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 | 132,185 | G→A | 100% | D560N (GAC→AAC) | fusA → | elongation factor G |
| RA | 266,830 | T→A | 7.3% | I45I (ATT→ATA) | kdgD → | 5‑dehydro‑4‑deoxyglucarate dehydratase |
| RA | 266,842 | T→C | 8.3% | C49C (TGT→TGC) | kdgD → | 5‑dehydro‑4‑deoxyglucarate dehydratase |
| RA | 266,857 | T→C | 7.6% | F54F (TTT→TTC) | kdgD → | 5‑dehydro‑4‑deoxyglucarate dehydratase |
| RA | 316,262 | C→A | 14.4% | Q28K (CAA→AAA) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 452,125 | T→A | 100% | K146I (AAA→ATA) | EO946_RS02320 ← | dienelactone hydrolase family protein |
| RA | 549,137 | T→A | 16.2% | I50N (ATC→AAC) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 607,277 | C→G | 5.3% | A40A (GCC→GCG) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,322 | G→C | 5.5% | A55A (GCG→GCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,359 | A→C | 15.8% | T68P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| JC | 607,424 | 27 bp→108 bp | 53.9% | coding (267‑293/1125 nt) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,529 | G→C | 5.2% | A124A (GCG→GCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,638 | G→C | 13.7% | A161P (GCC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,838 | A→G | 5.1% | T227T (ACA→ACG) | EO946_RS03185 → | collagen‑like protein |
| RA | 704,769 | G→C | 5.0% | E136D (GAG→GAC) | EO946_RS03655 → | phosphotransferase enzyme family protein |
| RA | 755,531 | A→C | 10.2% | Q22H (CAA→CAC) | EO946_RS03880 → | rhamnogalacturonan acetylesterase |
| RA | 813,489 | A→G | 5.3% | E51E (GAA→GAG) | nosA → | nitric oxide synthase |
| RA | 813,490 | A→C | 6.6% | I52L (ATC→CTC) ‡ | nosA → | nitric oxide synthase |
| RA | 813,492 | C→G | 5.3% | I52M (ATC→ATG) ‡ | nosA → | nitric oxide synthase |
| RA | 813,501 | G→A | 5.5% | G55G (GGG→GGA) | nosA → | nitric oxide synthase |
| RA | 847,255 | T→A | 6.0% | D277V (GAT→GTT) | EO946_RS04305 ← | NAD(P)‑dependent oxidoreductase |
| RA | 871,761 | G→A | 5.0% | T312T (ACG→ACA) | EO946_RS04420 → | ABC transporter ATP‑binding protein/permease |
| RA | 871,770 | T→C | 5.0% | D315D (GAT→GAC) | EO946_RS04420 → | ABC transporter ATP‑binding protein/permease |
| RA | 871,787 | T→C | 5.2% | I321T (ATC→ACC) | EO946_RS04420 → | ABC transporter ATP‑binding protein/permease |
| RA | 1,111,635 | C→A | 11.0% | T577K (ACA→AAA) | addB → | helicase‑exonuclease AddAB subunit AddB |
| RA | 1,112,969 | C→T | 100% | L1022F (CTT→TTT) | addB → | helicase‑exonuclease AddAB subunit AddB |
| RA | 1,136,748 | T→C | 5.5% | F172F (TTT→TTC) | EO946_RS05840 → | AraC family transcriptional regulator |
| RA | 1,176,173 | G→T | 91.9% | G135V (GGT→GTT) | med → | transcriptional regulator Med |
| RA | 1,347,639 | T→G | 5.0% | L175L (CTT→CTG) | purU → | formyltetrahydrofolate deformylase |
| RA | 1,347,645 | A→G | 5.2% | Q177Q (CAA→CAG) | purU → | formyltetrahydrofolate deformylase |
| RA | 1,347,648 | T→C | 5.2% | Y178Y (TAT→TAC) | purU → | formyltetrahydrofolate deformylase |
| RA | 1,347,693 | C→T | 5.6% | T193T (ACC→ACT) | purU → | formyltetrahydrofolate deformylase |
| RA | 1,448,868 | A→C | 6.2% | intergenic (+88/‑46) | EO946_RS07560 → / → abbA | ribonuclease H‑like YkuK family protein/AbrB antirepressor AbbA |
| RA | 1,496,370 | T→C | 6.2% | D245D (GAT→GAC) | pdhC → | pyruvate dehydrogenase complex dihydrolipoyllysine‑residue acetyltransferase |
| RA | 1,733,974 | C→G | 5.9% | V80V (GTC→GTG) | EO946_RS09000 → | serine hydrolase |
| RA | 1,789,771 | C→A | 5.8% | P4386T (CCT→ACT) | EO946_RS09130 → | type I polyketide synthase |
| RA | 1,898,213 | A→T | 7.7% | T288T (ACA→ACT) | parE → | DNA topoisomerase IV subunit B |
| RA | 1,898,222 | A→G | 7.9% | T291T (ACA→ACG) | parE → | DNA topoisomerase IV subunit B |
| RA | 1,898,276 | A→G | 6.3% | K309K (AAA→AAG) | parE → | DNA topoisomerase IV subunit B |
| RA | 1,898,282 | G→T | 6.2% | L311L (CTG→CTT) | parE → | DNA topoisomerase IV subunit B |
| RA | 1,898,291 | T→C | 8.2% | T314T (ACT→ACC) | parE → | DNA topoisomerase IV subunit B |
| RA | 1,898,327 | T→C | 5.7% | V326V (GTT→GTC) | parE → | DNA topoisomerase IV subunit B |
| RA | 1,898,330 | G→C | 5.6% | R327R (CGG→CGC) | parE → | DNA topoisomerase IV subunit B |
| RA | 2,070,279 | G→T | 10.8% | A1338A (GCC→GCA) | EO946_RS10385 ← | NTTRR‑F1 domain |
| RA | 2,073,402 | G→T | 6.9% | A297A (GCC→GCA) | EO946_RS10385 ← | NTTRR‑F1 domain |
| RA | 2,214,555 | C→A | 6.4% | V48L (GTA→TTA) | nth ← | endonuclease III |
| RA | 2,219,522 | A→T | 5.8% | T742T (ACT→ACA) | dinG ← | ATP‑dependent DNA helicase DinG |
| RA | 2,452,637 | C→T | 6.3% | S216S (TCG→TCA) | pstB ← | phosphate ABC transporter ATP‑binding protein PstB |
| RA | 2,502,278 | C→G | 14.8% | E262Q (GAA→CAA) | hrcA ← | heat‑inducible transcriptional repressor HrcA |
| RA | 2,717,319 | T→G | 6.0% | G399G (GGA→GGC) | sdhA ← | succinate dehydrogenase flavoprotein subunit |
| RA | 2,717,334 | G→A | 5.7% | S394S (TCC→TCT) | sdhA ← | succinate dehydrogenase flavoprotein subunit |
| RA | 2,717,337 | G→C | 5.8% | L393L (CTC→CTG) | sdhA ← | succinate dehydrogenase flavoprotein subunit |
| RA | 2,729,937 | C→A | 8.6% | E277* (GAA→TAA) | lcfA ← | long‑chain‑fatty‑acid‑‑CoA ligase LcfA |
| RA | 2,921,055 | C→T | 6.0% | L59L (TTG→TTA) | ytrB ← | ABC transporter ATP‑binding protein YtrB |
| RA | 2,921,064 | C→T | 5.9% | G56G (GGG→GGA) | ytrB ← | ABC transporter ATP‑binding protein YtrB |
| RA | 2,921,073 | G→A | 5.8% | A53A (GCC→GCT) | ytrB ← | ABC transporter ATP‑binding protein YtrB |
| RA | 2,921,106 | T→C | 6.4% | T42T (ACA→ACG) | ytrB ← | ABC transporter ATP‑binding protein YtrB |
| RA | 2,940,109 | C→T | 7.7% | T88T (ACG→ACA) | EO946_RS15145 ← | DNA starvation/stationary phase protection protein |
| RA | 2,940,121 | T→A | 7.6% | A84A (GCA→GCT) | EO946_RS15145 ← | DNA starvation/stationary phase protection protein |
| RA | 2,940,124 | C→A | 7.5% | A83A (GCG→GCT) | EO946_RS15145 ← | DNA starvation/stationary phase protection protein |
| RA | 2,940,133 | T→G | 7.5% | V80V (GTA→GTC) | EO946_RS15145 ← | DNA starvation/stationary phase protection protein |
| RA | 2,980,160 | G→A | 29.2% | noncoding (641/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,981,253 | C→T | 20.0% | noncoding (1267/1550 nt) | EO946_RS15435 ← | 16S ribosomal RNA |
| RA | 3,177,161 | T→G | 5.1% | I326I (ATA→ATC) | EO946_RS16445 ← | acetyl‑CoA C‑acetyltransferase |
| RA | 3,183,699 | G→A | 5.6% | T204T (ACG→ACA) | mdtP → | multidrug efflux MFS transporter MdtP |
| RA | 3,183,711 | G→T | 5.7% | G208G (GGG→GGT) | mdtP → | multidrug efflux MFS transporter MdtP |
| RA | 3,183,714 | T→G | 5.4% | V209V (GTT→GTG) | mdtP → | multidrug efflux MFS transporter MdtP |
| RA | 3,183,726 | T→G | 5.5% | L213L (CTT→CTG) | mdtP → | multidrug efflux MFS transporter MdtP |
| RA | 3,183,733 | C→T | 5.1% | L216L (CTA→TTA) | mdtP → | multidrug efflux MFS transporter MdtP |
| RA | 3,193,459 | C→G | 8.0% | E56Q (GAA→CAA) | htrB ← | serine protease Do‑like protein HtrB |
| RA | 3,218,214 | C→T | 5.0% | intergenic (‑30/‑174) | sigO ← / → EO946_RS20875 | RNA polymerase sigma factor SigO/YvrJ family protein |
| RA | 3,247,065 | C→T | 100% | intergenic (‑11/+110) | bdbD ← / ← cadA | disulfide bond formation protein BdbD/cadmium‑translocating P‑type ATPase |
| RA | 3,280,377 | G→T | 7.2% | Q115K (CAA→AAA) | EO946_RS16965 ← | lantibiotic dehydratase |
| RA | 3,285,567 | C→T | 29.1% | L278L (CTG→CTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,575 | T→G | 29.0% | N276H (AAT→CAT) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,580 | A→G | 33.5% | I274T (ATA→ACA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,647 | C→A | 34.4% | V252L (GTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,713 | G→A | 27.0% | L230L (CTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,394,360 | T→G | 10.9% | K180N (AAA→AAC) | ppaX ← | pyrophosphatase PpaX |
| RA | 3,447,038 | T→G | 9.8% | N183T (AAC→ACC) | degU ← | two‑component system response regulator DegU |
| RA | 3,637,344 | T→A | 100% | Y44N (TAC→AAC) | EO946_RS18740 → | DUF2529 domain‑containing protein |
| RA | 3,851,237 | G→T | 10.1% | I46I (ATC→ATA) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,936,148 | T→C | 5.2% | S144S (TCT→TCC) | EO946_RS20250 → | aldehyde dehydrogenase family protein |
| RA | 3,936,166 | A→G | 5.4% | T150T (ACA→ACG) | EO946_RS20250 → | aldehyde dehydrogenase family protein |
| RA | 3,936,178 | C→T | 5.4% | A154A (GCC→GCT) | EO946_RS20250 → | aldehyde dehydrogenase family protein |
| RA | 3,936,181 | A→T | 5.5% | A155A (GCA→GCT) | EO946_RS20250 → | aldehyde dehydrogenase family protein |
| RA | 3,992,887 | G→A | 13.6% | T258I (ACA→ATA) | walK ← | cell wall metabolism sensor histidine kinase WalK |
| RA | 4,040,429 | C→A | 7.5% | R197L (CGT→CTT) | mnmG ← | tRNA uridine‑5‑carboxymethylaminomethyl(34) synthesis enzyme MnmG |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NZ_CP034943 | 3954252 | 3954416 | 165 | 59 [50] | [42] 59 | gnd/ahpC | decarboxylating NADP(+)‑dependent phosphogluconate dehydrogenase/alkyl hydroperoxide reductase subunit C |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP034943 | = 91969 | NA (NA) | 15 (0.080) | 6/250 | 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 | |||||
| * | ? | NZ_CP034943 | = 607210 | 255 (1.360) | 9 (0.060) | 7/188 | NT | 6.1% | coding (53/1125 nt) | EO946_RS03185 | collagen‑like protein |
| ? | NZ_CP034943 | 607715 = | 88 (0.630) | coding (558/1125 nt) | EO946_RS03185 | collagen‑like protein | |||||