mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 37,255 | A→C | 27.1% | G190G (GGT→GGG) | caiC ← | putative crotonobetaine/carnitine‑CoA ligase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 342,510 | C→G | 12.5% | intergenic (+3/‑374) | yahJ → / → yahK | putative metallo‑dependent hydrolase domain deaminase/broad specificity NADPH‑dependent aldehyde reductase, Zn‑containing |
| RA | 425,249 | T→G | 11.1% | V80G (GTG→GGG) | queA → | S‑adenosylmethionine:tRNA ribosyltransferase‑isomerase |
| RA | 429,830 | T→G | 21.5% | V109G (GTG→GGG) | secF → | SecYEG protein translocase auxillary subunit |
| RA | 458,189 | A→G | 15.9% | D255G (GAT→GGT) | clpX → | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease |
| JC JC | 458,790 | IS186 (–) +6 bp :: Δ1 bp | 47.6% | intergenic (+90/‑93) | clpX → / → lon | ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La |
| RA | 467,118 | T→C | 16.3% | G65G (GGA→GGG) | ybaE ← | putative ABC transporter periplasmic binding protein |
| RA | 489,597 | T→G | 13.4% | V1021G (GTG→GGG) | mscK → | mechanosensitive channel protein, intermediate conductance, K+ regulated |
| RA | 760,032 | A→C | 17.5% | T443P (ACC→CCC) | sucA → | 2‑oxoglutarate decarboxylase, thiamine triphosphate‑binding |
| RA | 776,058 | T→G | 11.4% | G70G (GGT→GGG) | tolR → | membrane spanning protein in TolA‑TolQ‑TolR complex |
| RA | 1,065,745 | A→G | 19.0% | E54G (GAG→GGG) | agp → | glucose‑1‑phosphatase/inositol phosphatase |
| RA | 1,078,659 | T→G | 19.9% | H75P (CAC→CCC) | putA ← | fused DNA‑binding transcriptional regulator/proline dehydrogenase/pyrroline‑5‑carboxylate dehydrogenase |
| JC | 1,195,194 | Δ3 bp | 9.3% | coding (72‑74/1251 nt) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,131 | G→A | 20.4% | A337T (GCC→ACC) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,305 | C→T | 46.8% | R395C (CGT→TGT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,378,289 | A→C | 12.4% | T136P (ACT→CCT) | ycjT → | putative family 65 glycosyl hydrolase |
| RA | 1,406,283 | T→G | 21.5% | V102G (GTG→GGG) | smrA → | DNA endonuclease |
| RA | 1,425,607 | G→T | 9.6% | L77L (CTG→CTT) | ynaK → | Rac prophage; conserved protein |
| RA | 1,530,890 | A→T | 6.0% | pseudogene (305/738 nt) | yncI → | pseudogene |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,126,514 | T→C | 18.0% | E226G (GAG→GGG) | wcaG ← | bifunctional GDP‑fucose synthetase: GDP‑4‑dehydro‑6‑deoxy‑D‑mannose epimerase/ GDP‑4‑dehydro‑6‑L‑deoxygalactose reductase |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,360 | Δ1 bp | 14.0% | pseudogene (3/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,216,209 | T→A | 13.7% | I90F (ATT→TTT) | yehW ← | putative ABC transporter permease |
| RA | 2,274,349 | T→G | 24.7% | G57G (GGT→GGG) | yejB → | microcin C ABC transporter permease |
| RA | 2,525,307 | G→T | 13.4% | E61* (GAA→TAA) | yfeN → | putative outer membrane protein |
| RA | 2,745,097 | G→C | 12.8% | G81G (GGC→GGG) | trmD ← | tRNA m(1)G37 methyltransferase, SAM‑dependent |
| RA | 2,849,513 | T→G | 23.8% | T113P (ACC→CCC) | hycB ← | hydrogenase 3, Fe‑S subunit |
| RA | 2,950,173 | A→G | 18.6% | E311G (GAG→GGG) | argA → | amino acid N‑acetyltransferase and inactive acetylglutamate kinase |
| RA | 3,006,050 | G→A | 10.6% | intergenic (‑264/‑212) | ygeV ← / → ygeW | putative sigma‑54‑interacting transcriptional activator/putative carbamoyltransferase |
| RA | 3,090,130 | A→C | 17.4% | T126P (ACC→CCC) | yggI → | Zn‑dependent metalloprotease‑related protein |
| RA | 3,206,438 | G→A | 19.4% | intergenic (‑182/‑25) | ttdR ← / → ttdA | transcriptional activator of ttdABT/L‑tartrate dehydratase, alpha subunit |
| RA | 3,216,975 | T→G | 19.7% | V66G (GTG→GGG) | yqjI → | PadR family putative transcriptional regulator |
| RA | 3,251,685 | A→G | 11.6% | E221G (GAG→GGG) | yqjG → | putative S‑transferase |
| RA | 3,277,500 | T→G | 17.2% | V55G (GTG→GGG) | yhaV → | toxin of the SohB(PrlF)‑YhaV toxin‑antitoxin system |
| RA | 3,289,059 | G→A | 12.4% | L82L (CTG→CTA) | yraJ → | putative outer membrane protein |
| RA | 3,289,078 | C→A | 16.0% | Q89K (CAG→AAG) | yraJ → | putative outer membrane protein |
| RA | 3,296,181 | A→T | 11.3% | I125F (ATT→TTT) | diaA → | DnaA initiator‑associating factor for replication initiation |
| RA | 3,429,967 | A→C | 12.3% | C19W (TGT→TGG) | yrdB ← | DUF1488 family protein |
| RA | 3,514,938 | T→G | 11.8% | H41P (CAC→CCC) | rpe ← | D‑ribulose‑5‑phosphate 3‑epimerase |
| RA | 3,532,543 | A→T | 10.3% | intergenic (‑104/‑275) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| RA | 3,532,595 | C→A | 13.3% | intergenic (‑156/‑223) | yhgE ← / → pck | DUF4153 family putative inner membrane protein/phosphoenolpyruvate carboxykinase [ATP] |
| RA | 3,560,455:1 | +G | 100% | 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 | 3,662,719 | T→G | 12.9% | V769G (GTG→GGG) | mdtF → | anaerobic multidrug efflux transporter, ArcA‑regulated |
| RA | 3,665,652 | G→A | 16.7% | F53F (TTC→TTT) | gadX ← | acid resistance regulon transcriptional activator; autoactivator |
| RA | 3,665,655 | T→A | 10.6% | V52V (GTA→GTT) | gadX ← | acid resistance regulon transcriptional activator; autoactivator |
| RA | 3,665,707 | A→C | 20.0% | V35G (GTT→GGT) | gadX ← | acid resistance regulon transcriptional activator; autoactivator |
| RA | 3,755,363 | A→C | 11.1% | G383G (GGT→GGG) | aldB ← | aldehyde dehydrogenase B |
| RA | 3,757,532 | G→A | 15.7% | S99F (TCT→TTT) | yiaY ← | L‑threonine dehydrogenase |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,820,994 | A→C | 9.1% | G59G (GGT→GGG) | ligB ← | DNA ligase, NAD(+)‑dependent |
| RA | 3,860,856 | A→C | 11.5% | T192P (ACT→CCT) | yidL → | AraC family putative transcriptional regulator |
| RA | 3,891,533 | A→C | 9.3% | intergenic (+50/‑82) | tnaB → / → mdtL | tryptophan transporter of low affinity/multidrug efflux system protein |
| RA | 3,895,216 | T→A | 12.9% | *189K (TAA→AAA) | chrR → | chromate reductase, Class I, flavoprotein |
| RA | 3,996,586 | T→G | 12.9% | G100G (GGT→GGG) | xerC → | site‑specific tyrosine recombinase |
| JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,019,672 | A→C | 6.6% | T17P (ACC→CCC) | ubiJ → | aerobic ubiquinone synthesis protein, SCP2 family protein |
| RA | 4,029,690 | T→G | 10.7% | T428P (ACT→CCT) | fadB ← | fused 3‑hydroxybutyryl‑CoA epimerase/delta(3)‑cis‑delta(2)‑trans‑enoyl‑CoA isomerase/enoyl‑CoA hydratase/3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,065,580 | T→A | 13.0% | T63S (ACC→TCC) | yihO ← | putative sulphoquinovose importer |
| RA | 4,065,596 | C→A | 15.0% | L57L (CTG→CTT) | yihO ← | putative sulphoquinovose importer |
| RA | 4,065,604 | T→A | 14.6% | I55F (ATC→TTC) | yihO ← | putative sulphoquinovose importer |
| RA | 4,096,769 | T→C | 11.0% | E227G (GAG→GGG) | rhaB ← | rhamnulokinase |
| RA | 4,103,633 | A→C | 16.1% | V448G (GTG→GGG) | cpxA ← | sensory histidine kinase in two‑component regulatory system with CpxR |
| RA | 4,150,396 | T→A | 10.7% | intergenic (‑131/+51) | eptC ← / ← ppc | LPS heptose I phosphoethanolamine transferase/phosphoenolpyruvate carboxylase |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,241,801 | C→A | 12.6% | A152S (GCG→TCG) | xylE ← | D‑xylose transporter |
| RA | 4,241,994 | T→G | 14.8% | S87S (TCA→TCC) | xylE ← | D‑xylose transporter |
| RA | 4,242,022 | C→A | 12.8% | C78F (TGC→TTC) | xylE ← | D‑xylose transporter |
| RA | 4,296,060 | C→T | 26.0% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,297,510 | A→C | 11.6% | G619G (GGT→GGG) | fdhF ← | formate dehydrogenase‑H, selenopolypeptide subunit |
| RA | 4,300,840 | A→G | 9.6% | L64P (CTC→CCC) | mdtP ← | outer membrane factor of efflux pump |
| RA | 4,449,045 | T→G | 26.8% | intergenic (+3/+77) | chpB → / ← ppa | toxin of the ChpB‑ChpS toxin‑antitoxin system/inorganic pyrophosphatase |
| RA | 4,594,550 | C→G | 20.8% | R58P (CGC→CCC) | lgoT ← | putative L‑galactonate:H+ symporter |
| RA | 4,617,666 | A→G | 17.0% | E115G (GAG→GGG) | deoC → | 2‑deoxyribose‑5‑phosphate aldolase, NAD(P)‑linked |
| RA | 4,621,986 | C→G | 10.1% | A73G (GCG→GGG) | yjjJ → | putative protein kinase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 4233732 | 4235409 | 1678 | 21 [20] | [20] 23 | pgi | pgi |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 225739 = | 160 (1.820) | 8 (0.090) +ACTTCA |
3/420 | NT | 5.6% | intergenic (+164/‑20) | alaV/rrlH | tRNA‑Ala/23S ribosomal RNA of rrnH operon |
| ? | NC_000913 | = 4037483 | 117 (1.330) | intergenic (+148/‑36) | alaT/rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon | |||||
| * | ? | NC_000913 | 279163 = | NA (NA) | 57 (0.650) | 4/432 | NT | 50.0% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2760086 | 57 (0.650) | coding (1102/1410 nt) | yfjI | CP4‑57 prophage; uncharacterized protein | |||||
| * | ? | NC_000913 | 1207790 = | 11 (0.120) | 58 (0.710) | 46/400 | NT | 81.0% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 17 (0.210) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 12 (0.140) | 69 (0.850) | 42/400 | NT | 83.1% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 17 (0.210) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 1470336 = | 25 (0.280) | 31 (0.350) | 3/432 | NT | 55.4% | noncoding (1041/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1979270 | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||