mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 39,219 | G→T | intergenic (‑104/+25) | caiB ← / ← caiA | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase/crotonobetainyl‑CoA reductase |
| RA | 209,615 | G→T | intergenic (+35/‑64) | accA → / → ldcC | acetyl‑CoA carboxyltransferase subunit alpha/lysine decarboxylase 2 |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 344,676 | C→T | Y167Y (TAC→TAT) | yahL → | uncharacterized protein YahL |
| RA | 605,177 | A→G | V83A (GTG→GCG) | nfsB ← | NAD(P)H nitroreductase NfsB |
| RA | 689,676 | C→A | P402P (CCG→CCT) | lnt ← | apolipoprotein N‑acyltransferase |
| RA | 844,373 | G→T | L370M (CTG→ATG) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,042,437 | C→A | A592S (GCA→TCA) | etk ← | protein‑tyrosine kinase Etk |
| RA | 1,462,806 | C→A | R228S (CGT→AGT) | paaK → | phenylacetate‑CoA ligase |
| RA | 1,571,925 | C→T | V41I (GTC→ATC) | gadB ← | glutamate decarboxylase B |
| RA | 1,586,888 | G→T | Q283K (CAA→AAA) | ydeQ ← | putative fimbrial adhesin protein YdeQ |
| RA | 1,594,707 | G→T | pseudogene (3380/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,738,025 | C→A | S61Y (TCT→TAT) | purR → | DNA‑binding transcriptional repressor PurR |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,890,435 | C→A | S33I (AGC→ATC) | yeaY ← | Slp family lipoprotein YeaY |
| RA | 1,906,222 | G→T | V179F (GTC→TTC) | mntP → | Mn(2(+)) exporter |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,286,657 | G→T | pseudogene (2258/2525 nt) | yejO ← | adhesin‑like autotransporter YejO |
| RA | 2,307,351 | G→T | P422Q (CCG→CAG) | yojI ← | ABC transporter family protein/microcin J25 efflux protein |
| RA | 2,477,621 | G→T | P3P (CCC→CCA) | dsdC ← | DNA‑binding transcriptional dual regulator DsdC |
| RA | 2,521,499 | C→A | intergenic (+171/+94) | lysV → / ← xapR | tRNA‑Lys/DNA‑binding transcriptional activator XapR |
| RA | 2,615,136 | G→T | S249* (TCG→TAG) | yfgO ← | putative transporter YfgO |
| RA | 2,886,193 | C→A | A343S (GCC→TCC) | cas3 ← | CRISPR‑associated endonuclease/helicase Cas3 |
| RA | 3,044,990 | C→A | G443G (GGC→GGA) | bglA → | 6‑phospho‑beta‑glucosidase A |
| RA | 3,216,092 | C→A | V134L (GTG→TTG) | nfeF ← | NADPH‑dependent ferric chelate reductase |
| RA | 3,317,324 | A→G | V68A (GTC→GCC) | nusA ← | transcription termination/antitermination protein NusA |
| RA | 3,331,197 | C→A | V186V (GTG→GTT) | obgE ← | GTPase ObgE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,397,022 | C→A | E258D (GAG→GAT) | rng ← | RNase G |
| RA | 3,488,966 | C→A | G405G (GGG→GGT) | argD ← | N‑acetylornithine aminotransferase/N‑succinyldiaminopimelate aminotransferase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,565,112 | G→T | G490G (GGC→GGA) | glgP ← | glycogen phosphorylase |
| RA | 3,617,537 | G→T | A175S (GCA→TCA) | nikD → | Ni(2(+)) ABC transporter ATP binding subunit NikD |
| RA | 3,734,742 | G→T | V341V (GTG→GTT) | xylH → | xylose ABC transporter membrane subunit |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,926,823 | G→T | P61T (CCG→ACG) | asnC ← | DNA‑binding transcriptional dual regulator AsnC |
| RA | 4,224,158 | G→T | A111S (GCG→TCG) | metH → | cobalamin‑dependent methionine synthase |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,352,911 | G→T | A2S (GCA→TCA) | ghoT → | toxin of the GhoTS toxin‑antitoxin system |
| RA | 4,357,514 | C→A | L368L (CTG→CTT) | cadA ← | lysine decarboxylase 1 |
| RA | 4,576,834 | G→T | pseudogene (2700/2721 nt) | yjiV → | putative uncharacterized protein YjiV |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102972 | 3104055 | 1084 | 32 [31] | [30] 32 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423761–3424233 | 3424540–3424239 | 7–780 | 32 [31] | [31] 33 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 128 (1.140) | 40 (0.400) | 33/246 | 1.3 | 28.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 86 (0.870) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 141 (1.300) | 75/270 | 0.1 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 194 (1.730) | 155 (1.400) | 74/276 | 0.1 | 61.0% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 151 (1.350) | 65/278 | 0.2 | 96.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 6 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||