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 | 38,132 | C→A | L328L (CTG→CTT) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| JC | 490,962 | (GTATTACCG)2→3 | coding (81/378 nt) | ybaN → | conserved inner membrane protein YbaN |
| JC JC | 568,908 | IS2 (–) +5 bp | coding (7‑11/1527 nt) | ybcK → | DLP12 prophage; putative recombinase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 951,454 | C→T | E701K (GAA→AAA) | pflB ← | pyruvate formate‑lyase |
| 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 | 1,449,784 | C→A | V522V (GTG→GTT) | tynA ← | copper‑containing amine oxidase |
| JC JC | 1,580,223 | IS5 (–) +4 bp | coding (565‑568/1158 nt) | ydeM ← | putative anaerobic sulfatase maturation enzyme YdeM |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| 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 | 2,154,736 | C→G | P241A (CCG→GCG) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,505,811 | G→C | R274R (CGC→CGG) | ypdF ← | aminopeptidase |
| RA | 2,734,747 | G→T | P96P (CCC→CCA) | pgeF ← | polyphenol oxidase YfiH |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,588,006 | C→A | K36N (AAG→AAT) | ugpQ ← | glycerophosphodiester phosphodiesterase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,941,766 | G→T | intergenic (‑439/‑42) | yieP ← / → rrsC | putative transcriptional regulator YieP/16S ribosomal RNA |
| 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 |
| MC | 4,326,086 | Δ153 bp | between other | yjdN ← / ← yjdM | conserved protein YjdN/conserved protein YjdM |
| RA | 4,505,167 | C→A | G370G (GGC→GGA) | yjhB → | putative sialic acid transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196275 | 1211428 | 15154 | 13 [9] | [10] 12 | [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 | 3103013 | 3104051 | 1039 | 11 [9] | [9] 11 | mutY | adenine DNA glycosylase |
| * | * | ÷ | NC_000913 | 3423782–3424234 | 3424531–3424239 | 6–750 | 12 [10] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 41 (0.850) | 14/258 | 2.0 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 18 (0.480) | 8/200 | 2.4 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377430 = | NA (NA) | intergenic (+119/+105) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 51 (1.450) | 16/188 | 0.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 375160 | NA (NA) | 32 (0.630) +T |
14/272 | 2.1 | NA | noncoding (28/34 nt) | other | REP31e |
| ? | NC_000913 | = 377491 | NA (NA) | noncoding (32/34 nt) | other | REP32d | |||||
| * | ? | NC_000913 | 377321 = | NA (NA) | 27 (0.730) +38 bp |
9/198 | 2.2 | NA | intergenic (+10/+214) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | 2347281 = | NA (NA) | noncoding (34/34 nt) | other | REP164c | |||||
| * | ? | NC_000913 | 608007 = | NA (NA) | 20 (0.480) | 12/222 | 1.9 | 26.0% | noncoding (1/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 609352 = | 57 (1.370) | intergenic (+175/+107) | insL‑2/entD | IS186/IS421 transposase/phosphopantetheinyl transferase EntD | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 58 (1.160) | 38/266 | 0.2 | 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 = | 65 (1.260) | 68 (1.330) | 45/272 | 0.1 | 67.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 55 (1.070) | 41/274 | 0.2 | 94.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4373295 = | NA (NA) | 21 (0.440) | 11/254 | 2.5 | NA | noncoding (2/34 nt) | other | REP328b |
| ? | NC_000913 | 4374499 = | NA (NA) | noncoding (1/34 nt) | other | REP329a | |||||