mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision aa8f2595a244
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 7,686 | C→T | V92I (GTC→ATC) | yaaJ ← | putative transporter |
| RA | 105,107 | T→C | Y376H (TAT→CAT) | ftsA → | ATP‑binding cell division FtsK recruitment protein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 319,348 | G→A | L218L (CTC→CTT) | rclA ← | reactive chlorine stress species (RCS) resistance protein, pyridine nucleotide‑dependent disulfide oxidoreductase family |
| RA | 445,781 | A→G | W296R (TGG→CGG) | yajR ← | putative transporter |
| RA | 468,662 | C→T | L94L (CTG→TTG) | ybaO → | putative DNA‑binding transcriptional regulator |
| RA | 529,055 | (T)8→7 | pseudogene (416/491 nt) | ybbD → | pseudogene |
| RA | 573,440 | C→T | R24C (CGC→TGC) | rusA → | DLP12 prophage, endonuclease RUS |
| RA | 585,217 | C→T | W139* (TGG→TGA) | ompT ← | DLP12 prophage, outer membrane protease VII, outer membrane protein 3b |
| RA | 632,923 | A→G | A185A (GCT→GCC) | ybdH ← | putative oxidoreductase |
| RA | 671,531 | A→G | G25G (GGT→GGC) | holA ← | DNA polymerase III, delta subunit |
| RA | 685,425 | T→C | T169A (ACC→GCC) | gltK ← | glutamate/aspartate ABC transporter permease |
| RA | 752,248 | T→C | Y183C (TAC→TGC) | ybgD ← | putative fimbrial‑like adhesin protein |
| RA | 865,423 | A→G | P314P (CCT→CCC) | moeA ← | molybdopterin molybdenumtransferase, molybdopterin biosynthesis protein |
| RA | 935,542 | G→A | A773A (GCG→GCA) | ftsK → | DNA translocase at septal ring sorting daughter chromsomes |
| RA | 1,121,934 | A→G | I225T (ATC→ACC) | pyrC ← | dihydro‑orotase |
| RA | 1,190,202 | T→C | E82E (GAA→GAG) | phoP ← | response regulator in two‑component regulatory system with PhoQ |
| RA | 1,235,563 | A→G | Y209C (TAC→TGC) | fadR → | fatty acid metabolism regulon transcriptional regulator |
| RA | 1,287,826 | C→T | A267T (GCA→ACA) | purU ← | formyltetrahydrofolate hydrolase |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,334,893 | A→G | intergenic (+64/‑231) | cysB → / → ymiA | N‑acetylserine‑responsive cysteine regulon transcriptional activator, autorepressor/uncharacterized protein |
| RA | 1,458,617 | A→G | A118A (GCA→GCG) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,458,625 | (G)6→7 | coding (362/789 nt) | paaG → | 1,2‑epoxyphenylacetyl‑CoA isomerase, oxepin‑CoA‑forming |
| RA | 1,594,132 | (C)8→9 | pseudogene (3856/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,595,427 | A→G | pseudogene (2561/3861 nt) | yneO ← | pseudogene, AidA homolog |
| RA | 1,644,142 | G→A | Q55* (CAG→TAG) | ydfU ← | Qin prophage, uncharacterized protein |
| RA | 1,657,767 | G→A | C68Y (TGC→TAC) | ynfD → | DUF1161 family periplasmic protein |
| RA | 1,684,038 | G→A | G386D (GGC→GAC) | rstB → | sensory histidine kinase of RstAB two‑component system |
| RA | 1,719,281 | C→T | V108M (GTG→ATG) | anmK ← | anhydro‑N‑acetylmuramic acid kinase |
| RA | 1,820,136 | G→A | P360L (CCG→CTG) | chbC ← | N,N'‑diacetylchitobiose‑specific enzyme IIC component of PTS |
| RA | 1,825,480 | T→C | D49G (GAC→GGC) | spy ← | periplasmic ATP‑independent protein refolding chaperone, stress‑induced |
| RA | 1,897,952 | G→A | G341S (GGC→AGC) | sdaA → | L‑serine dehydratase 1 |
| RA | 1,904,586 | T→C | V231A (GTC→GCC) | manZ → | mannose‑specific enzyme IID component of PTS |
| RA | 1,905,787 | T→C | S34P (TCT→CCT) | mntP → | putative Mn(2+) efflux pump, mntR‑regulated |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 1,995,769 | T→C | intergenic (‑410/‑49) | uvrY ← / → yecF | response regulator in two‑component regulatory system with BarA/DUF2594 family protein |
| RA | 2,072,728 | G→A | G397D (GGT→GAT) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| RA | 2,073,225 | T→C | W563R (TGG→CGG) | flu → | CP4‑44 prophage, antigen 43 (Ag43) phase‑variable biofilm formation autotransporter |
| 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 | 2,193,417 | T→C | D251G (GAC→GGC) | mrp ← | antiporter inner membrane protein |
| RA | 2,203,362 | A→G | I1028M (ATA→ATG) | yehI → | DUF4132 domain‑containing protein |
| RA | 2,228,728 | C→T | pseudogene (31/150 nt) | mdtQ ← | pseudogene, putative channel/filament proteins |
| RA | 2,233,485 | (T)6→7 | coding (608/720 nt) | sanA → | DUF218 superfamily vancomycin high temperature exclusion protein |
| RA | 2,248,780 | C→T | R280Q (CGG→CAG) | yeiE ← | putative DNA‑binding transcriptional regulator |
| RA | 2,298,294 | G→A | T142I (ACC→ATC) | napB ← | nitrate reductase, small, cytochrome C550 subunit, periplasmic |
| RA | 2,314,992 | T→C | L502P (CTG→CCG) | rcsD → | phosphotransfer intermediate protein in two‑component regulatory system with RcsBC |
| RA | 2,340,022 | C→T | G152G (GGC→GGT) | ubiG → | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase/ 2‑octaprenyl‑6‑hydroxy phenol methylase |
| RA | 2,401,103 | G→A | T151T (ACC→ACT) | nuoF ← | NADH:ubiquinone oxidoreductase, chain F |
| RA | 2,563,520 | G→T | intergenic (+403/‑72) | yffP → / → yffQ | CPZ‑55 prophage, uncharacterized protein/CPZ‑55 prophage, uncharacterized protein |
| RA | 2,763,869 | (T)7→8 | coding (1285/1617 nt) | yfjL ← | CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein |
| RA | 2,842,591 | T→C | L151L (TTA→TTG) | hycI ← | protease involved in processing C‑terminal end of HycE |
| RA | 2,933,613 | T→C | T26A (ACA→GCA) | fucA ← | L‑fuculose‑1‑phosphate aldolase |
| RA | 2,937,802 | A→G | D112G (GAC→GGC) | fucK → | L‑fuculokinase |
| RA | 3,007,295 | T→C | V345A (GTG→GCG) | ygeW → | putative carbamoyltransferase |
| RA | 3,139,583 | G→A | R286H (CGT→CAT) | yghU → | putative S‑transferase |
| RA | 3,207,686 | G→A | G106R (GGG→AGG) | ttdB → | L‑tartrate dehydratase, beta subunit |
| RA | 3,226,690 | A→G | T153A (ACC→GCC) | ygjI → | putative transporter |
| RA | 3,271,600 | (C)5→6 | coding (171/1146 nt) | garK ← | glycerate kinase I |
| JC | 3,304,813 | (C)7→10 | coding (1005/1245 nt) | mtr ← | tryptophan transporter of high affinity |
| RA | 3,366,953 | G→A | G10R (GGA→AGA) | yhcF → | putative transcriptional regulator |
| RA | 3,457,094 | A→G | I240V (ATC→GTC) | gspD → | general secretory pathway component, cryptic |
| 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 | 3,591,739 | A→T | I196N (ATC→AAC) | ugpB ← | sn‑glycerol‑3‑phosphate ABC transporter periplasmic binding protein |
| RA | 3,624,198 | T→C | pseudogene (312/351 nt) | yrhC → | pseudogene fragment |
| RA | 3,634,940 | A→G | S34G (AGC→GGC) | yhiM → | acid resistance protein, inner membrane |
| RA | 3,655,564 | G→A | S113S (AGC→AGT) | yhiD ← | putative Mg(2+) transport ATPase, inner membrane protein |
| RA | 3,791,004 | A→G | G114G (GGT→GGC) | tdh ← | 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 | 3,844,805 | T→C | L281P (CTC→CCC) | adeD → | cryptic adenine deaminase |
| RA | 3,865,112 | Δ1 bp | coding (1162/1662 nt) | yidE ← | putative transporter |
| RA | 3,897,086 | T→C | C105R (TGT→CGT) | yieH → | phosphoenolpyruvate and 6‑phosphogluconate phosphatase |
| RA | 3,901,765 | G→A | G152G (GGC→GGT) | bglH ← | carbohydrate‑specific outer membrane porin, cryptic |
| RA | 3,926,801 | A→G | V68A (GTA→GCA) | asnC ← | transcriptional activator of asnA, autorepressor |
| RA | 3,936,381 | C→T | T35M (ACG→ATG) | rbsB → | D‑ribose ABC transporter periplasmic binding protein, ribose chemotaxis receptor |
| RA | 4,185,540 | C→T | P64L (CCG→CTG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,281,472 | A→G | E498G (GAG→GGG) | 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 | 4,312,566 | T→C | R142R (AGA→AGG) | alsR ← | d‑allose‑inducible als operon transcriptional repressor, autorepressor, repressor of rpiR |
| RA | 4,340,898 | C→T | R244H (CGC→CAC) | melR ← | melibiose operon transcriptional regulator, autoregulator |
| RA | 4,351,093 | G→A | G190G (GGC→GGT) | dcuS ← | sensory histidine kinase in two‑component regulatory system with DcuR, regulator of anaerobic fumarate respiration |
| RA | 4,490,935 | A→G | L69L (TTG→CTG) | idnR ← | transcriptional repressor, 5‑gluconate‑binding |
| RA | 4,538,491 | C→T | G92D (GGC→GAC) | nanM ← | N‑acetylneuraminic acid mutarotase |
| RA | 4,544,191 | A→G | K155R (AAA→AGA) | fimI → | fimbrial protein involved in type 1 pilus biosynthesis |
| RA | 4,574,259 | A→G | pseudogene (341/2937 nt) | yjiV → | pseudogene, conserved hypothetical protein |
| RA | 4,606,094 | (G)8→7 | noncoding (72/87 nt) | leuV ← | tRNA‑Leu |
| RA | 4,628,576 | A→G | intergenic (+29/+279) | nadR → / ← ettA | trifunctional protein: nicotinamide mononucleotide adenylyltransferase, ribosylnicotinamide kinase, transcriptional repressor/energy‑dependent translational throttle A |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 807341 | 810360 | 3020 | 2 [1] | [1] 2 | ybhB–[bioB] | ybhB, bioA, [bioB] |
| * | * | ÷ | NC_000913 | 1465204 | 1465212 | 9 | 2 [1] | [1] 2 | ynbG | uncharacterized protein |
| * | * | ÷ | NC_000913 | 2033861 | 2033908 | 48 | 2 [0] | [1] 3 | rseX/yedS | sRNA antisense regulator of ompA and ompC translation, Hfq‑dependent/pseudogene, outer membrane protein homology, putative outer membrane protein |
| * | * | ÷ | NC_000913 | 2211733 | 2211777 | 45 | 3 [1] | [1] 2 | yehS | DUF1456 family protein |
| * | * | ÷ | NC_000913 | 2857138 | 2859608 | 2471 | 7 [0] | [0] 3 | mutS | methyl‑directed mismatch repair protein |
| * | * | ÷ | NC_000913 | 3423794–3424234 | 3424523–3424243 | 10–730 | 2 [1] | [1] 3 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3623984–3624038 | 3624122 | 85–139 | 2 [1] | [1] 2 | yrhC | pseudogene fragment |
| * | * | ÷ | NC_000913 | 4035872–4037090 | 4037349–4037094 | 5–1478 | 2 [1] | [1] 2 | [rrsA]–alaT | [rrsA], ileT, alaT |
| * | * | ÷ | NC_000913 | 4304524 | 4304563 | 40 | 3 [1] | [1] 3 | ytcA/yjcS | putative inner membrane efflux pump‑associated DUF1656 family protein/metallo‑beta‑lactamase superfamily protein |
| * | * | ÷ | NC_000913 | 4410069 | 4410113 | 45 | 6 [1] | [1] 2 | rlmB/yjfI | 23S rRNA mG2251 2'‑O‑ribose methyltransferase, SAM‑dependent/DUF2170 family protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 27 (1.060) | 12 (0.540) | 11/208 | 0.7 | 35.1% | coding (290/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | 1209619 = | 21 (0.950) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 27 (1.060) | 6 (0.270) | 6/208 | 1.4 | 21.3% | coding (305/630 nt) | stfP | e14 prophage, uncharacterized protein |
| ? | NC_000913 | = 1209602 | 21 (0.950) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage, side tail fiber protein fragment family,Phage or Prophage Related | |||||