mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 112,531 | A→C | 5.1% | intergenic (+209/‑95) | gltX → / → cysE | glutamate‑‑tRNA ligase/serine O‑acetyltransferase |
| RA | 112,586 | G→T | 8.0% | intergenic (+264/‑40) | gltX → / → cysE | glutamate‑‑tRNA ligase/serine O‑acetyltransferase |
| RA | 112,636 | G→T | 6.0% | R4I (AGA→ATA) | cysE → | serine O‑acetyltransferase |
| RA | 112,660 | C→A | 5.2% | T12K (ACA→AAA) | cysE → | serine O‑acetyltransferase |
| RA | 131,088 | C→A | 100% | S194Y (TCT→TAT) | fusA → | elongation factor G |
| RA | 154,410 | C→T | 77.8% | R95C (CGT→TGT) | rpsI → | 30S ribosomal protein S9 |
| RA | 177,011 | T→G | 8.1% | intergenic (+184/‑88) | EO946_RS01020 → / → EO946_RS01025 | alcohol dehydrogenase/SulP family inorganic anion transporter |
| RA | 177,029 | G→C | 13.3% | intergenic (+202/‑70) | EO946_RS01020 → / → EO946_RS01025 | alcohol dehydrogenase/SulP family inorganic anion transporter |
| RA | 183,034 | A→G | 26.7% | M104T (ATG→ACG) | feuA ← | iron ABC transporter substrate‑binding protein FeuA |
| RA | 196,535 | C→G | 6.2% | S99* (TCA→TGA) | cdaA → | diadenylate cyclase CdaA |
| RA | 240,190 | G→T | 14.5% | F114L (TTC→TTA) | EO946_RS01360 ← | hypothetical protein |
| RA | 240,193 | G→T | 5.0% | N113K (AAC→AAA) | EO946_RS01360 ← | hypothetical protein |
| RA | 240,198 | G→T | 16.4% | Q112K (CAA→AAA) | EO946_RS01360 ← | hypothetical protein |
| RA | 240,207 | G→T | 10.3% | Q109K (CAA→AAA) | EO946_RS01360 ← | hypothetical protein |
| RA | 240,211 | G→T | 16.3% | A107A (GCC→GCA) | EO946_RS01360 ← | hypothetical protein |
| RA | 316,262 | C→A | 7.0% | Q28K (CAA→AAA) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 316,282 | G→C | 14.9% | K34N (AAG→AAC) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 316,300 | G→C | 9.0% | L40L (CTG→CTC) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 316,303 | A→C | 5.0% | K41N (AAA→AAC) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 438,766 | G→T | 5.1% | intergenic (‑32/‑74) | gabR ← / → gabT | transcriptional regulator GabR/4‑aminobutyrate‑‑2‑oxoglutarate transaminase |
| RA | 549,085 | C→A | 11.7% | Q33K (CAA→AAA) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 549,119 | T→G | 9.4% | L44R (CTG→CGG) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 607,359 | A→C | 10.0% | T68P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,413 | A→C | 11.4% | T86P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,430 | G→C | 5.4% | A91A (GCG→GCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,562 | G→C | 9.0% | G135G (GGG→GGC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,638 | G→C | 7.0% | A161P (GCC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,671 | C→G | 8.0% | P172A (CCA→GCA) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,676 | C→G | 5.4% | T173T (ACC→ACG) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,682 | G→C | 6.7% | A175A (GCG→GCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,688 | A→G | 8.7% | G177G (GGA→GGG) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,694 | C→T | 16.5% | T179T (ACC→ACT) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,700 | A→C | 22.3% | E181D (GAA→GAC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,702 | C→T | 20.5% | A182V (GCC→GTC) | EO946_RS03185 → | collagen‑like protein |
| JC | 607,835 | Δ9 bp | 7.2% | coding (678‑686/1125 nt) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,844 | C→G | 7.3% | A229A (GCC→GCG) | EO946_RS03185 → | collagen‑like protein |
| RA | 634,052 | T→G | 15.5% | E573D (GAA→GAC) | EO946_RS03330 ← | ABC‑F family ATP‑binding cassette domain‑containing protein |
| RA | 634,108 | C→A | 7.6% | V555F (GTT→TTT) | EO946_RS03330 ← | ABC‑F family ATP‑binding cassette domain‑containing protein |
| RA | 755,531 | A→C | 14.2% | Q22H (CAA→CAC) | EO946_RS03880 → | rhamnogalacturonan acetylesterase |
| RA | 886,736 | G→C | 6.8% | S51* (TCA→TGA) | EO946_RS04490 ← | MFS transporter |
| RA | 886,747 | A→C | 8.1% | P47P (CCT→CCG) | EO946_RS04490 ← | MFS transporter |
| RA | 886,754 | A→C | 8.3% | V45G (GTT→GGT) | EO946_RS04490 ← | MFS transporter |
| RA | 886,758 | C→A | 5.7% | A44S (GCC→TCC) | EO946_RS04490 ← | MFS transporter |
| RA | 986,786 | C→A | 6.8% | Q367K (CAA→AAA) | spoVR → | stage V sporulation protein SpoVR |
| RA | 986,801 | G→T | 9.3% | D372Y (GAT→TAT) | spoVR → | stage V sporulation protein SpoVR |
| RA | 1,000,541 | C→A | 6.3% | G74G (GGC→GGA) | EO946_RS05160 → | aldo/keto reductase |
| RA | 1,036,283 | C→A | 8.7% | S43Y (TCT→TAT) | EO946_RS05355 → | ABC transporter permease |
| RA | 1,038,838 | C→A | 6.7% | Q30K (CAA→AAA) | EO946_RS05365 → | AAA family ATPase |
| RA | 1,097,455 | C→A | 11.4% | I66I (ATC→ATA) | EO946_RS05675 → | MarR family transcriptional regulator |
| RA | 1,097,474 | G→T | 15.0% | E73* (GAA→TAA) | EO946_RS05675 → | MarR family transcriptional regulator |
| RA | 1,152,026 | G→C | 8.0% | G59G (GGC→GGG) | EO946_RS05920 ← | GNAT family N‑acetyltransferase |
| RA | 1,167,036 | G→T | 18.5% | D192Y (GAC→TAC) | argB → | acetylglutamate kinase |
| RA | 1,279,924 | C→A | 5.9% | I50I (ATC→ATA) | EO946_RS06645 → | altronate dehydratase family protein |
| RA | 1,293,306 | G→T | 7.3% | V127L (GTA→TTA) | EO946_RS06740 → | sigma‑70 family RNA polymerase sigma factor |
| RA | 1,427,023 | C→T | 82.2% | L80F (CTC→TTC) | ptsP → | phosphoenolpyruvate‑‑protein phosphotransferase |
| RA | 1,485,790 | G→T | 5.8% | D52Y (GAT→TAT) | ktrC → | Ktr system potassium transporter KtrC |
| RA | 1,582,926 | C→A | 5.7% | I39I (ATC→ATA) | ylyA → | sporulation‑related RNA polymerase‑binding protein YlyA |
| RA | 1,669,737 | C→T | 100% | Q88* (CAG→TAG) | fliM → | flagellar motor switch protein FliM |
| RA | 1,720,748 | C→A | 8.9% | S224R (AGC→AGA) | spoIIIE → | DNA translocase SpoIIIE |
| RA | 1,753,584 | G→T | 8.4% | intergenic (+275/‑230) | fabD → / → EO946_RS09090 | ACP S‑malonyltransferase/acyltransferase domain‑containing protein |
| RA | 1,820,732 | C→A | 7.4% | S361Y (TCT→TAT) | EO946_RS09145 → | thioesterase domain‑containing protein |
| RA | 1,925,447 | C→A | 7.5% | R1870L (CGA→CTA) | EO946_RS09730 ← | non‑ribosomal peptide synthetase |
| RA | 2,034,593 | C→A | 18.4% | intergenic (‑259/‑135) | EO946_RS10175 ← / → EO946_RS10180 | UPF0715 family protein/hypothetical protein |
| RA | 2,103,774 | C→A | 12.5% | V4L (GTA→TTA) | azoJ ← | FMN‑dependent NADH‑azoreductase AzoJ |
| RA | 2,139,480 | A→C | 8.4% | A119A (GCT→GCG) | deoD ← | purine‑nucleoside phosphorylase |
| RA | 2,169,199 | C→G | 100% | G81G (GGG→GGC) | EO946_RS10950 ← | class I SAM‑dependent methyltransferase |
| RA | 2,194,168 | G→T | 15.4% | Q247K (CAA→AAA) | kdgR ← | pectin utilization transcriptional regulator KdgR |
| RA | 2,214,518 | T→G | 6.5% | K60T (AAA→ACA) | nth ← | endonuclease III |
| RA | 2,214,528 | G→T | 6.2% | Q57K (CAA→AAA) | nth ← | endonuclease III |
| RA | 2,214,541 | G→T | 6.7% | T52T (ACC→ACA) | nth ← | endonuclease III |
| RA | 2,350,865 | A→T | 5.6% | pseudogene (916/1182 nt) | EO946_RS12020 ← | IS3 family transposase |
| RA | 2,387,066 | T→G | 13.5% | S354R (AGC→CGC) | EO946_RS12195 ← | acetyl‑CoA C‑acetyltransferase |
| RA | 2,387,114 | C→A | 8.3% | V338L (GTA→TTA) | EO946_RS12195 ← | acetyl‑CoA C‑acetyltransferase |
| RA | 2,729,932 | C→A | 7.2% | M278I (ATG→ATT) | lcfA ← | long‑chain‑fatty‑acid‑‑CoA ligase LcfA |
| RA | 2,729,937 | C→A | 6.1% | E277* (GAA→TAA) | lcfA ← | long‑chain‑fatty‑acid‑‑CoA ligase LcfA |
| RA | 2,812,790 | T→G | 8.6% | E199D (GAA→GAC) | EO946_RS14520 ← | SDR family oxidoreductase |
| RA | 2,851,294 | G→T | 6.2% | P60T (CCC→ACC) | murC ← | UDP‑N‑acetylmuramate‑‑L‑alanine ligase |
| RA | 2,865,416 | C→A | 6.8% | P134P (CCG→CCT) | pulA ← | type I pullulanase |
| RA | 2,900,726 | G→T | 5.2% | G96V (GGA→GTA) | EO946_RS14945 → | extracellular solute‑binding protein |
| RA | 2,901,667 | T→A | 9.0% | Y410N (TAC→AAC) | EO946_RS14945 → | extracellular solute‑binding protein |
| RA | 2,901,671 | A→C | 15.4% | K411T (AAA→ACA) | EO946_RS14945 → | extracellular solute‑binding protein |
| RA | 2,910,798 | C→A | 5.7% | M1M (ATG→ATT) † | EO946_RS14985 ← | MFS transporter |
| RA | 2,978,569 | C→T | 18.0% | noncoding (2232/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,979,628 | T→A | 12.6% | noncoding (1173/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,160 | G→A | 21.0% | noncoding (641/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,981,239 | T→A | 13.1% | noncoding (1281/1550 nt) | EO946_RS15435 ← | 16S ribosomal RNA |
| RA | 2,982,148 | G→T | 18.9% | noncoding (372/1550 nt) | EO946_RS15435 ← | 16S ribosomal RNA |
| RA | 2,991,245 | G→T | 22.9% | intergenic (+46/‑161) | gbsR → / → bslA | transcriptional regulator GbsR/biofilm‑surface layer protein BslA |
| RA | 2,991,247 | A→T | 10.4% | intergenic (+48/‑159) | gbsR → / → bslA | transcriptional regulator GbsR/biofilm‑surface layer protein BslA |
| RA | 2,991,252 | C→A | 29.5% | intergenic (+53/‑154) | gbsR → / → bslA | transcriptional regulator GbsR/biofilm‑surface layer protein BslA |
| RA | 2,991,262 | G→T | 21.2% | intergenic (+63/‑144) | gbsR → / → bslA | transcriptional regulator GbsR/biofilm‑surface layer protein BslA |
| MC JC | 3,191,671 | (ATTATAATT)2→1 | 100% | intergenic (+3/‑66) | EO946_RS16520 → / → mrgA | oxidoreductase/metalloregulation DNA‑binding stress protein MgrA |
| RA | 3,201,029 | C→A | 8.9% | Y216* (TAC→TAA) | EO946_RS16570 → | spore germination protein |
| RA | 3,201,042 | G→T | 9.6% | A221S (GCG→TCG) | EO946_RS16570 → | spore germination protein |
| RA | 3,219,734 | C→A | 6.6% | Q358K (CAA→AAA) | oxdC → | oxalate decarboxylase |
| RA | 3,219,805 | G→T | 11.8% | K381N (AAG→AAT) | oxdC → | oxalate decarboxylase |
| RA | 3,280,312 | C→A | 6.0% | L136F (TTG→TTT) | EO946_RS16965 ← | lantibiotic dehydratase |
| RA | 3,280,341 | C→A | 8.0% | E127* (GAG→TAG) | EO946_RS16965 ← | lantibiotic dehydratase |
| RA | 3,280,377 | G→T | 8.9% | Q115K (CAA→AAA) | EO946_RS16965 ← | lantibiotic dehydratase |
| RA | 3,285,567 | C→T | 34.6% | L278L (CTG→CTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,575 | T→G | 34.2% | N276H (AAT→CAT) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,580 | A→G | 37.6% | I274T (ATA→ACA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,647 | C→A | 39.9% | V252L (GTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,713 | G→A | 26.9% | L230L (CTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,299,548 | T→G | 6.8% | intergenic (‑246/+63) | EO946_RS17065 ← / ← gap | phosphoglycerate kinase/type I glyceraldehyde‑3‑phosphate dehydrogenase |
| RA | 3,348,441 | C→G | 5.5% | S147C (TCT→TGT) | EO946_RS17300 → | carboxylesterase/lipase family protein |
| RA | 3,349,666 | T→G | 5.4% | intergenic (+1/+26) | EO946_RS17305 → / ← padC | hypothetical protein/phenolic acid decarboxylase |
| RA | 3,362,393 | G→C | 9.8% | L99L (CTG→CTC) | EO946_RS17380 → | MazG‑like family protein |
| RA | 3,375,849 | T→G | 5.5% | N263H (AAC→CAC) | trxB ← | thioredoxin‑disulfide reductase |
| RA | 3,394,417 | G→T | 8.0% | A161A (GCC→GCA) | ppaX ← | pyrophosphatase PpaX |
| RA | 3,394,434 | T→G | 5.9% | S156R (AGC→CGC) | ppaX ← | pyrophosphatase PpaX |
| RA | 3,446,964 | T→A | 7.3% | M208L (ATG→TTG) | degU ← | two‑component system response regulator DegU |
| RA | 3,446,970 | G→T | 20.8% | Q206K (CAA→AAA) | degU ← | two‑component system response regulator DegU |
| RA | 3,447,038 | T→G | 9.5% | N183T (AAC→ACC) | degU ← | two‑component system response regulator DegU |
| RA | 3,465,110 | C→G | 7.1% | G711A (GGA→GCA) | EO946_RS17885 ← | SpoIID/LytB domain‑containing protein |
| RA | 3,496,440 | G→T | 6.1% | Q330K (CAA→AAA) | EO946_RS17995 ← | glucosaminidase domain‑containing protein |
| RA | 3,498,703 | G→T | 7.1% | intergenic (‑198/‑69) | manA ← / → EO946_RS18005 | mannose‑6‑phosphate isomerase, class I/spore germination protein |
| RA | 3,562,015 | A→C | 7.8% | intergenic (‑661/‑137) | EO946_RS18300 ← / → EO946_RS21105 | response regulator/HAMP domain‑containing histidine kinase |
| RA | 3,569,139 | C→T | 83.1% | M166I (ATG→ATA) | mbl ← | cell shape‑determining protein Mbl |
| RA | 3,584,283 | G→T | 7.0% | D322Y (GAT→TAT) | EO946_RS18420 → | N‑acetylneuraminate synthase family protein |
| RA | 3,584,291 | G→T | 5.6% | S324S (TCG→TCT) | EO946_RS18420 → | N‑acetylneuraminate synthase family protein |
| RA | 3,584,358 | C→A | 6.3% | L347I (CTA→ATA) | EO946_RS18420 → | N‑acetylneuraminate synthase family protein |
| RA | 3,635,983 | G→C | 16.4% | D171E (GAC→GAG) | EO946_RS18730 ← | fructose‑bisphosphate aldolase |
| RA | 3,719,864 | T→G | 5.5% | S79R (AGC→CGC) | EO946_RS19145 ← | YwdI family protein |
| RA | 3,746,893 | T→G | 7.4% | N59H (AAC→CAC) | EO946_RS19275 ← | galactokinase |
| RA | 3,746,962 | C→A | 6.4% | D36Y (GAT→TAT) | EO946_RS19275 ← | galactokinase |
| RA | 3,769,576 | T→G | 6.5% | I281S (ATT→AGT) | sacX → | SacY negative regulator SacX |
| RA | 3,790,764 | T→G | 13.4% | N203H (AAC→CAC) | EO946_RS19525 ← | BglG family transcription antiterminator |
| RA | 3,790,777 | C→A | 9.4% | L198L (CTG→CTT) | EO946_RS19525 ← | BglG family transcription antiterminator |
| RA | 3,846,624 | G→T | 6.7% | Q195K (CAA→AAA) | dbpA ← | ATP‑dependent RNA helicase DbpA |
| RA | 3,851,220 | G→T | 7.3% | T52K (ACG→AAG) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,237 | G→T | 9.0% | I46I (ATC→ATA) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,254 | G→C | 6.2% | L41V (CTT→GTT) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,945,908 | T→G | 7.4% | L388R (CTT→CGT) | EO946_RS20305 → | Na+/H+ antiporter |
| RA | 3,945,938 | T→G | 10.1% | L398R (CTT→CGT) | EO946_RS20305 → | Na+/H+ antiporter |
| RA | 3,976,149 | G→T | 6.2% | G19G (GGC→GGA) | rlmH ← | 23S rRNA (pseudouridine(1915)‑N(3))‑methyltransferase RlmH |
| RA | 4,040,429 | C→A | 6.3% | R197L (CGT→CTT) | mnmG ← | tRNA uridine‑5‑carboxymethylaminomethyl(34) synthesis enzyme MnmG |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP034943 | = 91969 | NA (NA) | 15 (0.030) | 12/248 | NT | NA | intergenic (+131/‑39) | EO946_RS00485/EO946_RS00490 | 16S ribosomal RNA/23S ribosomal RNA |
| ? | NZ_CP034943 | 91973 = | NA (NA) | intergenic (+135/‑35) | EO946_RS00485/EO946_RS00490 | 16S ribosomal RNA/23S ribosomal RNA | |||||