mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.29.0 revision 8f9c342918e4
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 89,556 | A→G | intergenic (+524/‑78) | cra → / → mraZ | transcriptional repressor‑activator for carbon metabolism/RsmH methytransferase inhibitor |
| RA | 134,458 | T→C | V24A (GTC→GCC) | yacL → | UPF0231 family protein |
| RA | 170,334 | T→C | V186A (GTG→GCG) | fhuC → | iron(3+)‑hydroxamate import ABC transporter ATPase |
| RA | 187,251 | G→A | T467M (ACG→ATG) | glnD ← | uridylyltransferase |
| RA | 218,835 | (A)8→7 | intergenic (‑60/+52) | proS ← / ← tsaA | prolyl‑tRNA synthetase/tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 277,333 | A→G | T207A (ACG→GCG) | mmuM → | CP4‑6 prophage; S‑methylmethionine:homocysteine methyltransferase |
| RA | 284,450 | A→G | E417G (GAG→GGG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | ECP production outer membrane protein |
| RA | 339,842 | T→C | intergenic (+99/‑323) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 339,848 | T→C | intergenic (+105/‑317) | yahG → / → yahI | DUF1116 family protein/carbamate kinase‑like protein |
| RA | 346,248 | (A)7→8 | coding (90/672 nt) | yahN ← | amino acid exporter for proline, lysine, glutamate, homoserine |
| RA | 376,673 | T→C | intergenic (+3/‑99) | mhpT → / → yaiL | 3‑hydroxyphenylpropionic transporter/DUF2058 family protein |
| RA | 384,199 | C→T | V140I (GTT→ATT) | yaiS ← | putative PIG‑L family deacetylase |
| RA | 404,111 | (G)5→6 | coding (409/1116 nt) | yaiC → | diguanylate cyclase, cellulose regualtor |
| RA | 483,535 | C→T | G290E (GGG→GAG) | acrB ← | multidrug efflux system protein |
| RA | 484,337 | (C)6→7 | coding (67/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 487,092 | T→C | L186P (CTG→CCG) | mscK → | mechanosensitive channel protein, intermediate conductance, K+ regulated |
| RA | 657,377 | T→C | V29A (GTG→GCG) | cspE → | constitutive cold shock family transcription antitermination protein; negative regulator of cspA transcription; RNA melting protein; ssDNA‑binding protein |
| RA | 702,598 | A→G | S52P (TCC→CCC) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 713,720 | A→G | S55G (AGC→GGC) | pgm → | phosphoglucomutase |
| RA | 736,382 | T→C | intergenic (+163/‑63) | ybfC → / → ybfQ | putative secreted protein/pseudogene, H repeat‑associated protein |
| RA | 807,696 | C→T | D72N (GAT→AAT) | ybhB ← | kinase inhibitor homolog, UPF0098 family |
| RA | 810,116 | A→G | Y258C (TAC→TGC) | bioB → | biotin synthase |
| RA | 851,958 | G→A | P214S (CCG→TCG) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 878,968 | A→G | D76G (GAC→GGC) | yliI → | soluble aldose sugar dehydrogenase |
| RA | 886,290 | A→G | A350A (GCT→GCC) | ybjJ ← | putative drug efflux MFS transporter, inner membrane protein |
| RA | 942,738 | C→T | R594W (CGG→TGG) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 1,010,679 | A→G | D239G (GAC→GGC) | uup → | replication regulatory ABC‑F family DNA‑binding ATPase |
| RA | 1,132,321 | C→T | T156T (ACC→ACT) | flgD → | flagellar hook assembly protein |
| RA | 1,151,492 | (G)6→7 | intergenic (+88/‑123) | fabG → / → acpP | 3‑oxoacyl‑[acyl‑carrier‑protein] reductase/acyl carrier protein (ACP) |
| RA | 1,212,088 | (C)8→9 | intergenic (‑85/+615) | iraM ← / ← ycgX | RpoS stabilzer during Mg starvation, anti‑RssB factor/DUF1398 family protein |
| RA | 1,259,406 | G→A | G466G (GGC→GGT) | dauA ← | C4‑dicarboxylic acid transporter |
| RA | 1,270,861 | A→G | V330A (GTG→GCG) | chaA ← | calcium/sodium:proton antiporter |
| RA | 1,307,516 | A→G | V377A (GTC→GCC) | clsA ← | cardiolipin synthase 1 |
| 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 | 1,407,641 | A→G | V52A (GTC→GCC) | ydaM ← | diguanylate cyclase, csgD regulator |
| RA | 1,419,721 | (G)7→6 | intergenic (‑265/+44) | ydaG ← / ← racR | Rac prophage; uncharacterized protein/Rac prophage; putative DNA‑binding transcriptional regulator |
| RA | 1,444,706 | C→T | G552G (GGC→GGT) | ydbH → | putative membrane‑anchored protein, function unknown |
| RA | 1,449,092 | A→G | L753P (CTG→CCG) | tynA ← | tyramine oxidase, copper‑requiring |
| RA | 1,472,600 | T→C | pseudogene (2084/3497 nt) | ydbA → | pseudogene, autotransporter homolog; interrupted by IS2 and IS30 |
| RA | 1,490,800 | A→G | intergenic (‑87/‑102) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| RA | 1,494,068 | A→G | E533E (GAA→GAG) | trg → | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| RA | 1,496,777 | T→C | intergenic (+146/‑79) | ydcJ → / → opgD | putative metalloenzyme/OPG biosynthetic periplasmic protein |
| RA | 1,570,469 | T→C | T7T (ACA→ACG) | gadC ← | glutamate:gamma‑aminobutyric acid antiporter |
| RA | 1,594,053 | (C)6→7 | pseudogene (73/1461 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,660 | A→G | pseudogene (2328/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,597,313 | (C)7→8 | pseudogene (675/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,636,877 | T→C | V41A (GTC→GCC) | ynfO → | uncharacterized protein, Qin prophage |
| RA | 1,639,617 | T→C | G147G (GGA→GGG) | rrrQ ← | Qin prophage; putative lysozyme |
| RA | 1,646,854 | C→T | intergenic (+117/+320) | flxA → / ← intK | Qin prophage; uncharacterized protein/pseudogene, integrase fragment, Qin prophage;Phage or Prophage Related |
| RA | 1,664,083 | T→C | L159L (TTG→CTG) | ynfH → | oxidoreductase, membrane subunit |
| RA | 1,691,784 | A→G | S356S (AGT→AGC) | uidC ← | putative outer membrane porin for beta‑glucuronides porin protein |
| RA | 1,710,621 | G→A | D140N (GAC→AAC) | rsxG → | SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide and tripeptide permease A/glutathionine S‑transferase |
| RA | 1,719,070 | A→G | I178T (ATT→ACT) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,833,205 | G→A | A260T (GCC→ACC) | xthA → | exonuclease III |
| RA | 1,862,504 | Δ1 bp | intergenic (‑75/‑267) | msrB ← / → gapA | methionine sulfoxide reductase B/glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,877,132 | A→G | H75R (CAC→CGC) | yeaO → | DUF488 family protein |
| RA | 1,967,082 | T→C | K119R (AAA→AGA) | cheY ← | chemotaxis regulator transmitting signal to flagellar motor component |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,045,143 | T→C | V69A (GTG→GCG) | yeeJ → | putative adhesin |
| RA | 2,081,148 | T→C | S39G (AGC→GGC) | sbmC ← | DNA gyrase inhibitor |
| RA | 2,114,010 | T→C | E106E (GAA→GAG) | wcaN ← | putative regulatory subunit for GalU |
| RA | 2,130,464 | T→C | T139A (ACC→GCC) | wcaD ← | putative colanic acid polymerase |
| RA | 2,140,009 | T→C | D535G (GAC→GGC) | asmA ← | suppressor of OmpF assembly mutants; putative outer membrane protein assembly factor; inner membrane‑anchored periplasmic protein |
| RA | 2,160,028 | C→T | P548L (CCG→CTG) | mdtC → | multidrug efflux system, subunit C |
| 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 | 2,210,118 | T→C | pseudogene (1019/2001 nt) | yehQ → | pseudogene |
| RA | 2,223,301 | T→C | F373L (TTC→CTC) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,264,624 | C→T | A254A (GCC→GCT) | setB → | lactose/glucose efflux system |
| RA | 2,279,534 | G→A | P76L (CCG→CTG) | bcr ← | bicyclomycin/cysteine/sulfonamide efflux transporter |
| RA | 2,464,296 | C→T | A238T (GCA→ACA) | mlaA ← | ABC transporter maintaining OM lipid asymmetry, OM lipoprotein component |
| RA | 2,536,495 | G→A | A248V (GCG→GTG) | pdxK ← | pyridoxal‑pyridoxamine kinase/hydroxymethylpyrimidine kinase |
| RA | 2,575,242 | A→G | H72H (CAT→CAC) | eutP ← | putative P‑loop NTPase ethanolamine utilization protein |
| RA | 2,657,699 | T→C | T413A (ACC→GCC) | hscA ← | DnaK‑like molecular chaperone specific for IscU |
| RA | 2,665,669 | A→G | T79A (ACA→GCA) | csiE → | stationary phase inducible protein |
| RA | 2,747,020 | G→A | A259V (GCG→GTG) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| RA | 2,809,534 | T→C | intergenic (+41/‑83) | ygaY → / → ygaZ | pseudogene, major facilitator transporter superfamily;putative transport; Not classified; putative transport protein/putative L‑valine exporter, norvaline resistance protein |
| RA | 2,812,356 | T→C | G310G (GGT→GGC) | emrA → | multidrug efflux system |
| RA | 2,832,456 | C→T | intergenic (‑167/‑20) | norR ← / → norV | anaerobic nitric oxide reductase DNA‑binding transcriptional activator/anaerobic nitric oxide reductase flavorubredoxin |
| RA | 2,858,929 | A→C | T613P (ACC→CCC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,913,035 | A→G | L206P (CTC→CCC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,913,196 | T→C | K152K (AAA→AAG) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| MC JC | 3,018,356 | (GTC)4→3 | coding (2297‑2299/3099 nt) | ygfK → | putative Fe‑S subunit oxidoreductase subunit |
| RA | 3,350,184 | (C)7→8 | coding (276/654 nt) | elbB ← | isoprenoid biosynthesis protein with amidotransferase‑like domain |
| RA | 3,356,384 | T→C | S554P (TCG→CCG) | gltB → | glutamate synthase, large subunit |
| RA | 3,400,928 | C→T | A54T (GCA→ACA) | mreB ← | cell wall structural complex MreBCD, actin‑like component MreB |
| RA | 3,404,872 | T→C | pseudogene (141/300 nt) | yrdE → | pseudogene, yedZ paralog |
| RA | 3,439,982 | A→G | S6S (AGT→AGC) | rplQ ← | 50S ribosomal subunit protein L17 |
| RA | 3,440,068 | C→T | W321* (TGG→TAG) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,440,822 | T→C | T70A (ACC→GCC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,462,301 | A→G | T110A (ACG→GCG) | gspI → | general secretory pathway component, cryptic |
| RA | 3,486,190 | A→G | Y24C (TAC→TGC) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,497,615 | T→C | F205L (TTC→CTC) | nirC → | nitrite transporter |
| RA | 3,505,884 | A→G | L46P (CTG→CCG) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| 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 | 3,588,203 | A→G | H326H (CAT→CAC) | ugpC ← | sn‑glycerol‑3‑phosphate ABC transporter ATPase |
| RA | 3,606,883 | G→A | E145K (GAG→AAG) | zntA → | zinc, cobalt and lead efflux system |
| RA | 3,629,003 | T→C | D179G (GAC→GGC) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,831,451 | A→G | E332G (GAA→GGA) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,844,146 | T→C | G61G (GGT→GGC) | adeD → | cryptic adenine deaminase |
| RA | 3,903,155 | C→T | G183S (GGC→AGC) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 3,967,132 | A→G | H239R (CAC→CGC) | rho → | transcription termination factor |
| RA | 4,106,405 | T→C | intergenic (+85/‑64) | cpxP → / → fieF | inhibitor of the cpx response; periplasmic adaptor protein/ferrous iron and zinc transporter |
| RA | 4,109,551 | C→T | P240S (CCA→TCA) | sbp → | sulfate transporter subunit |
| RA | 4,114,622 | A→G | S320P (TCC→CCC) | glpX ← | fructose 1,6‑bisphosphatase II |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,134,394 | A→G | D187G (GAC→GGC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,180,463 | T→C | A156A (GCT→GCC) | rplJ → | 50S ribosomal subunit protein L10 |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,338,117 | (A)8→7 | intergenic (‑188/+137) | adiY ← / ← adiA | adi system transcriptional activator/arginine decarboxylase |
| RA | 4,346,191 | A→G | V379A (GTA→GCA) | fumB ← | anaerobic class I fumarate hydratase (fumarase B) |
| RA | 4,381,504 | T→C | E272G (GAA→GGA) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,382,478 | C→A | intergenic (‑160/‑165) | frdA ← / → epmA | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit/Elongation Factor P Lys34 lysyltransferase |
| RA | 4,407,982 | T→C | R443R (CGT→CGC) | rnr → | exoribonuclease R, RNase R |
| RA | 4,485,819 | C→T | A45T (GCC→ACC) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,533,553 | A→G | L78L (TTG→CTG) | yjhQ ← | GNAT family putative N‑acetyltransferase |
| RA | 4,556,769 | (T)9→8 | intergenic (‑449/‑224) | yjiC ← / → iraD | uncharacterized protein/RpoS stabilzer after DNA damage, anti‑RssB factor |
| RA | 4,600,526 | A→G | G150G (GGT→GGC) | dnaC ← | DNA biosynthesis protein |
| RA | 4,619,018 | A→G | T264A (ACG→GCG) | deoA → | thymidine phosphorylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423719–3424234 | 3424586–3424238 | 5–868 | 32 [28] | [30] 31 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| * | * | ÷ | NC_000913 | 4166365–4168219 | 4171617–4168572 | 354–5253 | 31 [30] | [30] 33 | rrsB–rrlB | rrsB, gltT, rrlB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 58 (0.970) | 51/290 | 0.3 | 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 | |||||