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 | 28,094 | G→A | V268M (GTG→ATG) | rihC → | ribonucleoside hydrolase 3 |
| RA | 121,578 | (T)7→6 | intergenic (‑27/‑514) | aroP ← / → pdhR | aromatic amino acid transporter/pyruvate dehydrogenase complex repressor; autorepressor |
| RA | 218,942 | A→G | V218A (GTT→GCT) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| RA | 240,865 | G→A | A813A (GCC→GCT) | fadE ← | acyl coenzyme A dehydrogenase |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,465 | C→A | E90* (GAG→TAG) | ykfG ← | CP4‑6 prophage; RadC‑like JAB domain protein |
| RA | 282,993 | C→T | A239V (GCC→GTC) | yagE → | 2‑keto‑3‑deoxy gluconate (KDG) aldolase; CP4‑6 prophage |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | ECP production outer membrane protein |
| RA | 328,638 | A→G | G32G (GGT→GGC) | betB ← | betaine aldehyde dehydrogenase, NAD‑dependent |
| RA | 401,576 | Δ1 bp | coding (191/261 nt) | iraP → | anti‑RssB factor, RpoS stabilzer during Pi starvation; anti‑adapter protein |
| RA | 449,925 | A→G | I239I (ATT→ATC) | cyoB ← | cytochrome o ubiquinol oxidase subunit I |
| RA | 468,271 | (T)8→7 | intergenic (+41/‑112) | cof → / → ybaO | thiamine pyrimidine pyrophosphate hydrolase; HMP‑PP phosphatase/putative DNA‑binding transcriptional regulator |
| RA | 482,315 | G→A | Q697* (CAG→TAG) | acrB ← | multidrug efflux system protein |
| RA | 503,650 | A→G | G349G (GGT→GGC) | fsr ← | putative fosmidomycin efflux system protein |
| RA | 518,730 | A→G | R140R (CGT→CGC) | ybbO ← | putative oxidoreductase |
| RA | 520,191 | A→G | Q153Q (CAA→CAG) | ybbA → | putative ABC transporter ATPase |
| RA | 577,085 | G→A | intergenic (‑260/‑313) | nmpC ← / → essD | DLP12 prophage; truncated outer membrane porin (pseudogene);IS, phage, Tn; Phage or Prophage Related; outer membrane porin protein; locus of qsr prophage/DLP12 prophage; putative phage lysis protein |
| RA | 588,485 | G→A | R824C (CGC→TGC) | nfrA ← | bacteriophage N4 receptor, outer membrane subunit |
| RA | 655,949 | A→G | L7P (CTC→CCC) | dcuC ← | anaerobic C4‑dicarboxylate transport |
| RA | 741,429 | A→G | S376S (TCT→TCC) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 750,456 | T→C | S572G (AGC→GGC) | ybgQ ← | putative outer membrane protein |
| RA | 781,084 | T→C | noncoding (17/76 nt) | valZ → | tRNA‑Val |
| RA | 807,115 | T→C | Q56R (CAA→CGA) | ybhC ← | acyl‑CoA thioesterase, lipoprotein |
| 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 | 971,855 | A→G | D35G (GAC→GGC) | ycbJ → | protein kinase‑like domain protein |
| RA | 976,403 | C→T | D26D (GAC→GAT) | mukB → | chromosome condensin MukBEF, ATPase and DNA‑binding subunit |
| RA | 1,097,480 | A→G | intergenic (+651/+85) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,116,797 | A→G | intergenic (‑215/‑10) | lpxL ← / → yceA | lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase/putative rhodanese‑related sulfurtransferase |
| RA | 1,129,249 | T→C | L471L (TTG→CTG) | murJ → | putative lipid II flippase |
| RA | 1,145,762 | A→G | T275A (ACG→GCG) | rluC → | 23S rRNA pseudouridine(955,2504,2580) synthase |
| RA | 1,154,782 | A→G | E224G (GAA→GGA) | yceG → | septation protein, ampicillin sensitivity |
| RA | 1,203,225 | C→T | intergenic (+1/‑43) | croE → / → ymfL | e14 prophage; putative DNA‑binding transcriptional regulator/e14 prophage; putative DNA‑binding transcriptional regulator |
| RA | 1,246,015 | T→C | A454A (GCA→GCG) | treA ← | periplasmic trehalase |
| RA | 1,307,391 | T→C | T419A (ACA→GCA) | clsA ← | cardiolipin synthase 1 |
| RA | 1,314,744 | T→C | T161A (ACT→GCT) | yciE ← | putative rubrerythrin/ferritin‑like metal‑binding protein |
| RA | 1,336,738 | T→C | I303T (ATT→ACT) | acnA → | aconitate hydratase 1; aconitase A |
| RA | 1,363,578 | A→G | D279G (GAC→GGC) | puuC → | gamma‑glutamyl‑gamma‑aminobutyraldehyde dehydrogenase; succinate semialdehyde dehydrogenase |
| RA | 1,370,155 | A→G | intergenic (+152/‑61) | pspE → / → ycjM | thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein |
| RA | 1,490,770 | A→G | intergenic (‑57/‑132) | gapC ← / → cybB | pseudogene, GAP dehydrogenase; glyceraldehyde‑3‑phosphate dehydrogenase (second fragment)/cytochrome b561 |
| RA | 1,492,550 | T→C | G27G (GGT→GGC) | trg → | methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor |
| RA | 1,515,171 | T→C | V137A (GTG→GCG) | ydcV → | putative ABC transporter permease |
| RA | 1,539,343 | T→C | E1083G (GAA→GGA) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,567,815 | C→T | A337T (GCT→ACT) | yddW ← | liprotein, glycosyl hydrolase homolog |
| RA | 1,577,803 | T→C | T514A (ACC→GCC) | yddA ← | putative multidrug ABC transporter permease/ATPase |
| RA | 1,630,461 | A→G | N151N (AAT→AAC) | ydfI ← | putative NAD‑dependent D‑mannonate oxidoreductase |
| RA | 1,631,501 | C→T | pseudogene (785/1284 nt) | ydfJ ← | pseudogene, MFS transporter family; interrupted by Qin prophage;Phage or Prophage Related; putative transport protein |
| RA | 1,756,590 | T→C | V298A (GTT→GCT) | pykF → | pyruvate kinase I |
| RA | 1,832,946 | T→C | R173R (CGT→CGC) | xthA → | exonuclease III |
| RA | 1,863,313 | T→C | A181A (GCT→GCC) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,888,023 | (A)8→9 | intergenic (‑32/+38) | rnd ← / ← fadD | ribonuclease D/acyl‑CoA synthetase (long‑chain‑fatty‑acid‑‑CoA ligase) |
| RA | 1,926,559 | T→C | L147P (CTT→CCT) | exoX → | exodeoxyribonuclease 10; DNA exonuclease X |
| RA | 1,929,306 | G→A | A134A (GCC→GCT) | yebE ← | DUF533 family inner membrane protein |
| RA | 1,944,247 | A→G | intergenic (+48/+99) | znuB → / ← ruvB | zinc ABC transporter permease/ATP‑dependent DNA helicase, component of RuvABC resolvasome |
| RA | 1,956,520 | T→C | N163S (AAC→AGC) | torZ ← | trimethylamine N‑oxide reductase system III, catalytic subunit |
| RA | 1,967,290 | C→T | G50S (GGT→AGT) | cheY ← | chemotaxis regulator transmitting signal to flagellar motor component |
| RA | 1,974,562 | T→C | T255A (ACG→GCG) | cheA ← | fused chemotactic sensory histidine kinase in two‑component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,000,046 | G→A | R114C (CGC→TGC) | fliY ← | cystine transporter subunit |
| RA | 2,028,056 | T→C | intergenic (‑39/+132) | yedQ ← / ← yodC | putative membrane‑anchored diguanylate cyclase/uncharacterized protein |
| RA | 2,051,242 | T→C | V2102A (GTG→GCG) | yeeJ → | putative adhesin |
| RA | 2,083,091 | A→G | T112T (ACA→ACG) | sbcB → | exodeoxyribonuclease I; exonuclease I |
| RA | 2,110,993 | T→C | L9L (TTA→TTG) | rfbA ← | glucose‑1‑phosphate thymidylyltransferase |
| RA | 2,117,002 | T→C | T42T (ACA→ACG) | wcaL ← | putative glycosyl transferase |
| RA | 2,124,650 | G→A | A366V (GCG→GTG) | wcaI ← | putative glycosyl transferase |
| RA | 2,134,397 | A→G | V419A (GTG→GCG) | wzc ← | colanic acid production tyrosine‑protein kinase; autokinase; Ugd phosphorylase |
| RA | 2,136,954 | A→G | V97A (GTC→GCC) | wza ← | colanic acid export protein; outer membrane auxillary lipoprotein |
| RA | 2,150,590 | A→G | A132A (GCT→GCC) | yegI ← | protein kinase‑related putative non‑specific DNA‑binding 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 | 2,224,908 | C→T | intergenic (‑38/+136) | pbpG ← / ← yohC | D‑alanyl‑D‑alanine endopeptidase/Yip1 family inner membrane protein |
| RA | 2,241,409 | T→C | Q87R (CAG→CGG) | galS ← | galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor; mgl operon transcriptional repressor; autorepressor |
| RA | 2,258,247 | A→G | F41L (TTC→CTC) | psuG ← | pseudouridine 5'‑phosphate glycosidase |
| RA | 2,367,269 | A→G | S67G (AGC→GGC) | arnC → | undecaprenyl phosphate‑L‑Ara4FN transferase |
| RA | 2,409,038 | A→G | E59E (GAA→GAG) | yfbR → | 5'‑nucleotidase |
| RA | 2,467,027 | C→T | R161R (CGC→CGT) | intS → | CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase |
| RA | 2,467,446 | A→G | K301R (AAG→AGG) | intS → | CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase |
| RA | 2,473,322 | T→C | pseudogene (264/708 nt) | oweS ← | pseudogene, CPS‑53 (KpLE1) prophage; bacteriophage replication protein O family;Phage or Prophage Related |
| RA | 2,498,862 | T→C | V64V (GTT→GTC) | ypdA → | sensor kinase regulating yhjX; pyruvate‑responsive YpdAB two‑component system |
| RA | 2,519,524 | T→C | V383V (GTA→GTG) | gltX ← | glutamyl‑tRNA synthetase |
| RA | 2,602,739 | A→G | T308A (ACC→GCC) | hyfB → | hydrogenase 4, membrane subunit |
| RA | 2,609,458 | T→C | R324R (CGT→CGC) | hyfG → | hydrogenase 4, subunit |
| RA | 2,624,906 | T→C | R621R (CGT→CGC) | ppk → | polyphosphate kinase, component of RNA degradosome |
| JC | 2,636,790 | (TTC)3→2 | coding (565‑567/1473 nt) | der ← | GTPase; multicopy suppressor of ftsJ |
| RA | 2,647,150 | G→A | A59V (GCT→GTT) | pbpC ← | penicillin‑insensitive murein repair transglycosylase; inactive transpeptidase domain protein |
| RA | 2,662,523 | A→G | intergenic (‑392/+60) | iscR ← / ← trmJ | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor/tRNA mC32,mU32 2'‑O‑methyltransferase, SAM‑dependent |
| RA | 2,730,879 | T→C | noncoding (279/1542 nt) | rrsG ← | 16S ribosomal RNA of rrnG operon |
| RA | 2,764,190 | A→G | F322L (TTC→CTC) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,767,140 | T→C | L53L (TTG→CTG) | rnlB → | CP4‑57 prophage; uncharacterized protein |
| RA | 2,780,330 | G→A | G799G (GGC→GGT) | ypjA ← | adhesin‑like autotransporter |
| RA | 2,793,819 | A→G | D362G (GAC→GGC) | gabT → | 4‑aminobutyrate aminotransferase, PLP‑dependent |
| RA | 2,828,902 | A→G | L94L (TTA→TTG) | srlM → | sorbitol=responsive srl operon transcriptional activator |
| RA | 2,912,885 | A→G | I256T (ATC→ACC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,975,171 | G→A | P282S (CCC→TCC) | aas ← | fused 2‑acylglycerophospho‑ethanolamine acyl transferase/acyl‑acyl carrier protein synthetase |
| RA | 3,073,252 | T→C | H147R (CAC→CGC) | epd ← | D‑erythrose 4‑phosphate dehydrogenase |
| RA | 3,086,618 | A→G | intergenic (+216/‑88) | yqgC → / → metK | uncharacterized protein/S‑adenosylmethionine synthetase |
| RA | 3,151,501 | T→C | T162A (ACG→GCG) | exbB ← | membrane spanning protein in TonB‑ExbB‑ExbD complex |
| RA | 3,176,250 | T→C | H195R (CAC→CGC) | cpdA ← | 3',5' cAMP phosphodiesterase |
| RA | 3,196,367 | A→T | D129E (GAT→GAA) | hldE ← | heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| RA | 3,272,271 | Δ1 bp | coding (481/885 nt) | garR ← | tartronate semialdehyde reductase |
| RA | 3,312,212 | (T)5→6 | coding (566/945 nt) | truB ← | tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase |
| RA | 3,313,236 | T→C | intergenic (‑58/+106) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,375,895 | (G)6→7 | coding (1027/1368 nt) | dcuD → | putative transporter |
| RA | 3,376,403 | T→C | D125G (GAC→GGC) | sspB ← | ClpXP protease specificity enhancing factor |
| 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 | 3,394,694 | T→C | D522G (GAC→GGC) | yhdP ← | DUF3971‑AsmA2 domains protein |
| RA | 3,440,116 | T→C | D305G (GAC→GGC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,449,100 | T→C | T24A (ACG→GCG) | rplP ← | 50S ribosomal subunit protein L16 |
| RA | 3,485,605 | A→G | S72P (TCT→CCT) | yhfA ← | OsmC family protein |
| RA | 3,515,565 | A→G | Y117H (TAC→CAC) | dam ← | DNA adenine methyltransferase |
| RA | 3,544,043 | T→C | *293Q (TAA→CAA) | yhgA → | transposase_31 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 | 3,571,851 | C→T | R551H (CGC→CAC) | glgB ← | 1,4‑alpha‑glucan branching enzyme |
| RA | 3,576,697 | A→G | I122T (ATA→ACA) | gntU ← | gluconate transporter, low affinity GNT 1 system |
| RA | 3,612,540 | T→C | W226R (TGG→CGG) | yhhT → | UPF0118 family putative transporter |
| RA | 3,662,633 | G→A | A740A (GCG→GCA) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,725,236 | A→G | V28A (GTT→GCT) | glyQ ← | glycine tRNA synthetase, alpha subunit |
| RA | 3,788,944 | T→C | F282L (TTT→CTT) | yibQ → | putative polysaccharide deacetylase |
| RA | 3,790,211 | T→C | intergenic (‑130/+109) | waaH ← / ← tdh | LPS(HepIII)‑glucuronic acid glycosyltransferase/L‑threonine 3‑dehydrogenase, NAD(P)‑binding |
| RA | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 3,831,329 | A→G | E291E (GAA→GAG) | yicH → | putative inner membrane‑anchored periplasmic AsmA family protein |
| RA | 3,877,783 | C→T | T779T (ACG→ACA) | gyrB ← | DNA gyrase, subunit B |
| RA | 3,920,989 | A→T | A67A (GCT→GCA) | atpE ← | F0 sector of membrane‑bound ATP synthase, subunit c |
| RA | 3,940,308 | A→G | L102P (CTG→CCG) | hsrA ← | putative multidrug or homocysteine efflux system |
| RA | 3,949,005 | T→C | Q322R (CAG→CGG) | yifB ← | magnesium chelatase family protein and putative transcriptional regulator |
| RA | 3,992,016 | T→C | R288R (CGT→CGC) | cyaA → | adenylate cyclase |
| RA | 4,003,303 | A→G | R292R (CGT→CGC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,017,296 | T→C | intergenic (+104/‑37) | udp → / → rmuC | uridine phosphorylase/DNA recombination protein |
| RA | 4,102,930 | C→T | L37L (CTG→TTG) | yiiM → | 6‑N‑hydroxylaminopurine resistance protein |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,146,023 | A→G | T677A (ACG→GCG) | pflD → | putative glycine radical domain‑containing pyruvate formate‑lyase |
| RA | 4,185,098 | A→G | Y1285C (TAC→TGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,185,894 | C→T | A182V (GCG→GTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,217,392 | T→C | V95A (GTA→GCA) | aceA → | isocitrate lyase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,302,141 | T→C | E313G (GAG→GGG) | mdtO ← | membrane translocase (MDR) of MdtNOP efflux pump, PET family |
| RA | 4,308,664 | C→T | G269D (GGC→GAC) | alsC ← | D‑allose ABC transporter permease |
| RA | 4,342,193 | A→G | T95A (ACG→GCG) | melA → | alpha‑galactosidase, NAD(P)‑binding |
| RA | 4,366,223 | A→G | F184S (TTC→TCC) | dcuA ← | C4‑dicarboxylate antiporter |
| RA | 4,399,151 | Δ1 bp | coding (1740/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,453,330 | A→G | N254D (AAC→GAC) | ytfT → | putative sugar ABC transporter permease |
| RA | 4,478,921 | Δ1 bp | intergenic (+32/+113) | rraB → / ← yjgM | protein inhibitor of RNase E/GNAT family putative N‑acetyltransferase |
| RA | 4,485,872 | C→T | R27H (CGC→CAC) | pepA ← | multifunctional aminopeptidase A: a cyteinylglycinase, transcription regulator and site‑specific recombination factor |
| RA | 4,549,322 | A→G | N172S (AAT→AGT) | fimH → | minor component of type 1 fimbriae |
| RA | 4,564,425 | G→A | P89S (CCA→TCA) | yjiL ← | putative ATPase, activator of (R)‑hydroxyglutaryl‑CoA dehydratase |
| RA | 4,606,215 | (G)8→7 | noncoding (72/87 nt) | leuP ← | tRNA‑Leu |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423700–3424234 | 3424593–3424238 | 5–894 | 87 [85] | [85] 87 | [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) | 153 (1.120) | 124/290 | 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 | |||||