mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 87,468 | A→G | T38A (ACC→GCC) | ilvH → | acetolactate synthase 3, small subunit, valine‑sensitive |
| RA | 93,429 | C→T | S88S (AGC→AGT) | murE → | UDP‑N‑acetylmuramoyl‑L‑alanyl‑D‑glutamate:meso‑ diaminopimelate ligase |
| RA | 126,432 | T→C | A246A (GCT→GCC) | aceF → | pyruvate dehydrogenase, dihydrolipoyltransacetylase component E2 |
| RA | 147,824 | C→T | A286V (GCA→GTA) | yadD → | transposase_31 family protein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 703,866 | A→G | intergenic (‑255/‑78) | nagB ← / → nagE | glucosamine‑6‑phosphate deaminase/N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 709,223 | C→T | T297I (ACC→ATC) | chiP → | chitoporin, uptake of chitosugars |
| RA | 1,053,704 | G→A | I825I (ATC→ATT) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,089,446 | C→G | A138P (GCC→CCC) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine (PGA) N‑deacetylase outer membrane export lipoprotein |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,443,966 | C→T | Q306* (CAA→TAA) | ydbH → | putative membrane‑anchored protein, function unknown |
| RA | 1,449,947 | T→C | Y468C (TAT→TGT) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,594,132 | (C)8→7 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,594,256 | (C)8→9 | pseudogene (3732/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,691,529 | (A)6→7 | intergenic (+169/+57) | ydgA → / ← uidC | DUF945 family protein/putative outer membrane porin for beta‑glucuronides porin protein |
| RA | 1,756,208 | G→A | A171T (GCT→ACT) | pykF → | pyruvate kinase I |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,994,960 | C→T | A134T (GCG→ACG) | uvrY ← | response regulator in two‑component regulatory system with BarA |
| RA | 2,073,616 | A→G | D693G (GAC→GGC) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| 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 | 2,184,452 | G→A | A22V (GCC→GTC) | thiD ← | hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,268,372 | G→A | E182K (GAG→AAG) | yeiR → | Zn‑stimulated GTPase involved in zinc homeostasis, mutants are cadmium and EDTA sensitive, Zn(2+) binding protein |
| RA | 2,288,554 | G→C | pseudogene (361/2525 nt) | yejO ← | pseudogene, autotransporter outer membrane homology,putative transport, Not classified, putative ATP‑binding component of a transport system |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,635,578 | A→G | K449K (AAA→AAG) | xseA → | exonuclease VII, large subunit |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,017,777 | +G | coding (1718/3099 nt) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,161,267 | G→A | P468L (CCG→CTG) | ftsP ← | septal ring component that protects the divisome from stress, multicopy suppressor of ftsI(Ts) |
| RA | 3,232,207 | T→C | S181S (AGT→AGC) | fadH → | 2,4‑dienoyl‑CoA reductase, NADH and FMN‑linked |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,400,093 | G→A | A332V (GCG→GTG) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,459,354 | T→C | V339A (GTA→GCA) | gspE → | general secretory pathway component, cryptic |
| RA | 3,534,920 | G→A | R317W (CGG→TGG) | envZ ← | sensory histidine kinase in two‑component regulatory system with OmpR |
| 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 | 3,668,544 | (C)6→7 | coding (645/1398 nt) | yhjA ← | putative cytochrome C peroxidase |
| RA | 3,709,561 | (C)6→7 | coding (915/1692 nt) | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,949 | G→A | pseudogene (601/669 nt) | rph ← | ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,815,986 | G→A | pseudogene (564/669 nt) | rph ← | ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,823,249 | T→C | Y284H (TAC→CAC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,125,041 | T→C | K590K (AAA→AAG) | priA ← | Primosome factor n' (replication factor Y) |
| RA | 4,182,791 | A→G | D516G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,280,409 | (A)7→8 | coding (430/1650 nt) | yjcE → | putative cation/proton antiporter |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,345,727 | A→G | F534L (TTC→CTC) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,400,278 | A→G | intergenic (+76/‑10) | miaA → / → hfq | delta(2)‑isopentenylpyrophosphate tRNA‑adenosine transferase/global sRNA chaperone, HF‑I, host factor for RNA phage Q beta replication |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807329 | 810368 | 3040 | 23 [13] | [16] 19 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857129 | 2859643 | 2515 | 24 [16] | [16] 17 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423732–3424234 | 3424557–3424238 | 5–826 | 17 [15] | [16] 17 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 61 (0.940) | 24 (0.430) | 16/190 | 2.0 | 28.5% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 68 (1.230) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 44 (0.710) | 28/214 | 1.0 | 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 | |||||