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 | 21,581 | C→T | P59S (CCA→TCA) | ribF → | bifunctional riboflavin kinase/FAD synthetase |
| RA | 156,412 | T→G | T158P (ACA→CCA) | yadN ← | putative fimbrial‑like adhesin protein |
| RA | 199,121 | C→T | V398V (GTC→GTT) | bamA → | BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 630,819 | C→T | A309V (GCG→GTG) | cstA → | carbon starvation protein involved in peptide utilization, APC peptide transporter family protein |
| RA | 783,566 | (T)5→4 | coding (401/720 nt) | pnuC → | nicotinamide riboside transporter |
| RA | 1,042,246 | A→G | S655S (AGT→AGC) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,086,260 | G→A | A87V (GCC→GTC) | pgaD ← | biofilm PGA synthase PgaCD, regulatory subunit, c‑di‑GMP‑stimulated activity and dimerization |
| RA | 1,240,435 | T→C | Q546R (CAG→CGG) | cvrA ← | putative cation/proton antiporter |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,417,546 | (T)8→7 | coding (218/276 nt) | racC ← | Rac prophage, uncharacterized protein |
| RA | 1,426,252 | A→G | intergenic (+170/‑202) | ydaY → / → tmpR | pseudogene, Rac prophage,Phage or Prophage Related/Rac prophage, pseudogene, tail protein family,Phage or Prophage Related, putative alpha helix protein |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,467,061 | C→T | pseudogene (1670/2513 nt) | ydbA → | pseudogene, autotransporter homolog, interrupted by IS2 and IS30 |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,629,489 | G→A | G475G (GGC→GGT) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,756,216 | (A)5→4 | coding (519/1413 nt) | pykF → | pyruvate kinase I |
| RA | 1,818,550 | (C)7→8 | intergenic (‑50/+55) | chbF ← / ← chbR | phospho‑chitobiase, general 6‑phospho‑beta‑glucosidase activity/repressor of chb operon for N,N'‑diacetylchitobiose utilization |
| RA | 1,827,934 | G→A | A109V (GCC→GTC) | astB ← | succinylarginine dihydrolase |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,960,496 | T→C | T145T (ACT→ACC) | argS → | arginyl‑tRNA synthetase |
| RA | 1,973,169 | G→A | G57G (GGC→GGT) | cheW ← | purine‑binding chemotaxis protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,036,909 | T→C | Q415R (CAG→CGG) | yedV ← | putative sensory kinase in two‑component regulatory system with YedW |
| RA | 2,040,142 | T→C | V222A (GTA→GCA) | yedY → | membrane‑anchored, periplasmic TMAO, DMSO reductase |
| RA | 2,052,156 | C→T | intergenic (+142/+120) | yeeJ → / ← yeeL | putative adhesin/pseudogene, glycosyltransferase homology |
| 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 | 2,250,649 | C→T | H311H (CAC→CAT) | yeiH → | UPF0324 family inner membrane protein |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,509,025 | A→G | G134G (GGT→GGC) | glk ← | glucokinase |
| RA | 2,653,260 | T→C | V256A (GTG→GCG) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| 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 | 2,920,310 | A→G | V146A (GTC→GCC) | gudX ← | glucarate dehydratase‑related protein, substrate unknown |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,968,260 | (T)6→5 | coding (175/2247 nt) | ptsP ← | PEP‑protein phosphotransferase enzyme I, GAF domain containing protein |
| RA | 3,067,677 | G→A | A135V (GCG→GTG) | yggE ← | oxidative stress defense protein |
| RA | 3,081,469 | T→C | D56G (GAC→GGC) | tktA ← | transketolase 1, thiamine triphosphate‑binding |
| RA | 3,120,324 | A→G | V319A (GTG→GCG) | glcA ← | glycolate transporter |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,258,242 | (A)8→9 | intergenic (‑232/+43) | yhaO ← / ← tdcG | putative transporter/L‑serine dehydratase 3, anaerobic |
| RA | 3,269,600 | T→C | *396Q (TAG→CAG) | yhaC → | pentapetide repeats‑related protein |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| RA | 3,284,931 | A→G | T83A (ACC→GCC) | agaC → | N‑acetylgalactosamine‑specific enzyme IIC component of PTS |
| 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 | 3,560,455 | +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)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH |
| RA | 3,868,399 | C→T | C304Y (TGT→TAT) | yidR ← | DUF3748 family 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 |
| RA | 3,950,476 | (T)8→7 | intergenic (+56/‑31) | ilvL → / → ilvX | ilvG operon leader peptide/uncharacterized protein |
| RA | 4,185,540 | C→T | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime 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 | 4,490,935 | 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 | 4,554,430 | (T)7→8 | intergenic (+69/‑146) | uxuB → / → uxuR | D‑mannonate oxidoreductase, NAD‑dependent/fructuronate‑inducible hexuronate regulon transcriptional repressor, autorepressor |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| JC | 4,606,094 | (G)8→11 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,627,489 | T→C | F59L (TTT→CTT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,635,400 | (T)7→6 | intergenic (‑90/‑121) | rob ← / → creA | right oriC‑binding transcriptional activator, AraC family/putative periplasmic protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3754 | 3754 | 1 | 2 [0] | [0] 2 | thrC | L‑threonine synthase |
| * | * | ÷ | NC_000913 | 807332 | 810363 | 3032 | 2 [0] | [1] 2 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1530056 | 1530138 | 83 | 2 [1] | [1] 2 | ydcD | putative immunity protein for RhsE |
| * | * | ÷ | NC_000913 | 2857138 | 2859608 | 2471 | 9 [0] | [0] 4 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423793–3424232 | 3424520–3424240 | 9–728 | 2 [1] | [1] 2 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3455448 | 3455478 | 31 | 4 [0] | [1] 3 | gspA/gspC | general secretory pathway component, cryptic/general secretory pathway component, cryptic |
| * | * | ÷ | NC_000913 | 3603730 | 3603792 | 63 | 2 [0] | [1] 3 | ftsY | Signal Recognition Particle (SRP) receptor |