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 | 66,205 | T→C | T116A (ACC→GCC) | araD ← | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 199,912 | G→A | G662D (GGC→GAC) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 410,683 | A→G | K180K (AAA→AAG) | mak → | manno(fructo)kinase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 884,506 | G→A | L278L (CTG→CTA) | mdfA → | multidrug efflux system protein |
| RA | 1,022,508 | A→G | V459A (GTG→GCG) | yccS ← | putative transporter, FUSC superfamily inner membrane protein |
| RA | 1,116,482 | T→C | Y34C (TAC→TGC) | lpxL ← | lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,316,440 | C→T | P261P (CCG→CCA) | trpA ← | tryptophan synthase, alpha subunit |
| RA | 1,351,196 | (G)7→8 | intergenic (‑157/+211) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase, NADH‑dependent/DUF559 family endonuclease‑related protein |
| RA | 1,364,513 | T→C | R94R (CGT→CGC) | puuB → | gamma‑glutamylputrescine oxidoreductase |
| RA | 1,428,109 | C→T | L206L (CTG→CTA) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,625,476 | T→C | L635L (TTA→TTG) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,632,151 | T→C | pseudogene (135/1284 nt) | ydfJ ← | pseudogene, MFS transporter family, interrupted by Qin prophage,Phage or Prophage Related, putative transport protein |
| RA | 1,675,350 | A→G | G337G (GGT→GGC) | pntB ← | pyridine nucleotide transhydrogenase, beta subunit |
| RA | 1,708,192 | T→C | V425A (GTT→GCT) | rsxC → | SoxR iron‑sulfur cluster reduction factor component, putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,756,495 | (A)5→4 | coding (798/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,806,042 | (C)6→7 | coding (42/759 nt) | ydiY ← | acid‑inducible putative outer membrane protein |
| RA | 1,869,266 | G→A | Q104Q (CAG→CAA) | yeaH → | UPF0229 family protein |
| 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 | 2,073,225 | T→C | W563R (TGG→CGG) | 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 | 2,240,094 | T→C | A85A (GCA→GCG) | mglB ← | methyl‑galactoside transporter subunit |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,414,597 | T→C | G376G (GGT→GGC) | ackA → | acetate kinase A and propionate kinase 2 |
| RA | 2,421,553 | G→A | E77K (GAA→AAA) | folX → | D‑erythro‑7,8‑dihydroneopterin triphosphate 2'‑epimerase and dihydroneopterin aldolase |
| RA | 2,531,596 | (G)6→7 | coding (134/762 nt) | cysZ → | sulfate transporter, sulfite inhibited |
| RA | 2,650,996 | C→T | G431E (GGG→GAG) | yfhM ← | bacterial alpha2‑macroglobulin colonization factor ECAM, anti‑host protease defense factor, periplasmic inner membrane‑anchored lipoprotein |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | yfiH ← | UPF0124 family protein |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,772,200 | G→A | pseudogene (867/900 nt) | yfjV ← | pseudogene, CP4‑57 prophage,Phage or Prophage Related, putative pump protein |
| RA | 2,807,360 | G→A | G77S (GGC→AGC) | proX → | glycine betaine/proline ABC transporter periplasmic binding protein, cold shock protein |
| RA | 2,821,424 | G→C | G196G (GGC→GGG) | alaS ← | alanyl‑tRNA synthetase |
| 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 | 3,001,154 | T→C | C270C (TGT→TGC) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,005,344 | A→G | L148P (CTT→CCT) | ygeV ← | putative sigma‑54‑interacting transcriptional activator |
| RA | 3,026,239 | T→C | H158H (CAT→CAC) | guaD → | guanine deaminase |
| RA | 3,035,437 | T→C | K282R (AAG→AGG) | prfB ← | peptide chain release factor RF‑2 |
| RA | 3,084,730 | C→T | A394A (GCG→GCA) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,214,968 | (T)6→7 | coding (506/507 nt) | mug ← | G/U mismatch‑specific DNA glycosylase, xanthine DNA glycosylase |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,276,481 | G→A | S400S (TCG→TCA) | garD → | D‑galactarate dehydrogenase |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,505,331 | T→C | A230A (GCA→GCG) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,532,523 | (A)7→8 | intergenic (‑84/‑295) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| 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 | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,808 | A→G | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,867,575 | (T)8→7 | intergenic (‑153/‑153) | ibpA ← / → yidQ | heat shock chaperone/DUF1375 family outer membrane protein |
| 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 |
| MC JC | 3,970,427 | (ACG)4→3 | coding (295‑297/1131 nt) | wecB → | UDP‑N‑acetyl glucosamine‑2‑epimerase |
| RA | 4,182,791 | A→G | D516G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,219,119 | A→G | Y175C (TAC→TGC) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| 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 | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,490,935 | 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 | 4,556,610 | T→C | intergenic (‑290/‑383) | yjiC ← / → iraD | uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor |
| RA | 4,568,417 | C→T | G35R (GGG→AGG) | mdtM ← | multidrug efflux system protein |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,607,066 | A→G | V212A (GTT→GCT) | rsmC ← | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent |
| RA | 4,637,373 | T→C | V226V (GTT→GTC) | creC → | sensory histidine kinase in two‑component regulatory system with CreB or PhoB |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807329 | 810370 | 3042 | 16 [9] | [8] 14 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1429831 | 1429993 | 163 | 10 [9] | [9] 11 | stfR | Rac prophage, putative tail fiber protein |
| * | * | ÷ | NC_000913 | 2857138 | 2859614 | 2477 | 20 [0] | [5] 10 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423784–3424234 | 3424529–3424238 | 5–746 | 11 [7] | [9] 10 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 54 (1.010) | 15 (0.320) | 13/204 | 1.8 | 28.9% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 27 (0.580) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 69 (1.330) | 49/228 | 0.1 | 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 | |||||