruvate formate lyase activating enzyme |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 300045 | 300322 | 278 | 15 [12] | [12] 14 | paoC | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| * | * | ÷ | NC_000913 | 2099763 | 2101298 | 1536 | 14 [12] | [13] 14 | gnd | gnd |
| * | * | ÷ | NC_000913 | 3253572 | 3253892 | 321 | 15 [13] | [13] 14 | yhaJ | LysR family putative transcriptional regulator |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 70 (1.330) | 48/492 | NT | 100% | 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 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 647423 = | 63 (1.190) | 3 (0.060) | 3/478 | NT | 4.8% | coding (87/879 nt) | citG | 2‑(5''‑triphosphoribosyl)‑3'‑dephosphocoenzyme‑A synthase |
| ? | NC_000913 | 647850 = | 59 (1.150) | coding (186/552 nt) | citX | apo‑citrate lyase phosphoribosyl‑dephospho‑CoA transferase | |||||
| * | ? | NC_000913 | 1153312 = | 73 (1.380) | 3 (0.060) | 3/478 | NT | 4.6% | coding (13/810 nt) | pabC | 4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex |
| ? | NC_000913 | 1153646 = | 54 (1.050) | coding (347/810 nt) | pabC | 4‑amino‑4‑deoxychorismate lyase component of para‑aminobenzoate synthase multienzyme complex | |||||
| * | ? | NC_000913 | 1207790 = | 14 (0.270) | 19 (0.390) | 15/460 | NT | 59.3% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 13 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.250) | 30 (0.610) | 26/460 | NT | 70.5% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 13 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1293032 = | 1 (0.020) | 88 (1.670) | 63/492 | NT | 98.9% | 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 = | 0 (0.000) | 36 (0.680) | 26/492 | NT | 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 | 0 (0.000) | 50 (0.950) | 43/492 | NT | 100% | 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 | 2997110 = | NA (NA) | 4 (0.080) | 3/470 | NT | 29.5% | coding (166/906 nt) | insD1 | IS2 transposase TnpB |
| ? | NC_000913 | 2997476 = | 10 (0.190) | coding (123/366 nt) | insC1 | IS2 repressor TnpA | |||||
| * | ? | NC_000913 | 3034341 = | 42 (0.800) | 4 (0.080) | 3/470 | NT | 7.8% | coding (832/1518 nt) | lysS | lysine tRNA synthetase, constitutive |
| ? | NC_000913 | 3034584 = | 55 (1.090) | coding (589/1518 nt) | lysS | lysine tRNA synthetase, constitutive | |||||
| * | ? | NC_000913 | 4295831 = | NA (NA) | 4 (0.090) | 3/414 | NT | NA | intergenic (+38/+606) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296395 | NA (NA) | noncoding (562/602 nt) | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element, contains 11 REP sequences and 4 IHF sites | |||||