mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
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 | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 258,756 | G→T | pseudogene (81/331 nt) | crl → | RNA polymerase holoenzyme assembly factor Crl |
| MC JC | 260,173 | Δ13,782 bp | IS5‑mediated | proB–[ykfC] | 19 genes proB, proA, thrW, ykfI, yafW, ykfH, ykfG, yafX, ykfF, ykfB, yafY, yafZ, ykfA, perR, insN, insI1, insN, eyeA, [ykfC] |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 635,355 | G→A | R8* (CGA→TGA) N405N (AAC→AAT) |
ybdM ← ybdN ← |
ParB‑like nuclease domain‑containing protein YbdM putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| JC JC | 1,095,639 | IS5 (–) +4 bp | intergenic (‑202/‑201) | insE4 ← / → ycdU | IS3 element protein InsE/uncharacterized protein YcdU |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,306,736 | T→G | S325A (TCC→GCC) | oppF → | murein tripeptide ABC transporter/oligopeptide ABC transporter ATP binding subunit OppF |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| JC JC | 1,626,965 | IS2 (+) +5 bp | coding (412‑416/2046 nt) | dcp ← | peptidyl‑dipeptidase Dcp |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,705,108 | G→A | G54R (GGG→AGG) | cnu → | H‑NS‑ and StpA‑binding protein |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| JC JC | 2,108,146 | IS1 (–) +8 bp | coding (177‑184/1104 nt) | glf ← | UDP‑galactopyranose mutase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 3,266,540 | C→G | V176L (GTA→CTA) | tdcA ← | DNA‑binding transcriptional activator TdcA |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| MC JC | 3,678,269 | Δ42,364 bp | IS150‑mediated | [yhjG]–hokA | 36 genes [yhjG], pdeH, kdgK, yhjJ, dctA, pdeK, bcsC, bcsZ, bcsB, bcsA, yhjR, bcsE, bcsF, bcsG, ldrD, rdlD, yhjV, dppF, dppD, dppC, dppB, dppA, proK, eptB, yhjX, yhjY, tag, yiaC, bisC, yiaD, ghrB, yiaF, yiaG, cspA, ysaE, hokA |
| JC JC | 3,888,426 | IS2 (–) +5 bp | intergenic (+234/‑5) | mnmE → / → tnaC | 5‑carboxymethylaminomethyluridine‑tRNA synthase GTPase subunit/tnaAB operon leader peptide |
| RA | 4,132,697 | G→A | E28K (GAG→AAG) | metF → | 5,10‑methylenetetrahydrofolate reductase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,566,642 | G→A | S202L (TCG→TTG) | yjiN ← | DUF445 domain‑containing protein YjiN |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423806–3424233 | 3424446–3424239 | 7–641 | 38 [36] | [35] 37 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 4035352–4035730 | 4036902–4035736 | 7–1551 | 40 [35] | [36] 38 | [rrsA] | [rrsA] |
| * | * | ÷ | NC_000913 | 4038050–4038687 | 4040661 | 1975–2612 | 38 [35] | [36] 39 | [rrlA]–rrfA | [rrlA],rrfA |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 275149 | NA (NA) | 42 (0.410) | 37/598 | 1.8 | 29.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 725814 = | 103 (1.000) | coding (1223/2049 nt) | kdpB | K(+) transporting P‑type ATPase subunit KdpB | |||||
| * | ? | NC_000913 | = 566774 | 119 (1.150) | 98 (0.950) | 37/594 | 1.8 | 47.4% | pseudogene (91/93 nt) | renD | protein RenD |
| ? | NC_000913 | 568036 = | 99 (0.960) | pseudogene (2/213 nt) | renD | protein RenD | |||||
| * | ? | NC_000913 | 1207790 = | 36 (0.350) | 55 (0.560) | 44/566 | 1.1 | 60.8% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 37 (0.380) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 40 (0.390) | 62 (0.630) | 41/566 | 1.3 | 62.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 37 (0.380) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | 1396044 = | NA (NA) | 55 (0.530) | 41/598 | 1.5 | 49.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 1404867 = | 56 (0.540) | coding (127/909 nt) | abgR | putative LysR‑type DNA‑binding transcriptional regulator AbgR | |||||
| * | ? | NC_000913 | = 1404870 | 54 (0.520) | 72 (0.700) | 59/598 | 0.5 | 57.1% | coding (130/909 nt) | abgR | putative LysR‑type DNA‑binding transcriptional regulator AbgR |
| ? | NC_000913 | 2101749 = | NA (NA) | noncoding (1195/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 39 (0.380) | 31/598 | 2.5 | 30.2% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | 1790402 = | 90 (0.870) | coding (843/1437 nt) | selO | protein adenylyltransferase SelO | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 58 (0.560) | 44/596 | 1.2 | 42.3% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3262484 = | 79 (0.770) | coding (1177/1209 nt) | tdcD | propionate kinase | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 45 (0.430) | 34/598 | 2.2 | 36.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3262487 | 80 (0.770) | coding (1174/1209 nt) | tdcD | propionate kinase | |||||