mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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 | 418,960 | Δ1 bp | 100% | coding (1072/1296 nt) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| JC JC | 700,597 | IS1 (–) +9 bp | 100% | coding (990‑998/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 704,083 | C→A | 100% | A47E (GCG→GAG) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 1,157,896:1 | +A | 100% | coding (28/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| 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 | 1,464,303 | G→A | 5.9% | W255* (TGG→TGA) | paaX → | transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| RA | 1,726,390 | G→T | 100% | R123L (CGC→CTC) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,756,374 | G→A | 100% | G226D (GGC→GAC) | pykF → | pyruvate kinase I |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,066,465 | T→C | 100% | K286R (AAG→AGG) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,304,522 | G→T | 7.3% | intergenic (+129/+586) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,523 | G→C | 7.3% | intergenic (+130/+585) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,537 | A→G | 8.2% | intergenic (+144/+571) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,540 | C→T | 10.0% | intergenic (+147/+568) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 2,304,549 | C→T | 9.3% | intergenic (+156/+559) | eco → / ← mqo | ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| MC JC | 3,909,312 | Δ774 bp | 100% | [pstA]–[pstC] | [pstA], [pstC] | |
| RA | 3,922,565 | A→G | 5.6% | intergenic (‑125/+492) | atpI ← / ← rsmG | ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein |
| RA | 3,966,675 | C→T | 6.3% | R87C (CGC→TGC) | rho → | transcription termination factor |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,102,342 | T→G | 5.7% | V218G (GTG→GGG) | kdgT → | 2‑keto‑3‑deoxy‑D‑gluconate transporter |
| RA | 4,171,648 | A→C | 100% | noncoding (12/120 nt) | rrfB → | 5S ribosomal RNA of rrnB operon |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| JC | 4,189,483 | +CCGGC | 8.0% | coding (4134/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,189,483:2 | +C | 12.4% | coding (4134/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,189,512:1 | +C | 63.3% | coding (4163/4224 nt) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,060 | C→T | 14.4% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 18.8% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 24.8% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 21.5% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 12.6% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,304 | A→C | 8.2% | intergenic (+510/+132) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 954508 | 954855 | 348 | 43 [34] | [37] 38 | focA/ycaO | formate channel/ribosomal protein S12 methylthiotransferase accessory factor |
| * | * | ÷ | NC_000913 | 1211528 | 1212769 | 1242 | 40 [36] | [37] 39 | [icdC]–[ycgX] | [icdC],iraM,[ycgX] |
| * | * | ÷ | NC_000913 | 1529876 | 1530536 | 661 | 42 [35] | [37] 42 | [rhsE]–ydcD | [rhsE],ydcD |
| * | * | ÷ | NC_000913 | 1640598 | 1641185 | 588 | 39 [33] | [37] 38 | essQ/cspB | Qin prophage; putative S lysis protein/Qin prophage; cold shock protein |
| * | * | ÷ | NC_000913 | 2469008 | 2469812 | 805 | 40 [35] | [34] 42 | [gtrB]–[gtrS] | [gtrB],[gtrS] |
| * | * | ÷ | NC_000913 | 3268699 | 3269664 | 966 | 38 [36] | [35] 39 | [yhaC] | [yhaC] |
| * | * | ÷ | NC_000913 | 3287046 | 3287438 | 393 | 38 [37] | [37] 40 | [yraH] | [yraH] |
| * | * | ÷ | NC_000913 | 4110658 | 4111559 | 902 | 38 [36] | [37] 38 | [cdh]–tpiA | [cdh],tpiA |
| * | * | ÷ | NC_000913 | 4476646 | 4477215 | 570 | 38 [34] | [36] 40 | yjgL | SopA‑central‑domain‑like hexapeptide repeat protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 32 (0.320) | 62 (0.670) | 53/478 | NT | 67.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 29 (0.310) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 31 (0.310) | 81 (0.880) | 52/478 | NT | 73.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 29 (0.310) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1575208 = | 77 (0.780) | 4 (0.040) | 4/496 | NT | 5.1% | intergenic (‑6/+39) | pqqL/yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor |
| ? | NC_000913 | 1575230 = | 73 (0.760) | intergenic (‑28/+17) | pqqL/yddB | putative periplasmic M16 family zinc metalloendopeptidase/putative TonB‑dependent outer membrane receptor | |||||
| * | ? | NC_000913 | 2738913 = | NA (NA) | 4 (0.040) | 4/486 | NT | NA | intergenic (+8/+35) | pheA/tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase |
| ? | NC_000913 | 2738941 = | NA (NA) | intergenic (+36/+7) | pheA/tyrA | chorismate mutase and prephenate dehydratase, P‑protein/fused chorismate mutase T/prephenate dehydrogenase | |||||
| * | ? | NC_000913 | 4171223 = | 0 (0.000) | 4 (0.040) | 4/504 | NT | 100% | noncoding (2583/2904 nt) | rrlB | 23S ribosomal RNA of rrnB operon |
| ? | NC_000913 | 4212634 = | NA (NA) | noncoding (2592/2904 nt) | rrlE | 23S ribosomal RNA of rrnE operon | |||||