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 | 578,244 | A→G | L46L (CTA→CTG) | rzpD → | putative prophage endopeptidase RzpD |
| 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 |
| MC JC | 676,374 | Δ11,477 bp | IS5‑mediated | [ybeQ]–gltI | [ybeQ], ybeR, djlB, ybeT, ybeU, djlC, hscC, rihA, gltL, gltK, gltJ, sroC, gltI |
| RA | 696,582 | C→T | noncoding (35/75 nt) | glnV ← | tRNA‑Gln |
| RA | 771,504 | C→T | A16V (GCG→GTG) | cydA → | cytochrome bd‑I subunit 1 |
| RA | 811,531 | G→A | G384D (GGT→GAT) V4I (GTT→ATT) |
bioF → bioC → |
8‑amino‑7‑oxononanoate synthase malonyl‑acyl carrier protein methyltransferase |
| 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 |
| 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 | 2,718,740 | T→G | N2K (AAT→AAG) | trxC → | reduced thioredoxin 2 |
| RA | 2,774,080 | G→T | V255F (GTC→TTC) | yfjW → | uncharacterized protein YfjW |
| RA | 2,817,997 | A→G | intergenic (‑137/+62) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| 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 | 4,050,808 | IS2 (–) +5 bp | intergenic (‑43/‑224) | yihA ← / → csrC | GTP‑binding protein YihA/small regulatory RNA CsrC |
| 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 | 3423765–3424232 | 3424492–3424238 | 7–728 | 38 [37] | [37] 39 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 79 (0.740) | 58/598 | 0.5 | 58.1% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3888846 | 57 (0.530) | coding (117/1416 nt) | tnaA | tryptophanase | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 78 (0.730) | 55/598 | 0.7 | 53.8% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 3654624 = | 67 (0.630) | intergenic (+97/‑59) | slp/dctR | starvation lipoprotein/putative DNA‑binding transcriptional regulator DctR | |||||
| * | ? | NC_000913 | = 3187426 | NA (NA) | 67 (0.630) | 51/596 | 0.8 | 50.8% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 3654628 | 65 (0.610) | intergenic (+101/‑55) | slp/dctR | starvation lipoprotein/putative DNA‑binding transcriptional regulator DctR | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 57 (0.530) | 45/598 | 1.2 | 48.7% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3888838 = | 60 (0.560) | coding (109/1416 nt) | tnaA | tryptophanase | |||||