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 | 165,917 | C→T | A396A (GCC→GCT) | mrcB → | fused glycosyl transferase and transpeptidase |
| RA | 172,368 | A→G | M303V (ATG→GTG) | fhuB → | iron(3+)‑hydroxamate import ABC transporter permease |
| RA | 218,942 | A→G | V218A (GTT→GCT) | tsaA ← | tRNA‑Thr(GGU) m(6)t(6)A37 methyltransferase, SAM‑dependent |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 292,587 | T→C | Y121C (TAC→TGC) | yagK ← | CP4‑6 prophage; conserved protein |
| RA | 308,054 | (C)7→8 | coding (1279/2526 nt) | ecpC ← | ECP production outer membrane protein |
| RA | 389,169 | T→C | T187A (ACG→GCG) | hemB ← | 5‑aminolevulinate dehydratase (porphobilinogen synthase) |
| RA | 481,730 | A→G | Y892H (TAC→CAC) | acrB ← | multidrug efflux system protein |
| RA | 484,337 | (C)6→7 | coding (67/3150 nt) | acrB ← | multidrug efflux system protein |
| RA | 530,975 | C→T | R84R (CGG→CGA) | mnmH ← | tRNA 2‑selenouridine synthase, selenophosphate‑dependent |
| RA | 553,616 | G→C | R109G (CGG→GGG) | lpxH ← | UDP‑2,3‑diacylglucosamine pyrophosphohydrolase |
| RA | 566,457 | A→G | pseudogene (82/312 nt) | peaD → | pseudogene; DLP12 prophage; replication protein family;Phage or Prophage Related |
| 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 | 619,445 | A→G | V252A (GTT→GCT) | fepC ← | ferrienterobactin ABC transporter ATPase |
| RA | 630,669 | T→A | M259K (ATG→AAG) | cstA → | carbon starvation protein involved in peptide utilization; APC peptide transporter family protein |
| RA | 665,401 | C→T | V305I (GTC→ATC) | mrdB ← | cell wall shape‑determining protein |
| RA | 741,429 | A→G | S376S (TCT→TCC) | dtpD ← | dipeptide and tripeptide permease D |
| RA | 758,165 | T→C | C159C (TGT→TGC) | sdhB → | succinate dehydrogenase, FeS subunit |
| 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 |
| RA | 835,618 | T→C | V124A (GTG→GCG) | ybiB → | putative family 3 glycosyltransferase |
| 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 | 1,068,830 | A→G | F337S (TTT→TCT) | rutG ← | pyrimidine permease |
| RA | 1,097,492 | +G | intergenic (+663/+73) | ycdU → / ← serX | putative inner membrane protein/tRNA‑Ser |
| RA | 1,109,302 | A→G | intergenic (‑361/‑33) | opgC ← / → opgG | OPG biosynthetic transmembrane succinyltransferase/OPG biosynthetic periplasmic beta‑1,6 branching glycosyltransferase |
| RA | 1,115,423 | C→T | C23Y (TGT→TAT) | mdtG ← | putative drug efflux system protein |
| RA | 1,116,797 | A→G | intergenic (‑215/‑10) | lpxL ← / → yceA | lauryl‑acyl carrier protein (ACP)‑dependent acyltransferase/putative rhodanese‑related sulfurtransferase |
| RA | 1,154,782 | A→G | E224G (GAA→GGA) | yceG → | septation protein, ampicillin sensitivity |
| RA | 1,202,387 | T→C | T183A (ACA→GCA) | cohE ← | e14 prophage; repressor protein phage e14 |
| 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 | 1,226,979 | A→G | intergenic (+11/+92) | ycgJ → / ← pliG | uncharacterized protein/periplasmic inhibitor of g‑type lysozyme |
| RA | 1,246,015 | T→C | A454A (GCA→GCG) | treA ← | periplasmic trehalase |
| RA | 1,254,563 | T→C | T464A (ACA→GCA) | ycgV ← | putative adhesin |
| RA | 1,314,744 | T→C | T161A (ACT→GCT) | yciE ← | putative rubrerythrin/ferritin‑like metal‑binding protein |
| RA | 1,318,845 | T→C | H315R (CAC→CGC) | trpC ← | indole‑3‑glycerolphosphate synthetase and N‑(5‑phosphoribosyl)anthranilate isomerase |
| RA | 1,326,144 | C→T | P467S (CCA→TCA) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,370,155 | A→G | intergenic (+152/‑61) | pspE → / → ycjM | thiosulfate:cyanide sulfurtransferase (rhodanese)/alpha amylase catalytic domain family protein |
| RA | 1,399,978 | T→C | T87A (ACG→GCG) | ogt ← | O‑6‑alkylguanine‑DNA:cysteine‑protein methyltransferase |
| RA | 1,421,650 | (C)7→8 | coding (532/858 nt) | ydaU → | Rac prophage; conserved protein |
| RA | 1,539,343 | T→C | E1083G (GAA→GGA) | narZ ← | nitrate reductase 2 (NRZ), alpha subunit |
| RA | 1,594,132 | (C)8→7 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,724,344 | T→C | P104P (CCA→CCG) | sodC ← | superoxide dismutase, Cu, Zn, periplasmic |
| RA | 1,755,903 | G→A | G69D (GGT→GAT) | pykF → | pyruvate kinase I |
| RA | 1,776,173 | A→G | Y196C (TAC→TGC) | ydiF → | putative acetyl‑CoA:acetoacetyl‑CoA transferase: alpha subunit/beta subunit |
| RA | 1,833,916 | T→C | G172G (GGT→GGC) | ydjX → | TVP38/TMEM64 family inner membrane protein |
| RA | 1,863,313 | T→C | A181A (GCT→GCC) | gapA → | glyceraldehyde‑3‑phosphate dehydrogenase A |
| RA | 1,865,673 | A→G | intergenic (‑37/+53) | yeaE ← / ← mipA | aldo‑keto reductase, methylglyoxal to acetol, NADPH‑dependent/scaffolding protein for murein synthesizing machinery |
| RA | 1,919,775 | G→A | E756K (GAA→AAA) | yebT → | MCE domain protein |
| RA | 1,923,142 | G→A | intergenic (‑173/+223) | pphA ← / ← yebY | serine/threonine‑specific protein phosphatase 1/DUF2511 family protein |
| 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 | 1,992,730 | A→G | W30R (TGG→CGG) | pgsA ← | phosphatidylglycerophosphate synthetase |
| RA | 2,000,046 | G→A | R114C (CGC→TGC) | fliY ← | cystine transporter subunit |
| RA | 2,014,519 | A→G | S431G (AGC→GGC) | fliF → | flagellar basal‑body MS‑ring and collar protein |
| RA | 2,026,134 | C→T | T208T (ACC→ACT) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,033,044 | G→A | N12N (AAC→AAT) | yedJ ← | putative HD superfamily phosphohydrolase |
| RA | 2,117,002 | T→C | T42T (ACA→ACG) | wcaL ← | putative glycosyl transferase |
| RA | 2,161,057 | C→T | A891V (GCG→GTG) | 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 | 2,192,139 | Δ1 bp | coding (84/543 nt) | yehD ← | putative fimbrial‑like adhesin protein |
| RA | 2,209,036 | G→A | G357D (GGC→GAC) | yehP → | VMA domain putative YehL ATPase stimulator |
| RA | 2,213,249 | A→G | F466L (TTT→CTT) | yehU ← | inner membrane putative sensory kinase in two‑component system with YehT |
| 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 | 2,307,284 | A→G | R444R (CGT→CGC) | yojI ← | microcin J25 efflux ABC transporter permease/ATPase |
| RA | 2,317,816 | A→G | R687R (CGT→CGC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,458,429 | T→C | Y244C (TAT→TGT) | fadJ ← | enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 2,467,446 | A→G | K301R (AAG→AGG) | intS → | CPS‑53 (KpLE1) prophage; putative prophage CPS‑53 integrase |
| RA | 2,528,995 | T→C | E394E (GAA→GAG) | ligA ← | DNA ligase, NAD(+)‑dependent |
| RA | 2,585,998 | T→C | Y90H (TAT→CAT) | narQ → | sensory histidine kinase in two‑component regulatory system with NarP |
| RA | 2,609,458 | T→C | R324R (CGT→CGC) | hyfG → | hydrogenase 4, subunit |
| RA | 2,629,237 | T→C | intergenic (‑299/‑53) | yfgF ← / → yfgG | cyclic‑di‑GMP phosphodiesterase, anaerobic/uncharacterized protein |
| 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 | 2,705,211 | T→C | E33E (GAA→GAG) | lepB ← | leader peptidase (signal peptidase I) |
| 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 | 2,846,307 | G→A | G55G (GGC→GGT) | hycE ← | hydrogenase 3, large subunit |
| RA | 2,852,450 | A→G | K105K (AAA→AAG) | hypD → | hydrogenase maturation protein |
| RA | 2,858,154 | T→C | R354R (CGT→CGC) | mutS → | methyl‑directed mismatch repair protein |
| RA | 2,901,816 | T→C | F409L (TTC→CTC) | yqcE → | putative MFS transporter, inner membrane protein |
| RA | 2,912,885 | A→G | I256T (ATC→ACC) | relA ← | (p)ppGpp synthetase I/GTP pyrophosphokinase |
| RA | 2,932,540 | T→C | K158K (AAA→AAG) | fucO ← | L‑1,2‑propanediol oxidoreductase |
| RA | 2,986,123 | T→C | Y93H (TAC→CAC) | yqeG → | putative transporter |
| RA | 3,065,614 | T→C | R271R (CGT→CGC) | scpC → | propionyl‑CoA:succinate CoA transferase |
| RA | 3,086,618 | A→G | intergenic (+216/‑88) | yqgC → / → metK | uncharacterized protein/S‑adenosylmethionine synthetase |
| RA | 3,102,340 | (C)6→7 | coding (513/720 nt) | trmI ← | tRNA m(7)G46 methyltransferase, SAM‑dependent |
| RA | 3,135,026 | A→G | V449A (GTC→GCC) | pitB ← | phosphate transporter |
| RA | 3,159,137 | G→A | S670S (AGC→AGT) | ygiQ ← | Radical SAM superfamily protein |
| RA | 3,196,367 | A→T | D129E (GAT→GAA) | hldE ← | heptose 7‑phosphate kinase and heptose 1‑phosphate adenyltransferase |
| RA | 3,199,872 | T→C | Y365C (TAC→TGC) | ygiF ← | inorganic triphosphatase |
| RA | 3,272,271 | Δ1 bp | coding (481/885 nt) | garR ← | tartronate semialdehyde reductase |
| RA | 3,313,236 | T→C | intergenic (‑58/+106) | rbfA ← / ← infB | 30s ribosome binding factor/translation initiation factor IF‑2 |
| RA | 3,328,816 | (A)7→6 | intergenic (‑101/‑147) | greA ← / → dacB | transcript cleavage factor/D‑alanyl‑D‑alanine carboxypeptidase |
| 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 | 3,385,581 | T→C | V15A (GTT→GCT) | yhcN → | cadmium and peroxide resistance protein, stress‑induced |
| RA | 3,421,201 | G→A | T356T (ACG→ACA) | yhdX → | putative amino acid ABC transporter permease |
| RA | 3,431,418 | T→C | intergenic (‑3/+2) | tsaC ← / ← yrdD | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine‑dependent ADP‑forming ATPase/ssDNA‑binding protein, function unknown |
| RA | 3,440,116 | T→C | D305G (GAC→GGC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,447,416 | T→C | Y8C (TAC→TGC) | rplE ← | 50S ribosomal subunit protein L5 |
| RA | 3,449,100 | T→C | T24A (ACG→GCG) | rplP ← | 50S ribosomal subunit protein L16 |
| RA | 3,505,857 | A→G | V55A (GTG→GCG) | yhfS ← | FNR‑regulated pyridoxal phosphate‑dependent aminotransferase family protein |
| RA | 3,515,565 | A→G | Y117H (TAC→CAC) | dam ← | DNA adenine methyltransferase |
| RA | 3,546,863 | T→C | V102A (GTA→GCA) | gntT → | gluconate transporter, high‑affinity GNT I system |
| 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 | 3,612,540 | T→C | W226R (TGG→CGG) | yhhT → | UPF0118 family putative transporter |
| RA | 3,632,618 | G→A | intergenic (‑28/+234) | yhiJ ← / ← yhiL | DUF4049 family protein/pseudogene, DUF4049 family protein |
| 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 | 3,903,631 | T→C | Q24R (CAG→CGG) | bglB ← | cryptic phospho‑beta‑glucosidase B |
| RA | 3,904,425 | A→G | A391A (GCT→GCC) | bglF ← | fused beta‑glucoside‑specific PTS enzymes: IIA component/IIB component/IIC component |
| RA | 3,914,552 | G→A | P217S (CCG→TCG) | glmU ← | fused N‑acetyl glucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyl transferase |
| RA | 3,940,308 | A→G | L102P (CTG→CCG) | hsrA ← | putative multidrug or homocysteine efflux system |
| RA | 3,964,687 | A→G | V315A (GTT→GCT) | rhlB ← | ATP‑dependent RNA helicase |
| RA | 4,003,303 | A→G | R292R (CGT→CGC) | rarD ← | putative chloramphenical resistance permease |
| RA | 4,008,896 | A→G | V55A (GTG→GCG) | rhtB ← | homoserine, homoserine lactone and S‑methyl‑methionine efflux pump |
| RA | 4,017,296 | T→C | intergenic (+104/‑37) | udp → / → rmuC | uridine phosphorylase/DNA recombination protein |
| RA | 4,026,881 | C→T | R119C (CGC→TGC) | fre → | NAD(P)H‑flavin reductase |
| RA | 4,027,819 | A→G | C318C (TGT→TGC) | fadA ← | 3‑ketoacyl‑CoA thiolase (thiolase I) |
| RA | 4,128,316 | A→G | V27A (GTT→GCT) | metJ ← | transcriptional repressor, S‑adenosylmethionine‑binding |
| RA | 4,185,098 | A→G | Y1285C (TAC→TGC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,188,777 | A→G | D1143G (GAC→GGC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,240,380 | T→C | V19A (GTA→GCA) | psiE → | phosphate starvation inducible protein |
| RA | 4,272,615 | G→A | R419R (CGC→CGT) | uvrA ← | ATPase and DNA damage recognition protein of nucleotide excision repair excinuclease UvrABC |
| RA | 4,279,290 | A→G | D271G (GAT→GGT) | ghxP → | guanine/hypoxanthine permease, high affinity; guanine/hypoxanthine:H+ symporter |
| RA | 4,281,308 | A→G | A443A (GCA→GCG) | yjcE → | 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 | 4,342,193 | 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 | 4,381,596 | A→G | G241G (GGT→GGC) | frdA ← | anaerobic fumarate reductase catalytic and NAD/flavoprotein subunit |
| RA | 4,399,151 | Δ1 bp | coding (1740/1848 nt) | mutL → | methyl‑directed mismatch repair protein |
| RA | 4,428,008 | C→T | pseudogene (315/402 nt) | ytfA → | pseudogene, related to transcriptional regulators |
| RA | 4,453,330 | A→G | N254D (AAC→GAC) | ytfT → | putative sugar ABC transporter permease |
| RA | 4,475,822 | T→C | M129T (ATG→ACG) | yjgL → | SopA‑central‑domain‑like hexapeptide repeat protein |
| RA | 4,617,393 | A→G | D24G (GAC→GGC) | deoC → | 2‑deoxyribose‑5‑phosphate aldolase, NAD(P)‑linked |
| RA | 4,625,906 | T→C | intergenic (+43/‑6) | serB → / → radA | 3‑phosphoserine phosphatase/DNA repair protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 223795–224771 | 228611–226988 | 2218–4817 | 64 [62] | [62] 63 | [rrsH]–[rrlH] | [rrsH], ileV, alaV, [rrlH] |
| * | * | ÷ | NC_000913 | 3423730–3424234 | 3424588–3424238 | 5–859 | 63 [62] | [61] 63 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 13 (0.120) | 78 (0.800) | 65/266 | 0.8 | 85.4% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 15 (0.150) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 13 (0.120) | 92 (0.950) | 78/266 | 0.2 | 87.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 15 (0.150) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 120 (1.130) | 96/290 | 0.1 | 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 | |||||