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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 375,067 | A→G | intergenic (+186/‑392) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 375,075 | G→A | intergenic (+194/‑384) | mhpE → / → mhpT | 4‑hyroxy‑2‑oxovalerate/4‑hydroxy‑2‑oxopentanoic acid aldolase, class I/3‑hydroxyphenylpropionic transporter |
| RA | 380,021 | (G)10→8 | intergenic (‑140/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 404,123 | (C)5→4 | coding (421/1116 nt) | yaiC → | diguanylate cyclase, cellulose regualtor |
| RA | 467,458 | C→T | P16L (CCC→CTC) | cof → | thiamine pyrimidine pyrophosphate hydrolase, HMP‑PP phosphatase |
| RA | 543,768 | A→G | T93T (ACT→ACC) | allE ← | S‑ureidoglycine aminohydrolase |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 585,317 | C→T | W106* (TGG→TAG) | ompT ← | DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 593,467 | T→G | D435A (GAC→GCC) | cusS ← | copper‑sensing histidine kinase in two‑component regulatory system with CusR |
| RA | 600,470 | C→T | A586V (GCG→GTG) | cusA → | copper/silver efflux system, membrane component |
| RA | 738,087 | A→G | intergenic (+126/‑5) | ybfL → / → ybfD | pseudogene, DDE domain transposase family,putative factor, Not classified, putative receptor protein/H repeat‑associated putative transposase |
| RA | 746,063 | A→G | Q43Q (CAA→CAG) | nei → | endonuclease VIII and 5‑formyluracil/5‑hydroxymethyluracil DNA glycosylase |
| RA | 807,343 | C→G | intergenic (‑62/+90) | ybhC ← / ← ybhB | acyl‑CoA thioesterase, lipoprotein/kinase inhibitor homolog, UPF0098 family |
| RA | 857,298 | C→T | R446W (CGG→TGG) | ybiT → | ABC‑F family putative regulatory ATPase |
| RA | 867,319 | A→G | Y251C (TAC→TGC) | iaaA → | Isoaspartyl peptidase |
| RA | 936,202 | C→T | T993T (ACC→ACT) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 989,319 | (G)5→6 | coding (1038/1203 nt) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,036,083 | C→T | A105V (GCG→GTG) | hyaD → | hydrogenase 1 maturation protease |
| RA | 1,077,868 | G→A | R339C (CGC→TGC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| JC | 1,198,498 | (AATGATGA)6→5 | intergenic (‑261/‑190) | ymfE ← / → lit | e14 prophage, putative inner membrane protein/T4 phage exclusion protein, cell death peptidase, e14 prophage |
| RA | 1,276,337 | G→A | R428C (CGC→TGC) | narX ← | sensory histidine kinase in two‑component regulatory system with NarL |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| 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 | 1,421,650 | (C)7→8 | coding (532/858 nt) | ydaU → | Rac prophage, conserved protein |
| RA | 1,428,875 | T→C | pseudogene (80/189 nt) | lomR → | pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,504,515 | C→T | R267C (CGC→TGC) | insQ → | IS609 transposase B |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,702,700 | T→C | F156F (TTT→TTC) | add → | adenosine deaminase |
| RA | 1,722,854 | T→C | L245P (CTC→CCC) | ydhK → | putative efflux protein (PET) component of YdhJK efflux pump |
| RA | 1,873,602 | C→T | T10M (ACG→ATG) | yeaK → | aminoacyl‑tRNA editing domain 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 | 1,995,320 | G→A | R14C (CGC→TGC) | uvrY ← | response regulator in two‑component regulatory system with BarA |
| RA | 2,073,094 | T→C | L519P (CTG→CCG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,166,540 | T→C | R291R (CGT→CGC) | yegQ → | putative peptidase |
| 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 | 2,185,875 | (G)7→6 | intergenic (‑79/‑42) | rcnR ← / → rcnA | transcriptional repressor of rcnA/membrane protein conferring nickel and cobalt resistance |
| RA | 2,238,421 | T→C | E290G (GAG→GGG) | mglA ← | methyl‑galactoside ABC transporter ATPase |
| RA | 2,277,291 | C→T | A331V (GCG→GTG) | yejF → | microcin C ABC transporter ATPase |
| RA | 2,314,922 | T→C | S479P (TCC→CCC) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,380,852 | T→C | D59G (GAC→GGC) | elaB ← | putative membrane‑anchored DUF883 family ribosome‑binding protein |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,631,531 | G→A | G335G (GGC→GGT) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,771,806 | A→T | intergenic (+191/+196) | yfjT → / ← yfjU | CP4‑57 prophage, putative periplasmic protein/CP4‑57 prophage, conserved protein,Phage or Prophage Related |
| RA | 2,829,493 | G→A | S149S (TCG→TCA) | srlR → | sorbitol‑inducible srl operon transcriptional repressor |
| RA | 2,834,077 | G→A | A56T (GCC→ACC) | norW → | NADH:flavorubredoxin oxidoreductase |
| 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 | 2,968,916 | T→C | Q21R (CAG→CGG) | rppH ← | RNA pyrophosphohydrolase |
| RA | 3,066,288 | T→C | T296A (ACG→GCG) | ygfI ← | putative DNA‑binding transcriptional regulator |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,177,274 | G→A | R3C (CGT→TGT) | yqiB ← | DUF1249 protein YqiB |
| RA | 3,194,362 | (G)6→7 | coding (1499/1662 nt) | yqiK → | PHB family membrane protein, function unknown |
| RA | 3,271,600 | (C)5→7 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| 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 | 3,638,618 | T→C | V326A (GTG→GCG) | pitA → | phosphate transporter, low‑affinity, tellurite importer |
| RA | 3,709,561 | (C)6→7 | coding (915/1692 nt) | eptB ← | KDO phosphoethanolamine transferase, Ca(2+)‑inducible |
| RA | 3,720,202 | T→C | S52P (TCC→CCC) | cspA → | RNA chaperone and antiterminator, cold‑inducible |
| RA | 3,728,118 | (C)8→9 | coding (1254/1455 nt) | xylB ← | xylulokinase |
| RA | 3,790,538 | A→G | S270P (TCT→CCT) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,813 | A→G | intergenic (‑45/+21) | 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 | 3,920,872 | G→A | T6I (ACA→ATA) | atpF ← | F0 sector of membrane‑bound ATP synthase, subunit b |
| RA | 3,932,121 | A→G | N269S (AAC→AGC) | kup → | potassium transporter |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 3,959,758 | A→G | L19P (CTG→CCG) | ppiC ← | peptidyl‑prolyl cis‑trans isomerase C (rotamase C) |
| RA | 4,183,238 | C→T | A665V (GCG→GTG) | 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 | 4,304,888 | A→G | N570N (AAT→AAC) | yjcS ← | metallo‑beta‑lactamase superfamily 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 | 4,574,259 | 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807347 | 810368 | 3022 | 9 [0] | [7] 9 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 2857138 | 2859626 | 2489 | 12 [0] | [8] 9 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423785–3424233 | 3424530–3424241 | 9–746 | 9 [7] | [7] 9 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 59 (1.170) | 20 (0.460) | 19/192 | 0.9 | 32.4% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 33 (0.760) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 78 (1.600) | 52/216 | 0.0 | 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 | |||||