mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.0b
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 444,779 | C→T | 100% | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 877,748 | C→A | 15.1% | S148I (AGC→ATC) | deoR ← | deoxyribose‑5‑phosphate‑inducible deoxyribose operon transcriptional repressor; repressor of nupG and tsx |
| RA | 1,139,001 | T→A | 100% | I275F (ATC→TTC) | rne ← | fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein |
| RA | 1,313,853 | T→A | 57.5% | I65F (ATC→TTC) | trpC ← | fused indole‑3‑glycerolphosphate synthetase/N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,433,237 | C→T | 16.7% | W602* (TGG→TAG) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,563,861 | G→T | 100% | L296M (CTG→ATG) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 2,123,156 | T→C | 16.3% | N402D (AAT→GAT) | wcaD ← | putative colanic acid polymerase |
| RA | 2,215,597 | C→T | 32.2% | intergenic (‑129/‑67) | bglX ← / → dld | beta‑D‑glucoside glucohydrolase, periplasmic/D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,305,991 | G→T | 100% | Q80K (CAG→AAG) | ompC ← | outer membrane porin protein C |
| JC JC | 2,400,257 | IS5 (+) +4 bp | 59.1% | intergenic (‑137/‑780) | lrhA ← / → alaA | transcriptional repressor of flagellar, motility and chemotaxis genes/valine‑pyruvate aminotransferase 2 |
| RA | 2,419,720 | T→C | 23.9% | D183G (GAT→GGT) | hisJ ← | histidine/lysine/arginine/ornithine transporter subunit |
| RA | 2,420,353 | A→G | 64.4% | intergenic (‑86/+135) | hisJ ← / ← argT | histidine/lysine/arginine/ornithine transporter subunit/lysine/arginine/ornithine transporter subunit |
| RA | 2,598,477 | A→G | 18.2% | K103R (AAA→AGA) | hyfD → | hydrogenase 4, membrane subunit |
| RA | 3,280,415 | A→G | 23.6% | intergenic (+31/‑370) | agaI → / → yraH | galactosamine‑6‑phosphate isomerase/putative fimbrial‑like adhesin protein |
| JC | 3,528,829:1 | (GTTTTCAGCCAG)1→2 | 89.7% | coding (399/1353 nt) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| RA | 3,621,613 | A→T | 4.5% | L429* (TTA→TAA) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| JC | 3,676,833 | Δ3 bp | 95.3% | intergenic (‑26/+155) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,705,839 | G→A | 6.0% | G152G (GGC→GGT) | yhjY ← | autotransporter beta‑domain protein |
| RA | 4,444,286 | C→T | 26.7% | A296V (GCC→GTC) | yjfF → | inner membrane putative ABC superfamily sugar transporter permease |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1117462 | 1117734 | 273 | 4 [3] | [3] 4 | pyrC | dihydro‑orotase |
| * | * | ÷ | CP009273 | 1192548 | 1194262 | 1715 | 4 [3] | [3] 4 | [ymfD]–[lit] | [ymfD], ymfE, [lit] |
| * | * | ÷ | CP009273 | 1194385 | 1195425 | 1041 | 4 [3] | [3] 4 | [lit]–[intE] | [lit], [intE] |
| * | * | ÷ | CP009273 | 1196927 | 1198529 | 1603 | 4 [3] | [3] 4 | ymfI–[croE] | ymfI, ymfJ, cohE, [croE] |
| * | * | ÷ | CP009273 | 1198965 | 1199686 | 722 | 4 [3] | [3] 4 | [ymfL]–[oweE] | [ymfL], ymfM, [oweE] |
| * | * | ÷ | CP009273 | 1201077 | 1202087 | 1011 | 4 [3] | [3] 4 | [ymfR]–[jayE] | [ymfR], beeE, [jayE] |
| * | * | ÷ | CP009273 | 1202559 | 1202652 | 94 | 4 [3] | [3] 4 | ymfQ | prohage e14 tail protein homolog |
| * | * | ÷ | CP009273 | 1202866 | 1203206 | 341 | 4 [3] | [3] 4 | [ymfQ]–[stfP] | [ymfQ], [stfP] |
| * | * | ÷ | CP009273 | 1203262 | 1204889 | 1628 | 4 [1] | [3] 4 | [stfP]–[stfE] | [stfP], tfaP, tfaE, [stfE] |
| * | * | ÷ | CP009273 | 1205039 | 1206141 | 1103 | 4 [3] | [3] 4 | [stfE]–[mcrA] | [stfE], pinE, [mcrA] |
| * | * | ÷ | CP009273 | 1206394 | 1206627 | 234 | 4 [3] | [3] 4 | mcrA | putative 5‑methylcytosine/5‑hydroxymethylcytosine‑specific restriction nuclease; 5‑methylcytosine DNA binding protein; e14 prophage gene |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 28 (1.410) | 24/270 | NT | NA | intergenic (‑38/+557) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor |
| ? | CP009273 | = 360286 | NA (NA) | intergenic (‑220/+375) | lacZ/lacI | pseudogene, truncated/DNA‑binding transcriptional repressor | |||||
| * | ? | CP009273 | = 786311 | 16 (0.810) | 3 (0.160) | 3/258 | NT | 14.2% | coding (175/1047 nt) | galT | galactose‑1‑phosphate uridylyltransferase |
| ? | CP009273 | = 786404 | 21 (1.110) | coding (82/1047 nt) | galT | galactose‑1‑phosphate uridylyltransferase | |||||
| * | ? | CP009273 | 1045234 = | 24 (1.210) | 15 (0.760) | 14/270 | NT | 50.0% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 6 (0.300) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1203261 | 1 (0.050) | 3 (0.170) | 3/238 | NT | 87.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | CP009273 | = 1205058 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | CP009273 | 1973115 = | 5 (0.250) | 15 (0.760) | 15/270 | NT | 75.0% | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein |
| ? | CP009273 | = 3577555 | NA (NA) | intergenic (+15/‑1) | insB1/yrhA | IS1 transposase B/pseudogene, interrupted by IS1E | |||||
| * | ? | CP009273 | = 2096424 | NA (NA) | 11 (0.560) | 9/270 | NT | 45.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | CP009273 | = 2427745 | 13 (0.660) | coding (476/660 nt) | dedA | DedA family inner membrane protein | |||||