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 | 21,379 | G→T | G67* (GGA→TGA) | yaaY → | DUF2575 domain‑containing protein YaaY |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 288,809 | G→T | G118G (GGC→GGA) | xynR ← | CP4‑6 prophage; DNA‑binding transcriptional repressor XynR |
| RA | 711,559 | C→A | intergenic (‑94/+46) | fldA ← / ← ybfE | flavodoxin 1/LexA‑regulated protein |
| RA | 751,704 | C→A | V156F (GTC→TTC) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 794,407 | G→T | R80S (CGC→AGC) | modE ← | DNA‑binding transcriptional dual regulator ModE |
| RA | 810,479 | G→T | W33C (TGG→TGT) | bioF → | 8‑amino‑7‑oxononanoate synthase |
| RA | 845,414 | Δ1 bp | coding (67/2226 nt) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,100,596 | C→A | L101I (CTT→ATT) | ycdZ → | putative inner membrane protein |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,369,736 | C→A | P16P (CCC→CCA) | pspE → | thiosulfate sulfurtransferase PspE |
| RA | 1,457,108 | A→C | T227P (ACC→CCC) | paaE → | phenylacetyl‑CoA 1,2‑epoxidase, reductase subunit |
| RA | 1,479,173 | (T)7→6 | coding (36/1758 nt) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,663,870 | G→T | A88S (GCT→TCT) | ynfH → | putative menaquinol dehydrogenase |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,736,811 | C→T | M160I (ATG→ATA) | ydhP ← | putative transporter YdhP |
| RA | 1,774,957 | C→A | A91E (GCG→GAG) | aroD → | 3‑dehydroquinate dehydratase |
| RA | 1,831,689 | G→T | R98R (CGC→CGA) | astC ← | succinylornithine transaminase |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,029,494 | T→C | intergenic (‑128/‑45) | yedI ← / → yedA | conserved inner membrane protein YedI/putative transporter YedA |
| RA | 2,072,113 | C→A | A192E (GCG→GAG) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,226,878 | C→A | Q131H (CAG→CAT) | yohF ← | putative oxidoreductase with NAD(P)‑binding Rossmann‑fold domain |
| RA | 2,518,263 | C→A | intergenic (‑32/‑204) | alaW ← / → yfeC | tRNA‑Ala/putative DNA‑binding transcriptional regulator YfeC |
| RA | 2,625,040 | G→A | G666D (GGC→GAC) | ppk → | polyphosphate kinase |
| RA | 2,630,555 | C→A | A77E (GCG→GAG) | yfgI → | nalidixic acid resistance protein YfgI |
| RA | 2,790,155 | C→A | P58P (CCC→CCA) | lhgO → | L‑2‑hydroxyglutarate oxidase |
| RA | 2,841,419 | G→T | E144* (GAA→TAA) | ascB → | 6‑phospho‑beta‑glucosidase AscB |
| RA | 2,902,528 | G→T | P211P (CCG→CCT) | ygcE → | putative sugar kinase YgcE |
| RA | 2,920,701 | G→T | P16T (CCG→ACG) | gudX ← | glucarate dehydratase‑related protein |
| RA | 2,961,072 | C→A | A453S (GCG→TCG) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 2,963,965 | C→A | E71D (GAG→GAT) | ppdA ← | conserved protein PpdA |
| RA | 3,052,193 | G→T | A42E (GCG→GAG) | ubiI ← | 2‑octaprenylphenol hydroxylase |
| RA | 3,202,877 | G→T | W329C (TGG→TGT) | cca → | fused tRNA nucleotidyltransferase/2',3'‑cyclic phosphodiesterase/2' nucleotidase and phosphatase |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,554,444 | C→A | L454M (CTG→ATG) | malT → | DNA‑binding transcriptional activator MalT |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 4,215,356 | Δ1 bp | intergenic (+147/‑122) | metA → / → aceB | homoserine O‑succinyltransferase/malate synthase A |
| RA | 4,252,926 | C→A | R141R (CGA→AGA) | ubiC → | chorismate lyase |
| 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 | 4,337,342 | G→T | T196T (ACC→ACA) | adiY ← | DNA‑binding transcriptional activator AdiY |
| RA | 4,382,176 | G→T | A48D (GCT→GAT) | frdA ← | fumarate reductase flavoprotein subunit |
| RA | 4,399,968 | G→T | L239F (TTG→TTT) | miaA → | tRNA dimethylallyltransferase |
| RA | 4,406,938 | C→A | G95G (GGC→GGA) | rnr → | RNase R |
| RA | 4,640,034 | G→T | L91L (CTC→CTA) | arcA ← | DNA‑binding transcriptional dual regulator ArcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196277 | 1211431 | 15155 | 16 [14] | [13] 15 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3102973 | 3104076 | 1104 | 15 [14] | [14] 15 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423766–3424234 | 3424523–3424239 | 6–758 | 16 [14] | [9] 15 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3941746–3942013 | 3943292–3942038 | 26–1547 | 15 [13] | [14] 15 | [rrsC] | [rrsC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 89 (1.470) | 54/270 | 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 = | 103 (1.650) | 93 (1.500) | 55/276 | 0.1 | 64.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 65 (1.040) | 41/278 | 0.3 | 98.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||