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 | 47,849 | T→C | G27G (GGT→GGC) | kefC → | potassium:proton antiporter |
| RA | 134,458 | T→C | V24A (GTC→GCC) | yacL → | UPF0231 family protein |
| RA | 255,022 | A→G | V232A (GTG→GCG) | pepD ← | aminoacyl‑histidine dipeptidase (peptidase D) |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 284,450 | A→G | E417G (GAG→GGG) | yagF → | CP4‑6 prophage; dehydratase family protein |
| RA | 318,798 | T→C | M402V (ATG→GTG) | rclA ← | reactive chlorine stress species (RCS) resistance protein; pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 361,642 | A→G | G73G (GGT→GGC) | lacA ← | thiogalactoside acetyltransferase |
| RA | 380,022 | (G)10→9 | intergenic (‑141/+47) | frmR ← / ← yaiO | regulator protein that represses frmRAB operon/outer membrane protein |
| RA | 388,710 | T→C | intergenic (+64/+43) | tauD → / ← hemB | taurine dioxygenase, 2‑oxoglutarate‑dependent/5‑aminolevulinate dehydratase (porphobilinogen synthase) |
| RA | 400,157 | T→C | Y256C (TAC→TGC) | ddlA ← | D‑alanine‑D‑alanine ligase A |
| RA | 418,974 | A→G | A362A (GCA→GCG) | phoR → | sensory histidine kinase in two‑component regulatory system with PhoB |
| RA | 451,552 | A→G | V20A (GTA→GCA) | cyoA ← | cytochrome o ubiquinol oxidase subunit II |
| RA | 460,036 | C→T | G383G (GGC→GGT) | lon → | DNA‑binding ATP‑dependent protease La |
| RA | 585,303 | T→C | N111D (AAC→GAC) | ompT ← | DLP12 prophage; outer membrane protease VII; outer membrane protein 3b |
| RA | 599,828 | T→C | L372P (CTG→CCG) | cusA → | copper/silver efflux system, membrane component |
| 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 | 783,506 | C→T | A114V (GCG→GTG) | pnuC → | nicotinamide riboside transporter |
| RA | 871,451 | T→C | L162P (CTG→CCG) | gsiC → | glutathione ABC transporter permease |
| RA | 902,102 | A→G | L50P (CTG→CCG) | artQ ← | arginine ABC transporter permease |
| RA | 903,872 | (G)5→6 | intergenic (‑138/+80) | artP ← / ← ybjP | arginine ABC transporter ATPase/lipoprotein |
| RA | 909,056 | T→C | Q80R (CAG→CGG) | ltaE ← | L‑allo‑threonine aldolase, PLP‑dependent |
| RA | 910,826 | C→G | G75A (GGC→GCC) | poxB ← | pyruvate dehydrogenase, thiamine triphosphate‑binding, FAD‑binding |
| RA | 983,159 | T→C | F29L (TTT→CTT) | ycbK → | M15A protease‑related family periplasmic protein |
| RA | 1,042,089 | T→C | S708G (AGC→GGC) | etk ← | tyrosine‑protein kinase, role in O‑antigen capsule formation |
| RA | 1,076,582 | A→G | R767R (CGT→CGC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,133,069 | A→G | T166A (ACT→GCT) | flgE → | flagellar hook protein |
| RA | 1,140,553 | A→G | H174R (CAC→CGC) | flgL → | flagellar hook‑filament junction protein |
| RA | 1,169,838 | T→C | G179G (GGA→GGG) | ldtC ← | L,D‑transpeptidase linking Lpp to murein |
| RA | 1,216,705 | A→G | intergenic (+70/‑43) | ariR → / → ymgC | RcsB connector protein for regulation of biofilm and acid‑resistance/Blue light, low temperature and stress induced protein |
| RA | 1,242,307 | C→T | L258L (CTG→CTA) | ldcA ← | murein tetrapeptide carboxypeptidase; LD‑carboxypeptidase A |
| RA | 1,245,862 | (C)6→7 | coding (1515/1698 nt) | treA ← | periplasmic trehalase |
| RA | 1,297,386 | A→G | C246R (TGT→CGT) | adhE ← | fused acetaldehyde‑CoA dehydrogenase/iron‑dependent alcohol dehydrogenase/pyruvate‑formate lyase deactivase |
| RA | 1,307,916 | C→T | D244N (GAT→AAT) | clsA ← | cardiolipin synthase 1 |
| RA | 1,312,802 | A→T | I30N (ATC→AAC) | yciB ← | IspA family inner membrane protein |
| RA | 1,437,422 | T→C | A1121A (GCA→GCG) | pfo ← | pyruvate‑flavodoxin oxidoreductase |
| RA | 1,483,925 | A→G | S289G (AGC→GGC) | hrpA → | putative ATP‑dependent helicase |
| RA | 1,499,529 | A→G | G307G (GGT→GGC) | ydcK ← | uncharacterized protein |
| RA | 1,551,710 | T→C | F125L (TTC→CTC) | fdnI → | formate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible |
| RA | 1,597,313 | (C)7→8 | pseudogene (675/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,626,022 | A→G | A453A (GCT→GCC) | dcp ← | dipeptidyl carboxypeptidase II |
| RA | 1,708,662 | C→G | Q582E (CAA→GAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| RA | 1,756,617 | A→G | D307G (GAC→GGC) | pykF → | pyruvate kinase I |
| RA | 1,793,850 | (C)6→7 | coding (260/552 nt) | btuE ← | glutathione peroxidase |
| RA | 1,870,836 | T→C | L151P (CTG→CCG) | yeaI → | putative membrane‑anchored diguanylate cyclase |
| RA | 1,876,662 | G→A | A330A (GCG→GCA) | yeaN → | putative MFS transporter, inner membrane protein |
| RA | 1,954,322 | T→C | L294P (CTG→CCG) | cmoB → | tRNA (cmo5U34)‑carboxymethyltransferase, carboxy‑SAM‑dependent |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,025,559 | A→G | T17A (ACC→GCC) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,045,107 | T→C | V57A (GTT→GCT) | yeeJ → | putative adhesin |
| RA | 2,065,589 | T→C | E59G (GAG→GGG) | cobU ← | cobinamide kinase and cobinamide phosphate guanylyltransferase |
| RA | 2,143,684 | (G)6→7 | coding (419/3318 nt) | yegE → | putative diguanylate cyclase |
| 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 | 2,214,702 | T→C | intergenic (‑58/‑164) | yehU ← / → mlrA | inner membrane putative sensory kinase in two‑component system with YehT/transcriptional activator of csgD and csgBA |
| RA | 2,222,366 | T→C | V61A (GTG→GCG) | dld → | D‑lactate dehydrogenase, FAD‑binding, NADH independent |
| RA | 2,317,917 | T→C | T654A (ACC→GCC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,340,675 | T→C | L1165L (TTA→TTG) | yfaL ← | adhesin |
| RA | 2,405,949 | G→A | A231A (GCC→GCT) | lrhA ← | transcriptional repressor of flagellar, motility and chemotaxis genes |
| RA | 2,632,623 | T→C | N483S (AAC→AGC) | guaB ← | IMP dehydrogenase |
| RA | 2,747,020 | G→A | A259V (GCG→GTG) | ffh ← | Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) |
| JC | 2,765,463 | (TATGGCAC)6→7 | intergenic (‑310/+50) | yfjL ← / ← yfjM | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein |
| 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 | 2,858,929 | A→C | T613P (ACC→CCC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,862,057 | T→C | Y210H (TAT→CAT) | ygbJ → | putative dehydrogenase |
| RA | 2,863,006 | T→C | G224G (GGT→GGC) | ygbK → | FliA‑regulated DUF1537 family protein |
| RA | 2,892,270 | A→G | P19P (CCA→CCG) | queD → | 6‑pyruvoyl tetrahydrobiopterin synthase (PTPS) |
| RA | 2,910,582 | T→C | Y35C (TAC→TGC) | mazG ← | nucleoside triphosphate pyrophosphohydrolase |
| 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 |
| RA | 2,957,284 | A→G | V534A (GTG→GCG) | ptrA ← | protease III |
| RA | 2,999,717 | T→C | T59A (ACC→GCC) | ygeR ← | LysM domain‑containing M23 family putative peptidase; septation lipoprotein |
| RA | 3,012,795 | T→C | N482S (AAC→AGC) | yqeB ← | XdhC‑CoxI family protein with NAD(P)‑binding Rossman fold |
| RA | 3,122,268 | T→C | D513G (GAC→GGC) | glcB ← | malate synthase G |
| RA | 3,151,636 | G→A | R117C (CGT→TGT) | exbB ← | membrane spanning protein in TonB‑ExbB‑ExbD complex |
| RA | 3,179,019 | G→A | G302D (GGC→GAC) | tolC → | transport channel |
| RA | 3,355,080 | T→C | V119A (GTC→GCC) | gltB → | glutamate synthase, large subunit |
| RA | 3,370,354 | A→G | V228A (GTG→GCG) | nanE ← | putative N‑acetylmannosamine‑6‑P epimerase |
| RA | 3,410,937 | G→A | A220T (GCC→ACC) | dusB → | tRNA‑dihydrouridine synthase B |
| RA | 3,439,996 | G→A | R2C (CGC→TGC) | rplQ ← | 50S ribosomal subunit protein L17 |
| RA | 3,485,572 | T→C | T83A (ACG→GCG) | yhfA ← | OsmC family protein |
| RA | 3,507,955 | G→A | G212G (GGC→GGT) | php ← | phosphotriesterase homology 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 | 3,590,692 | T→C | T74A (ACG→GCG) | ugpA ← | sn‑glycerol‑3‑phosphate ABC transporter permease |
| RA | 3,628,031 | A→G | L503P (CTG→CCG) | rbbA ← | ribosome‑associated ATPase: ATP‑binding protein/ATP‑binding membrane protein |
| RA | 3,634,685 | G→A | intergenic (‑227/‑156) | yhiL ← / → yhiM | pseudogene, DUF4049 family protein/acid resistance protein, inner membrane |
| RA | 3,664,363 | (G)6→7 | coding (256/729 nt) | gadW ← | transcriptional activator of gadA and gadBC; repressor of gadX |
| RA | 3,684,183 | A→G | V479A (GTG→GCG) | yhjK ← | cyclic‑di‑GMP phosphodiesterase |
| RA | 3,723,735 | T→C | E221E (GAA→GAG) | glyS ← | glycine tRNA synthetase, beta subunit |
| RA | 3,797,933 | C→T | A329V (GCA→GTA) | waaL → | O‑antigen ligase |
| 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 | 3,844,629 | A→G | E222E (GAA→GAG) | adeD → | cryptic adenine deaminase |
| RA | 3,967,132 | A→G | H239R (CAC→CGC) | rho → | transcription termination factor |
| RA | 3,982,684 | (C)8→10 | noncoding (79/87 nt) | leuT → | tRNA‑Leu |
| RA | 4,011,598 | T→C | W175R (TGG→CGG) | yigM → | putative inner membrane EamA‑like transporter |
| RA | 4,031,161 | (A)6→7 | coding (1/1332 nt) | pepQ → | proline dipeptidase |
| RA | 4,128,197 | T→C | T67A (ACC→GCC) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,134,394 | A→G | D187G (GAC→GGC) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,135,451 | A→G | K539K (AAA→AAG) | katG → | catalase‑peroxidase HPI, heme b‑containing |
| RA | 4,279,976 | A→G | intergenic (+148/‑4) | ghxP → / → yjcE | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter/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 | 4,381,504 | T→C | E272G (GAA→GGA) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,382,351 | C→T | intergenic (‑33/‑292) | frdA ← / → epmA | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit/Elongation Factor P Lys34 lysyltransferase |
| RA | 4,410,053 | (T)9→8 | intergenic (+47/‑80) | rlmB → / → yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| RA | 4,640,125 | T→C | N61S (AAC→AGC) | arcA ← | response regulator in two‑component regulatory system with ArcB or CpxA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423739–3424234 | 3424577–3424238 | 5–839 | 58 [54] | [57] 59 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 382276 | NA (NA) | 74 (0.700) | 61/294 | 1.5 | NA | noncoding (1017/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 382590 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 85 (0.820) | 74/290 | 0.6 | 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 | |||||
| * | ? | NC_000913 | = 1468228 | NA (NA) | 86 (0.810) | 68/298 | 1.0 | NA | noncoding (1013/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469240 | NA (NA) | noncoding (1/1331 nt) | IS2 | repeat region | |||||