mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.27.1 revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 56,942 | A→G | A56A (GCT→GCC) | lptD ← | LPS assembly OM complex LptDE, beta‑barrel component |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 300,196 | A→G | F247L (TTC→CTC) | paoC ← | PaoABC aldehyde oxidoreductase, Moco‑containing subunit |
| RA | 323,369 | G→A | V344V (GTG→GTA) | ykgF → | ferridoxin‑like LutB family protein; putative electron transport chain YkgEFG component |
| RA | 796,454 | C→T | A198V (GCG→GTG) | modB → | molybdate ABC transporter permease; chlorate resistance protein |
| RA | 956,496 | A→G | V46A (GTA→GCA) | ycaO ← | ribosomal protein S12 methylthiotransferase accessory factor |
| RA | 1,055,493 | G→A | A229V (GCA→GTA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,334,244 | G→A | S130S (TCG→TCA) | cysB → | N‑acetylserine‑responsive cysteine regulon transcriptional activator; autorepressor |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,968,051 | G→A | P151S (CCG→TCG) | cheB ← | fused chemotaxis regulator: protein‑glutamate methylesterase in two‑component regulatory system with CheA |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,131,557 | G→A | R172C (CGC→TGC) | wcaC ← | putative glycosyl transferase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,230,157 | G→A | L77L (CTG→TTG) | dusC ← | tRNA‑dihydrouridine synthase C |
| RA | 2,526,308 | T→C | V183V (GTA→GTG) | yfeR ← | transcriptional regulator of yefH |
| RA | 2,810,153 | Δ1 bp | coding (537/738 nt) | ygaZ → | putative L‑valine exporter, norvaline resistance protein |
| RA | 3,032,861 | (T)5→4 | coding (45/126 nt) | yqfG → | uncharacterized protein |
| RA | 3,041,236 | G→A | intergenic (‑166/‑77) | sdhE ← / → ygfZ | flavinator of succinate dehydrogenase; antitoxin of CptAB toxin‑antitoxin pair/iron‑sulfur cluster repair protein, plumbagin resistance |
| RA | 3,168,604 | A→G | intergenic (‑60/+145) | mqsR ← / ← ygiV | GCU‑specific mRNA interferase toxin of the MqsR‑MqsA toxin‑antitoxin system; biofilm/motility regulator; anti‑repressor/transcriptional repressor for mcbR biofilm gene |
| RA | 3,270,488 | (C)7→8 | intergenic (+886/+137) | yhaC → / ← garK | pentapetide repeats‑related protein/glycerate kinase I |
| RA | 3,292,610 | T→C | L242L (TTA→TTG) | rsmI ← | 16S rRNA C1402 2'‑O‑ribose methyltransferase, SAM‑dependent |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,667,477 | T→C | H35R (CAC→CGC) | gadA ← | glutamate decarboxylase A, PLP‑dependent |
| RA | 3,672,577 | G→A | R55Q (CGG→CAG) | yhjC → | LysR family putative transcriptional regulator |
| RA | 3,750,962 | G→A | pseudogene (45/192 nt) | ysaD → | pseudogene, internal sequence remnant |
| RA | 3,758,369 | G→A | A498V (GCA→GTA) | selB ← | selenocysteinyl‑tRNA‑specific translation factor |
| RA | 3,815,810 | Δ1 bp | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,951,559 | +A | pseudogene (18/663 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
| RA | 3,964,812 | C→T | W273* (TGG→TGA) | rhlB ← | ATP‑dependent RNA helicase |
| RA | 3,991,485 | T→C | C111C (TGT→TGC) | cyaA → | adenylate cyclase |
| RA | 4,015,757 | A→G | V138A (GTT→GCT) | ysgA ← | putative carboxymethylenebutenolidase |
| RA | 4,068,334 | G→A | Q315* (CAA→TAA) | yihQ ← | putative sulpholipid alpha‑glucosidase; alpha‑glucosyl fluoride glucosidase |
| RA | 4,187,507 | A→C | N720H (AAC→CAC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,338,117 | (A)8→7 | intergenic (‑188/+137) | adiY ← / ← adiA | adi system transcriptional activator/arginine decarboxylase |
| RA | 4,367,579 | A→G | V250A (GTG→GCG) | aspA ← | aspartate ammonia‑lyase |
| RA | 4,389,327 | (C)6→7 | coding (44/3324 nt) | mscM ← | mechanosensitive channel protein, miniconductance |
| MC JC | 4,397,624 | (GCTGGC)3→2 | coding (213‑218/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,475,192 | A→G | T111A (ACA→GCA) | tabA → | biofilm modulator regulated by toxins; DUF386 family protein, cupin superfamily protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423753–3424536 | 3424536 | 1–784 | 67 [66] | [66] 67 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 124 (1.030) | 107/590 | 0.0 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||