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 | annotation | gene | description |
| RA | 444,779 | C→T | W440* (TGG→TAG) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 1,138,538 | T→G | E429A (GAA→GCA) | rne ← | fused ribonucleaseE: endoribonuclease/RNA‑binding protein/RNA degradosome binding protein |
| RA | 1,191,676 | C→T | H366H (CAC→CAT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,191,688 | C→T | T370T (ACC→ACT) | icd → | e14 prophage; isocitrate dehydrogenase, specific for NADP+ |
| RA | 1,563,861 | G→T | L296M (CTG→ATG) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 2,305,991 | G→T | Q80K (CAG→AAG) | ompC ← | outer membrane porin protein C |
| JC | 3,528,829 | (GTTTTCAGCCAG)1→2 | coding (399/1353 nt) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| JC | 3,676,833 | Δ3 bp | intergenic (‑26/+155) | dctA ← / ← yhjK | C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase |
| RA | 3,919,680 | C→T | A46T (GCC→ACC) | mioC ← | FMN‑binding protein MioC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP009273 | 1116965 | 1118123 | 1159 | 64 [62] | [61] 63 | pyrC | pyrC |
| * | * | ÷ | CP009273 | 1191701 | 1206927 | 15227 | 65 [60] | [62] 63 | [icd]–[icdC] | 25 genes [icd], ymfD, ymfE, lit, intE, xisE, ymfI, ymfJ, cohE, croE, ymfL, ymfM, oweE, aaaE, ymfR, beeE, jayE, ymfQ, stfP, tfaP, tfaE, stfE, pinE, mcrA, [icdC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009273 | 360104 = | NA (NA) | 218 (1.850) | 135/292 | 0.0 | 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 | 1045234 = | 135 (1.150) | 99 (0.840) | 75/292 | 0.6 | 58.2% | intergenic (‑34/‑55) | gfcA/insA | O‑antigen capsule production threonine‑rich inner membrane protein/IS1 repressor TnpA |
| ? | CP009273 | = 1973123 | 7 (0.060) | intergenic (‑669/‑111) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 1046001 | 114 (0.970) | 134 (1.140) | 92/292 | 0.1 | 69.1% | intergenic (+15/+418) | insB1/cspH | IS1 transposase B/stress protein, member of the CspA‑family |
| ? | CP009273 | 1973115 = | 6 (0.050) | intergenic (‑661/‑119) | flhD/uspC | flagellar class II regulon transcriptional activator, with FlhC/universal stress protein | |||||
| * | ? | CP009273 | = 3180785 | NA (NA) | 151 (1.280) | 99/292 | 0.0 | 93.2% | pseudogene (6/2445 nt) | yqiG | pseudogene; fimbrial export usher family;putative membrane; Not classified; putative membrane protein |
| ? | CP009273 | = 4334511 | 11 (0.090) | coding (1326/1422 nt) | melB | melibiose:sodium symporter | |||||
| * | ? | CP009273 | 4334507 = | 4 (0.030) | 147 (1.250) | 100/292 | 0.0 | 97.4% | coding (1322/1422 nt) | melB | melibiose:sodium symporter |
| ? | CP009273 | 4487998 = | NA (NA) | intergenic (+241/‑91) | intB/insC1 | pseudogene, integrase homology;IS, phage, Tn; Phage‑related functions and prophages; KpLE2 phage‑like element; P4‑like integrase/IS2 repressor TnpA | |||||