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 | 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 | 380,022 | (G)10→11 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| 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 | 1,044,785 | A→G | V340A (GTT→GCT) | gfcE ← | putative O‑antigen capsule outer membrane auxillary protein export channel |
| RA | 1,258,991 | A→G | E67E (GAA→GAG) | ychH → | DUF2583 family putative inner membrane protein |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,353,247 | G→A | R128C (CGT→TGT) | sapD ← | antimicrobial peptide ABC transporter ATPase |
| 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 | 1,554,117 | A→G | V518A (GTC→GCC) | maeA ← | malate dehydrogenase, decarboxylating, NAD‑requiring, malic enzyme |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,616,355 | T→C | V198A (GTC→GCC) | yneK → | uncharacterized protein |
| RA | 1,625,476 | T→C | L635L (TTA→TTG) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,675,350 | A→G | G337G (GGT→GGC) | pntB ← | pyridine nucleotide transhydrogenase, beta subunit |
| 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 | 1,904,586 | 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 | 2,366,415 | A→G | Y163C (TAC→TGC) | arnB → | uridine 5'‑(beta‑1‑threo‑pentapyranosyl‑4‑ulose diphosphate) aminotransferase, PLP‑dependent |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,445,253 | T→C | Y103C (TAC→TGC) | yfcA ← | TauE/TSUP family inner membrane protein |
| RA | 2,734,543 | (C)8→9 | coding (492/732 nt) | yfiH ← | UPF0124 family protein |
| RA | 2,736,687 | T→C | V181A (GTG→GCG) | bamD → | BamABCDE complex OM biogenesis lipoprotein |
| 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 | 2,821,424 | 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 | 2,845,226 | G→A | P416S (CCA→TCA) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| 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 | 3,129,594 | G→A | pseudogene (550/1101 nt) | yghO ← | pseudogene, IS‑interrupted |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,211,078 | C→T | intergenic (+82/‑29) | rpsU → / → dnaG | 30S ribosomal subunit protein S21/DNA primase |
| RA | 3,259,479 | G→A | G57G (GGC→GGT) | tdcG ← | L‑serine dehydratase 3, anaerobic |
| 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 | 3,411,139 | T→C | L287P (CTC→CCC) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,418,135 | T→C | *1035Q (TAA→CAA) | acrF → | multidrug efflux system protein |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| RA | 3,516,213 | G→A | A365V (GCG→GTG) | damX ← | cell division protein that binds to the septal ring |
| 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 | 3,802,147 | G→T | N304K (AAC→AAA) | waaO ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑ alpha‑1,3‑D‑galactosyltransferase |
| RA | 3,815,808 | A→G | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| 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 | 4,153,408 | A→G | intergenic (‑310/+288) | ppc ← / ← argE | phosphoenolpyruvate carboxylase/acetylornithine deacetylase |
| RA | 4,182,791 | A→G | D516G (GAC→GGC) | rpoB → | RNA polymerase, beta subunit |
| 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 | 4,328,811 | A→G | Q559Q (CAA→CAG) | crfC → | clamp‑binding sister replication fork colocalization protein, dynamin‑related |
| 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 | 4,366,113 | A→G | S221P (TCC→CCC) | dcuA ← | C4‑dicarboxylate antiporter |
| 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 | 4,606,215 | (G)8→9 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| 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 | 810368 | 3040 | 21 [13] | [13] 15 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857130 | 2859636 | 2507 | 15 [13] | [11] 15 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423769–3424232 | 3424545–3424240 | 9–777 | 15 [14] | [13] 15 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 4037941–4038687 | 4039303–4038731 | 45–1363 | 18 [14] | [14] 16 | rrlA | 23S ribosomal RNA of rrnA operon |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 20 (0.340) | 75 (1.470) | 48/192 | 0.0 | 84.2% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 11 (0.220) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 20 (0.340) | 27 (0.530) | 25/192 | 0.8 | 65.7% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 11 (0.220) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 47 (0.820) | 35/216 | 0.4 | 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 | |||||