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 | 41,317 | A→G | G205G (GGT→GGC) | caiT ← | putative transporter |
| RA | 92,682 | A→G | T424A (ACA→GCA) | ftsI → | transpeptidase involved in septal peptidoglycan synthesis; penicillin‑binding protein 3 |
| RA | 186,439 | C→T | A738T (GCA→ACA) | glnD ← | uridylyltransferase |
| RA | 209,483 | C→T | A288V (GCG→GTG) | accA → | acetyl‑CoA carboxylase, carboxytransferase, alpha subunit |
| RA | 217,580 | C→T | G399D (GGC→GAC) | proS ← | prolyl‑tRNA synthetase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 262,343 | G→A | G281S (GGC→AGC) | proA → | gamma‑glutamylphosphate reductase |
| RA | 279,852 | A→G | C8C (TGT→TGC) | insA ← | IS1 repressor TnpA |
| RA | 328,638 | A→G | G32G (GGT→GGC) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 351,040 | A→G | T343T (ACA→ACG) | prpC → | 2‑methylcitrate synthase |
| RA | 407,978 | A→G | D184G (GAT→GGT) | aroM → | AroM family protein |
| RA | 428,291 | C→T | S215S (AGC→AGT) | secD → | SecYEG protein translocase auxillary subunit |
| RA | 449,344 | A→G | F433S (TTC→TCC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 479,603 | C→T | V106I (GTT→ATT) | maa ← | maltose O‑acetyltransferase |
| RA | 484,337 | (C)6→7 | coding (67/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 496,931 | A→G | E604E (GAA→GAG) | htpG → | protein refolding molecular co‑chaperone Hsp90, Hsp70‑dependent; heat‑shock protein; ATPase |
| RA | 551,656 | A→G | R313R (CGT→CGC) | purK ← | N5‑carboxyaminoimidazole ribonucleotide synthase |
| RA | 600,631 | A→G | M640V (ATG→GTG) | cusA → | copper/silver efflux system, membrane component |
| RA | 615,301 | T→C | L382P (CTG→CCG) | entF → | enterobactin synthase multienzyme complex component, ATP‑dependent |
| RA | 627,982 | C→T | P97S (CCG→TCG) | entB → | isochorismatase |
| RA | 631,179 | A→G | N429S (AAC→AGC) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 723,528 | (T)8→7 | coding (887/2685 nt) | kdpD ← | fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein |
| RA | 751,969 | C→T | G67G (GGG→GGA) | ybgQ ← | putative outer membrane protein |
| RA | 769,691 | C→T | P572S (CCG→TCG) | mngB → | alpha‑mannosidase |
| RA | 788,591 | T→C | S83G (AGC→GGC) | galM ← | aldose 1‑epimerase; type‑1 mutarotase; galactose mutarotase |
| RA | 801,406 | A→G | E216E (GAA→GAG) | ybhH → | putative PrpF family isomerase |
| RA | 814,495 | A→G | T324A (ACG→GCG) | uvrB → | exision nuclease of nucleotide excision repair, DNA damage recognition component |
| RA | 852,223 | T→C | I125M (ATA→ATG) | opgE ← | OPG biosynthetic transmembrane phosphoethanolamine transferase |
| RA | 904,172 | A→G | L99S (TTG→TCG) | ybjP ← | lipoprotein |
| RA | 936,518 | C→T | P1099S (CCG→TCG) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| JC JC | 944,912 | Δ1 bp :: IS186 (+) +6 bp :: Δ1 bp | intergenic (+16/+14) | dmsC → / ← ycaC | dimethyl sulfoxide reductase, anaerobic, subunit C/putative isochorismatase family hydrolase |
| RA | 1,011,526 | C→T | G521G (GGC→GGT) | uup → | replication regulatory ABC‑F family DNA‑binding ATPase |
| RA | 1,025,076 | C→T | A202A (GCC→GCT) | helD → | DNA helicase IV |
| RA | 1,053,549 | A→G | L877P (CTA→CCA) | torS ← | hybrid sensory histidine kinase in two‑component regulatory system with TorR |
| RA | 1,066,324 | A→G | Q247R (CAG→CGG) | agp → | glucose‑1‑phosphatase/inositol phosphatase |
| RA | 1,077,452 | C→T | P477P (CCG→CCA) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| RA | 1,125,906 | G→A | W115* (TGG→TGA) | rimJ → | ribosomal‑protein‑S5‑alanine N‑acetyltransferase |
| RA | 1,140,385 | G→A | R118H (CGT→CAT) | flgL → | flagellar hook‑filament junction protein |
| RA | 1,148,553 | A→G | R311R (CGA→CGG) | plsX → | putative phosphate acyltransferase |
| RA | 1,259,033 | A→G | K81K (AAA→AAG) | ychH → | DUF2583 family putative inner membrane protein |
| RA | 1,262,619 | C→T | G87R (GGA→AGA) | ispE ← | 4‑diphosphocytidyl‑2‑C‑methylerythritol kinase |
| RA | 1,273,196 | C→T | F230F (TTC→TTT) | chaC → | cation transport regulator |
| RA | 1,382,640 | C→T | R232C (CGC→TGC) | ompG → | outer membrane porin G |
| RA | 1,429,407 | T→C | V120A (GTG→GCG) | stfR → | Rac prophage; putative tail fiber protein |
| RA | 1,437,231 | (T)9→8 | intergenic (‑338/+29) | ompN ← / ← pfo | outer membrane pore protein N, non‑specific/pyruvate‑flavodoxin oxidoreductase |
| RA | 1,460,132 | A→G | N360S (AAC→AGC) | paaH → | 3‑hydroxyadipyl‑CoA dehydrogenase, NAD+‑dependent |
| RA | 1,525,931 | C→T | R17H (CGC→CAC) | ansP ← | L‑asparagine transporter |
| RA | 1,529,542 | A→G | pseudogene (1641/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,560,722 | A→G | Y70H (TAC→CAC) | ddpB ← | D,D‑dipeptide ABC transporter permease |
| RA | 1,607,481 | A→G | T46A (ACC→GCC) | tam → | trans‑aconitate methyltransferase |
| RA | 1,681,679 | G→A | G235D (GGC→GAC) | folM → | dihydromonapterin reductase, NADPH‑dependent; dihydrofolate reductase isozyme |
| RA | 1,735,191 | T→C | Y253H (TAC→CAC) | mepH → | murein DD‑endopeptidase, space‑maker hydrolase |
| RA | 1,745,624 | T→C | E168E (GAA→GAG) | ydhQ ← | autotransporter adhesin‑related protein |
| RA | 1,756,377 | T→C | L227P (CTC→CCC) | pykF → | pyruvate kinase I |
| RA | 1,764,710 | T→C | intergenic (‑324/+224) | sufA ← / ← ydiH | Fe‑S cluster assembly protein/uncharacterized protein |
| RA | 1,789,056 | T→C | F208L (TTC→CTC) | aroH → | 3‑deoxy‑D‑arabino‑heptulosonate‑7‑phosphate synthase, tryptophan repressible |
| RA | 1,815,591 | A→G | P575P (CCA→CCG) | katE → | catalase HPII, heme d‑containing |
| RA | 1,881,694 | C→T | R39H (CGC→CAC) | dmlR ← | transcriptional activator of dmlA |
| RA | 1,882,431 | G→A | A174T (GCC→ACC) | dmlA → | D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
| RA | 1,897,602 | T→C | M224T (ATG→ACG) | sdaA → | L‑serine dehydratase 1 |
| RA | 1,906,622 | T→C | T147A (ACC→GCC) | rlmA ← | 23S rRNA m(1)G745 methyltransferase, SAM‑dependent |
| RA | 1,937,537 | T→C | intergenic (+16/‑112) | yebK → / → pykA | putative DNA‑binding transcriptional regulator/pyruvate kinase II |
| RA | 1,952,097 | A→G | T235A (ACG→GCG) | yecE → | UPF0759 family protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,993,219 | A→G | V496V (GTT→GTC) | uvrC ← | excinuclease UvrABC, endonuclease subunit |
| RA | 2,028,416 | A→G | intergenic (‑46/+33) | yodC ← / ← yedI | uncharacterized protein/DUF808 family inner membrane protein |
| RA | 2,045,163 | T→C | L76L (TTG→CTG) | yeeJ → | putative adhesin |
| RA | 2,064,506 | T→C | E239E (GAA→GAG) | cobS ← | cobalamin synthase |
| RA | 2,098,022 | T→C | T94A (ACG→GCG) | wzzB ← | regulator of length of O‑antigen component of lipopolysaccharide chains |
| RA | 2,131,812 | G→A | R87C (CGC→TGC) | wcaC ← | putative glycosyl transferase |
| RA | 2,165,605 | G→A | intergenic (+84/‑63) | yegP → / → yegQ | UPF0339 family protein/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 | 2,209,439 | G→A | pseudogene (340/2001 nt) | yehQ → | pseudogene |
| RA | 2,253,111 | A→G | A345A (GCT→GCC) | nupX ← | nucleoside permease |
| RA | 2,274,782 | T→C | F202L (TTC→CTC) | yejB → | microcin C ABC transporter permease |
| RA | 2,328,783 | (G)5→6 | coding (1015/1650 nt) | yfaQ ← | tandem DUF2300 domain protein, putative host defense protein |
| RA | 2,337,019 | G→A | A801V (GCC→GTC) | gyrA ← | DNA gyrase (type II topoisomerase), subunit A |
| RA | 2,341,415 | T→C | T919A (ACG→GCG) | yfaL ← | adhesin |
| RA | 2,344,828 | T→C | intergenic (‑659/‑37) | yfaL ← / → nrdA | adhesin/ribonucleoside‑diphosphate reductase 1, alpha subunit |
| RA | 2,353,790 | G→A | A382T (GCC→ACC) | glpA → | anaerobic sn‑glycerol‑3‑phosphate dehydrogenase, large FAD/NAD(P)‑binding subunit |
| RA | 2,421,732 | A→G | T9A (ACA→GCA) | yfcH → | putative NAD‑dependent nucleotide‑sugar epimerase |
| RA | 2,531,374 | (T)6→5 | intergenic (‑141/‑89) | zipA ← / → cysZ | FtsZ stabilizer/sulfate transporter, sulfite inhibited |
| RA | 2,548,346 | G→A | G82D (GGC→GAC) | yfeW → | penicillin binding protein PBP4B; weak DD‑carboxypeptidase activity |
| RA | 2,557,426 | T→C | L418L (TTA→TTG) | eutB ← | ethanolamine ammonia‑lyase, large subunit, heavy chain |
| RA | 2,565,229 | A→G | K236R (AAA→AGA) | yffS → | CPZ‑55 prophage; uncharacterized protein |
| RA | 2,584,258 | T→C | Y423C (TAC→TGC) | aegA ← | putative oxidoreductase, FeS binding subunit/NAD/FAD‑binding subunit |
| RA | 2,591,522 | T→C | R92R (CGT→CGC) | yffB → | putative ArsC family reductase |
| RA | 2,737,713 | (G)6→7 | intergenic (+67/‑32) | pheL → / → pheA | pheA gene leader peptide/chorismate mutase and prephenate dehydratase, P‑protein |
| RA | 2,754,034 | G→A | R89* (CGA→TGA) | ratB ← | UPF0125 family protein |
| RA | 2,775,762 | T→C | pseudogene (39/93 nt) | ypjI → | pseudogene, CP4‑57 putative prophage remnant;Phage or Prophage Related |
| RA | 2,780,291 | G→A | G812G (GGC→GGT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,811,185 | T→C | L139P (CTC→CCC) | mprA → | transcriptional repressor of microcin B17 synthesis and multidrug efflux |
| RA | 2,815,388 | T→C | D351G (GAC→GGC) | gshA ← | glutamate‑cysteine ligase |
| RA | 2,830,245 | G→A | E145K (GAA→AAA) | srlQ → | D‑arabinose 5‑phosphate isomerase |
| RA | 2,843,504 | G→A | P236L (CCG→CTG) | hycG ← | hydrogenase 3 and formate hydrogenase complex, HycG subunit |
| RA | 2,935,702 | T→C | L40P (CTG→CCG) | fucI → | L‑fucose isomerase |
| RA | 2,955,355 | T→C | T217A (ACG→GCG) | recB ← | exonuclease V (RecBCD complex), beta subunit |
| RA | 3,020,140 | T→C | F327S (TTT→TCT) | ssnA → | putative chlorohydrolase/aminohydrolase |
| RA | 3,025,265 | T→C | G305G (GGT→GGC) | xanQ → | xanthine permease |
| RA | 3,065,588 | A→G | N263D (AAT→GAT) | scpC → | propionyl‑CoA:succinate CoA transferase |
| RA | 3,084,257 | T→C | Y552C (TAC→TGC) | speA ← | biosynthetic arginine decarboxylase, PLP‑binding |
| RA | 3,213,764 | C→T | R240C (CGC→TGC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,214,545 | T→A | I500N (ATC→AAC) | rpoD → | RNA polymerase, sigma 70 (sigma D) factor |
| RA | 3,240,984 | (G)7→8 | coding (1041/1245 nt) | sstT → | sodium:serine/threonine symporter |
| RA | 3,297,484 | G→A | R219C (CGC→TGC) | yraQ ← | putative inner membrane permease |
| RA | 3,372,695 | T→C | Q294Q (CAA→CAG) | nanA ← | N‑acetylneuraminate lyase |
| RA | 3,375,075 | G→A | L69L (CTG→CTA) | dcuD → | putative transporter |
| RA | 3,377,215 | A→G | L69P (CTG→CCG) | sspA ← | stringent starvation protein A, phage P1 late gene activator, RNAP‑associated acid‑resistance protein, inactive glutathione S‑transferase homolog |
| RA | 3,542,564 | C→T | H720Y (CAT→TAT) | feoB → | ferrous iron transporter protein B and GTP‑binding protein; membrane 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 | 3,585,493 | T→C | Y444C (TAC→TGC) | ggt ← | gamma‑glutamyltranspeptidase |
| RA | 3,654,763 | A→G | I27M (ATA→ATG) | dctR → | Putative LuxR family repressor for dicarboxylate transport |
| RA | 3,668,330 | G→A | P287S (CCG→TCG) | yhjA ← | putative cytochrome C peroxidase |
| RA | 3,693,226 | T→C | S671G (AGT→GGT) | bcsA ← | cellulose synthase, catalytic subunit |
| RA | 3,750,344 | T→C | Y87H (TAT→CAT) | sgbE → | L‑ribulose‑5‑phosphate 4‑epimerase |
| RA | 3,755,937 | A→G | V192A (GTG→GCG) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,842,330 | T→C | R25G (AGA→GGA) | yicN ← | DUF1198 family protein |
| RA | 3,915,448 | (G)6→7 | intergenic (‑248/+105) | glmU ← / ← atpC | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase/F1 sector of membrane‑bound ATP synthase, epsilon subunit |
| RA | 3,918,289 | G→A | intergenic (‑24/+27) | atpG ← / ← atpA | F1 sector of membrane‑bound ATP synthase, gamma subunit/F1 sector of membrane‑bound ATP synthase, alpha subunit |
| RA | 4,016,062 | A→G | P36P (CCT→CCC) | ysgA ← | putative carboxymethylenebutenolidase |
| RA | 4,079,433 | T→C | V46A (GTG→GCG) | yiiE → | CopG family putative transcriptional regulator |
| RA | 4,123,177 | T→C | T55A (ACG→GCG) | ftsN ← | essential cell division protein |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,145,072 | C→T | P360S (CCG→TCG) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,161,466 | G→A | G115S (GGC→AGC) | fabR → | transcriptional repressor of fabA and fabB |
| RA | 4,183,795 | A→G | T851A (ACC→GCC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,204,350 | A→G | Q344R (CAG→CGG) | zraR → | fused DNA‑binding response regulator in two‑component regulatory system with ZraS: response regulator/sigma54 interaction protein |
| RA | 4,228,771 | A→G | E347E (GAA→GAG) | yjbB → | putative Na+/Pi‑cotransporter |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,339,912 | T→C | T204A (ACT→GCT) | adiA ← | arginine decarboxylase |
| RA | 4,352,500 | (A)8→7 | intergenic (+143/‑84) | yjdJ → / → ghoS | GNAT family putative N‑acetyltransferase/antitoxin of GhoTS toxin‑antitoxin pair; endonuclease for ghoT mRNA |
| RA | 4,399,151 | Δ1 bp | coding (1740/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,428,720 | T→C | intergenic (‑3/‑215) | ytfB ← / → fklB | OapA family protein/FKBP‑type peptidyl‑prolyl cis‑trans isomerase (rotamase) |
| RA | 4,430,267 | A→G | D135G (GAC→GGC) | cycA → | D‑alanine/D‑serine/glycine transporter |
| RA | 4,443,730 | C→T | T450M (ACG→ATG) | tamA → | translocation and assembly module for autotransporter export, outer membrane subunit |
| RA | 4,492,667 | C→T | V229M (GTG→ATG) | idnO ← | 5‑keto‑D‑gluconate‑5‑reductase |
| RA | 4,500,381 | T→C | pseudogene (154/942 nt) | yjgX ← | pseudogene fragment |
| RA | 4,601,428 | A→G | G30G (GGT→GGC) | dnaT ← | DNA biosynthesis protein (primosomal protein I) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2729633–2730949 | 2731291–2731080 | 132–1659 | 32 [31] | [31] 34 | [rrsG] | [rrsG] |
| * | * | ÷ | NC_000913 | 3423727–3424234 | 3424582–3424238 | 5–856 | 32 [31] | [30] 32 | [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) | 45 (0.730) | 42/290 | 0.9 | 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 | |||||