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 | 6,903 | T→C | T353A (ACC→GCC) | yaaJ ← | putative transporter |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 451,410 | C→T | W67* (TGG→TGA) | cyoA ← | cytochrome o ubiquinol oxidase subunit II |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 585,217 | C→T | W139* (TGG→TGA) | ompT ← | DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 852,261 | A→G | Y113H (TAC→CAC) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 856,434 | C→T | P158S (CCT→TCT) | ybiT → | ABC‑F family putative regulatory ATPase |
| RA | 1,043,741 | A→G | V157A (GTT→GCT) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,044,364 | T→C | T105A (ACA→GCA) | etp ← | O‑antigen capsule forming protein‑tyrosine‑phosphatase, Etk‑P dephosphorylase |
| RA | 1,112,317 | A→G | K485K (AAA→AAG) | opgH → | OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase, nutrient‑dependent cell size regulator, FtsZ assembly antagonist |
| RA | 1,136,783 | T→C | V170V (GTT→GTC) | flgI → | putative flagellar basal body protein |
| RA | 1,249,389 | G→A | A123A (GCC→GCT) | dhaL ← | dihydroxyacetone kinase, C‑terminal domain |
| RA | 1,276,719 | A→G | F300F (TTT→TTC) | narX ← | sensory histidine kinase in two‑component regulatory system with NarL |
| RA | 1,285,372 | A→G | E78E (GAA→GAG) | narJ → | molybdenum‑cofactor‑assembly chaperone delta subunit of nitrate reductase 1 |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| RA | 1,318,967 | G→A | D274D (GAC→GAT) | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| 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 | 1,399,120 | A→G | M136T (ATG→ACG) | fnr ← | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR, autorepressor |
| RA | 1,416,279 | A→G | S370P (TCC→CCC) | recE ← | Rac prophage, exonuclease VIII, 5' to 3' specific dsDNA exonuclease |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,474,310 | C→T | G30G (GGC→GGT) | ydbC → | putative NAD(P)‑binding oxidoreductase |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,610,596 | C→T | A29T (GCC→ACC) | uxaB ← | altronate oxidoreductase, NAD‑dependent |
| RA | 1,677,937 | T→C | intergenic (‑34/‑490) | pntA ← / → ydgH | pyridine nucleotide transhydrogenase, alpha subunit/DUF1471 family periplasmic protein |
| RA | 1,738,343 | A→G | Y167C (TAC→TGC) | purR → | transcriptional repressor, hypoxanthine‑binding |
| RA | 1,893,102 | G→A | A45V (GCA→GTA) | yoaA ← | putative ATP‑dependent helicase, DinG family |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,904,621 | G→A | V243I (GTA→ATA) | manZ → | mannose‑specific enzyme IID component of PTS |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,073,151 | T→C | L538P (CTG→CCG) | 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 | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,262,371 | G→A | G375G (GGC→GGT) | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| 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 | 2,346,057 | T→C | L398P (CTG→CCG) | nrdA → | ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,426,492 | A→G | R99R (CGT→CGC) | hisJ ← | histidine ABC transporter periplasmic binding protein |
| RA | 2,465,279 | T→C | intergenic (‑272/‑22) | mlaA ← / → yfdC | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component/putative inner membrane protein |
| RA | 2,547,591 | T→C | F307L (TTC→CTC) | murP → | N‑acetylmuramic acid permease, EIIBC component, PTS system |
| RA | 2,639,156 | T→C | N43S (AAC→AGC) | yfgM ← | ancillary SecYEG translocon subunit, putative anti‑RcsB factor |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,767,500 | T→C | intergenic (+145/‑210) | rnlB → / → yfjP | CP4‑57 prophage, uncharacterized protein/CP4‑57 prophage, 50S ribosome‑binding GTPase family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,867,926 | (C)6→7 | coding (828/1140 nt) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 2,910,133 | C→T | V185I (GTC→ATC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 2,966,732 | G→A | A568V (GCA→GTA) | ptsP ← | PEP‑protein phosphotransferase enzyme I, GAF domain containing protein |
| RA | 3,043,412 | G→A | A71V (GCA→GTA) | yqfB ← | UPF0267 family protein |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,222,930 | G→A | D100N (GAT→AAT) | ebgA → | evolved beta‑D‑galactosidase, alpha subunit |
| RA | 3,263,580 | A→G | C27C (TGT→TGC) | tdcD ← | propionate kinase/acetate kinase C, 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 | 3,386,276 | A→G | V638A (GTA→GCA) | aaeB ← | p‑hydroxybenzoic acid efflux system component |
| RA | 3,414,083 | A→T | I74F (ATC→TTC) | acrE → | cytoplasmic membrane lipoprotein |
| RA | 3,440,113 | A→G | V306A (GTG→GCG) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,450,125 | T→C | T37A (ACC→GCC) | rplV ← | 50S ribosomal subunit protein L22 |
| 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 |
| MC JC | 3,653,231 | Δ2,028 bp | IS5‑mediated | [yhiS]–[yhiD] | [yhiS], slp, dctR, [yhiD] |
| MC JC | 3,736,663 | (TTG)4→3 | coding (513‑515/825 nt) | bax ← | putative glucosaminidase |
| RA | 3,748,385 | G→A | A434A (GCG→GCA) | lyxK → | L‑xylulose kinase |
| 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 | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,928,356 | C→T | A416A (GCG→GCA) | viaA ← | stimulator of RavA ATPase activity, von Willebrand factor domain protein |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,142,011 | C→T | A71T (GCC→ACC) | frwA ← | putative PTS enzyme: Hpr, enzyme I and II components |
| RA | 4,185,540 | C→T | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,207,900 | C→T | intergenic (‑368/‑247) | purH ← / → rrsE | IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon |
| RA | 4,229,765 | A→G | A126A (GCT→GCC) | pepE ← | peptidase E, alpha‑aspartyl dipeptidase |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | yjcE → | putative cation/proton antiporter |
| RA | 4,285,518 | A→G | I618I (ATT→ATC) | acs ← | acetyl‑CoA synthetase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,318,211 | A→G | L185P (CTC→CCC) | phnK ← | carbon‑phosphorus lyase complex subunit, putative ATP transporter ATP‑binding 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 | 4,392,496 | C→T | noncoding (25/76 nt) | glyX → | tRNA‑Gly |
| 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 | 4,544,910 | G→A | V203M (GTG→ATG) | fimC → | periplasmic chaperone |
| RA | 4,565,986 | A→G | F421L (TTC→CTC) | yjiN ← | zinc‑type alcohol dehydrogenase‑like protein |
| RA | 4,574,101 | T→C | pseudogene (183/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| 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 | 807314 | 810368 | 3055 | 22 [20] | [18] 22 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857129 | 2859629 | 2501 | 22 [14] | [19] 21 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423763–3424233 | 3424558–3424242 | 10–796 | 21 [19] | [20] 26 | [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) | 61 (0.850) | 41/206 | 0.5 | 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 | |||||