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 | 7,361 | A→G | V200A (GTC→GCC) | yaaJ ← | putative transporter |
| RA | 96,614 | A→G | T205A (ACC→GCC) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide transferase |
| 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 | 191,580 | G→A | V242I (GTT→ATT) | tsf → | translation elongation factor EF‑Ts |
| 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 | 403,334 | C→T | T18T (ACC→ACT) | psiF → | PsiF family protein |
| RA | 429,170 | G→A | A508A (GCG→GCA) | secD → | SecYEG protein translocase auxillary subunit |
| 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 | 497,009 | A→G | intergenic (+15/‑166) | htpG → / → adk | protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase/adenylate kinase |
| 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 | 701,504 | Δ1 bp | coding (91/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 704,128 | C→T | S62F (TCC→TTC) | nagE → | N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components |
| RA | 713,720 | A→G | S55G (AGC→GGC) | pgm → | phosphoglucomutase |
| RA | 731,826 | C→T | G748G (GGC→GGT) | rhsC → | Rhs protein with putative toxin domain; putative neighboring cell growth inhibitor |
| RA | 736,382 | T→C | intergenic (+163/‑63) | ybfC → / → ybfQ | putative secreted protein/pseudogene, H repeat‑associated protein |
| RA | 890,338 | (T)7→6 | coding (250/378 nt) | ybjM → | inner membrane protein |
| RA | 942,738 | C→T | R594W (CGG→TGG) | dmsA → | dimethyl sulfoxide reductase, anaerobic, subunit A |
| RA | 1,068,545 | A→G | V432A (GTT→GCT) | rutG ← | pyrimidine permease |
| RA | 1,132,321 | C→T | T156T (ACC→ACT) | flgD → | flagellar hook assembly protein |
| RA | 1,165,959 | A→G | intergenic (+274/‑126) | ycfP → / → ndh | putative UPF0227 family esterase/respiratory NADH dehydrogenase 2/cupric reductase |
| RA | 1,188,526 | G→A | G417G (GGC→GGT) | phoQ ← | sensory histidine kinase in two‑component regulatory system with PhoP |
| 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 | 1,407,641 | 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 | 1,464,068 | T→C | L177P (CTT→CCT) | paaX → | transcriptional repressor of phenylacetic acid degradation paa operon, phenylacetyl‑CoA inducer |
| RA | 1,496,777 | T→C | intergenic (+146/‑79) | ydcJ → / → opgD | putative metalloenzyme/OPG biosynthetic periplasmic protein |
| RA | 1,595,660 | A→G | pseudogene (2328/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,596,244 | A→G | pseudogene (1744/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,597,313 | (C)7→8 | pseudogene (675/3861 nt) | yneO ← | pseudogene, AidA homolog |
| 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 | 1,655,247 | Δ1 bp | intergenic (‑106/+100) | rspA ← / ← ynfA | bifunctional D‑altronate/D‑mannonate dehydratase/UPF0060 family inner membrane protein |
| RA | 1,691,784 | A→G | S356S (AGT→AGC) | uidC ← | putative outer membrane porin for beta‑glucuronides porin protein |
| RA | 1,714,326 | (T)9→8 | intergenic (+55/‑51) | dtpA → / → gstA | dipeptide and tripeptide permease A/glutathionine S‑transferase |
| RA | 1,759,788 | T→C | M246V (ATG→GTG) | sufS ← | cysteine desulfurase, stimulated by SufE; selenocysteine lyase, PLP‑dependent |
| RA | 1,805,473 | A→G | L204P (CTG→CCG) | ydiY ← | acid‑inducible putative outer membrane protein |
| RA | 1,861,259 | C→T | G25D (GGC→GAC) | ydjL ← | putative Zn‑dependent NAD(P)‑binding oxidoreductase |
| RA | 1,876,677 | A→G | A335A (GCA→GCG) | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,877,132 | A→G | H75R (CAC→CGC) | yeaO → | DUF488 family protein |
| RA | 1,901,602 | A→G | intergenic (‑17/‑446) | yoaE ← / → manX | putative membrane protein/conserved protein/fused mannose‑specific PTS enzymes: IIA component/IIB component |
| 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 | 1,990,332 | T→C | F218L (TTT→CTT) | tyrP → | tyrosine transporter |
| RA | 2,113,546 | T→G | Y261S (TAC→TCC) | wcaN ← | putative regulatory subunit for GalU |
| 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 | 2,173,363 | 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 | 2,223,301 | 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 | 2,487,085 | A→G | L904L (TTA→TTG) | evgS → | hybrid sensory histidine kinase in two‑component regulatory system with EvgA |
| 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 | 2,682,677 | T→C | I23M (ATA→ATG) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,734,534 | +C | coding (501/732 nt) | yfiH ← | UPF0124 family protein |
| JC | 2,734,535 | Δ3 bp | coding (498‑500/732 nt) | yfiH ← | UPF0124 family 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 | 2,825,128 | A→G | V150A (GTA→GCA) | mltB ← | membrane‑bound lytic murein transglycosylase B |
| 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 | 2,851,919 | T→C | V19A (GTC→GCC) | hypC → | hydrogenase maturation protein |
| 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 | 3,103,474 | G→A | W154* (TGG→TGA) | mutY → | adenine DNA glycosylase |
| RA | 3,128,355 | T→C | G28G (GGT→GGC) | glcC → | glycolate‑inducible glc operon transcriptional repressor; autorepressor |
| RA | 3,356,384 | T→C | S554P (TCG→CCG) | gltB → | glutamate synthase, large subunit |
| RA | 3,404,872 | T→C | pseudogene (141/300 nt) | yrdE → | pseudogene, yedZ paralog |
| RA | 3,430,876 | A→G | D180D (GAT→GAC) | tsaC ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine‑dependent ADP‑forming ATPase |
| RA | 3,439,982 | A→G | S6S (AGT→AGC) | rplQ ← | 50S ribosomal subunit protein L17 |
| 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 | 3,551,418 | C→T | A352A (GCG→GCA) | malP ← | maltodextrin phosphorylase |
| 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 | 3,638,806 | G→A | A389T (GCG→ACG) | pitA → | phosphate transporter, low‑affinity; tellurite importer |
| RA | 3,664,969 | (T)8→7 | intergenic (‑351/+17) | gadW ← / ← gadX | transcriptional activator of gadA and gadBC; repressor of gadX/acid resistance regulon transcriptional activator; autoactivator |
| RA | 3,720,934 | T→C | A85A (GCT→GCC) | insJ → | IS150 transposase A |
| RA | 3,773,127 | A→G | T283A (ACG→GCG) | mtlA → | mannitol‑specific PTS enzyme: IIA, IIB and IIC components |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,844,146 | T→C | G61G (GGT→GGC) | adeD → | cryptic adenine deaminase |
| RA | 3,908,659 | A→G | F261L (TTT→CTT) | pstA ← | phosphate ABC transporter permease |
| RA | 3,967,132 | A→G | H239R (CAC→CGC) | rho → | transcription termination factor |
| 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 |
| JC JC | 4,160,984 | IS2 (+) +5 bp | intergenic (‑194/‑136) | sthA ← / → fabR | pyridine nucleotide transhydrogenase, soluble/transcriptional repressor of fabA and fabB |
| RA | 4,161,391 | A→G | T90A (ACC→GCC) | fabR → | transcriptional repressor of fabA and fabB |
| 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 | 4,351,421 | C→T | G81D (GGC→GAC) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,381,504 | T→C | E272G (GAA→GGA) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,407,982 | T→C | R443R (CGT→CGC) | rnr → | exoribonuclease R, RNase R |
| RA | 4,417,719 | C→T | G245G (GGG→GGA) | ulaR ← | transcriptional repressor for the L‑ascorbate utilization divergent operon |
| RA | 4,423,096 | T→C | L84P (CTG→CCG) | ulaE → | L‑xylulose 5‑phosphate 3‑epimerase |
| RA | 4,431,246 | T→C | G461G (GGT→GGC) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,441,918 | A→G | C87R (TGC→CGC) | msrA ← | methionine sulfoxide reductase A |
| RA | 4,485,819 | C→T | A45T (GCC→ACC) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,619,018 | A→G | T264A (ACG→GCG) | deoA → | thymidine phosphorylase |
| RA | 4,627,935 | C→T | S207S (AGC→AGT) | nadR → | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor |
| RA | 4,632,098 | T→C | W456R (TGG→CGG) | slt → | lytic murein transglycosylase, soluble |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423723–3424234 | 3424582–3424238 | 5–860 | 70 [66] | [69] 70 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 21 (0.180) | 83 (0.780) | 65/266 | 1.2 | 78.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 26 (0.250) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 21 (0.180) | 86 (0.810) | 75/266 | 0.5 | 79.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 26 (0.250) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 101 (0.880) | 74/290 | 1.0 | 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 | |||||