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 | 27,592 | A→C | 7.9% | T391P (ACG→CCG) | dnaX → | DNA polymerase III subunit gamma/tau |
| RA | 44,865 | T→A | 100% | intergenic (‑46/‑455) | abrB ← / → metG | transition state genes transcriptional regulator AbrB/methionine‑‑tRNA ligase |
| RA | 44,870 | 2 bp→TC | 100% | intergenic (‑51/‑449) | abrB ← / → metG | transition state genes transcriptional regulator AbrB/methionine‑‑tRNA ligase |
| RA | 112,586 | G→T | 7.4% | intergenic (+264/‑40) | gltX → / → cysE | glutamate‑‑tRNA ligase/serine O‑acetyltransferase |
| RA | 112,591 | A→T | 8.7% | intergenic (+269/‑35) | gltX → / → cysE | glutamate‑‑tRNA ligase/serine O‑acetyltransferase |
| RA | 112,600 | T→A | 5.5% | intergenic (+278/‑26) | gltX → / → cysE | glutamate‑‑tRNA ligase/serine O‑acetyltransferase |
| RA | 112,636 | G→T | 6.2% | R4I (AGA→ATA) | cysE → | serine O‑acetyltransferase |
| RA | 132,185 | G→A | 100% | D560N (GAC→AAC) | fusA → | elongation factor G |
| RA | 135,162 | C→A | 6.0% | intergenic (+209/‑29) | EO946_RS00715 → / → rpsJ | alpha/beta hydrolase/30S ribosomal protein S10 |
| RA | 240,211 | G→T | 13.1% | A107A (GCC→GCA) | EO946_RS01360 ← | hypothetical protein |
| RA | 316,262 | C→A | 6.1% | Q28K (CAA→AAA) | opuAA → | glycine/proline betaine ABC transporter ATP‑binding protein OpuAA |
| RA | 485,053 | G→T | 5.9% | L445F (TTG→TTT) | kimA → | potassium transporter KimA |
| RA | 549,057 | C→A | 7.1% | F23L (TTC→TTA) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 549,119 | T→G | 8.8% | L44R (CTG→CGG) | EO946_RS02865 → | PLP‑dependent aminotransferase family protein |
| RA | 595,203 | C→A | 13.0% | T30K (ACG→AAG) | EO946_RS03130 → | MMPL family transporter |
| RA | 607,359 | A→C | 13.6% | T68P (ACC→CCC) | EO946_RS03185 → | collagen‑like protein |
| JC | 607,424 | 27 bp→108 bp | 35.1% | coding (267‑293/1125 nt) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,469 | A→C | 5.8% | T104T (ACA→ACC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,484 | G→C | 6.7% | A109A (GCG→GCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,499 | G→C | 8.6% | G114G (GGG→GGC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,514 | T→G | 8.3% | A119A (GCT→GCG) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,562 | G→C | 7.4% | G135G (GGG→GGC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,638 | G→C | 13.6% | A161P (GCC→CCC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,694 | C→T | 10.9% | T179T (ACC→ACT) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,700 | A→C | 20.4% | E181D (GAA→GAC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,702 | C→T | 12.5% | A182V (GCC→GTC) | EO946_RS03185 → | collagen‑like protein |
| RA | 607,838 | A→G | 5.3% | T227T (ACA→ACG) | EO946_RS03185 → | collagen‑like protein |
| RA | 686,638 | C→G | 10.0% | L103V (CTT→GTT) | purM → | phosphoribosylformylglycinamidine cyclo‑ligase |
| RA | 755,530 | A→C | 6.2% | Q22P (CAA→CCA) | EO946_RS03880 → | rhamnogalacturonan acetylesterase |
| RA | 767,723 | A→C | 6.5% | I81S (ATT→AGT) | EO946_RS03930 ← | hypothetical protein |
| RA | 767,765 | A→C | 6.1% | I67S (ATT→AGT) | EO946_RS03930 ← | hypothetical protein |
| RA | 803,278 | G→T | 6.3% | Q29K (CAG→AAG) | yfmC ← | Fe(3+)‑citrate ABC transporter substrate‑binding protein YfmC |
| RA | 934,369 | G→T | 7.1% | A340S (GCA→TCA) | ssuD → | FMNH2‑dependent alkanesulfonate monooxygenase |
| RA | 1,151,967 | T→G | 12.5% | K79T (AAA→ACA) | EO946_RS05920 ← | GNAT family N‑acetyltransferase |
| RA | 1,263,936 | G→T | 7.7% | T83K (ACA→AAA) | fetB ← | iron export ABC transporter permease subunit FetB |
| RA | 1,488,182 | G→T | 8.1% | A575S (GCA→TCA) | ade → | adenine deaminase |
| RA | 1,720,712 | C→A | 8.0% | T212T (ACC→ACA) | spoIIIE → | DNA translocase SpoIIIE |
| RA | 1,730,084 | G→C | 17.7% | D169H (GAT→CAT) | rodZ → | cell shape determination protein RodZ |
| RA | 1,753,598 | G→T | 9.2% | intergenic (+289/‑216) | fabD → / → EO946_RS09090 | ACP S‑malonyltransferase/acyltransferase domain‑containing protein |
| RA | 2,034,593 | C→A | 16.1% | intergenic (‑259/‑135) | EO946_RS10175 ← / → EO946_RS10180 | UPF0715 family protein/hypothetical protein |
| RA | 2,139,480 | A→C | 7.3% | A119A (GCT→GCG) | deoD ← | purine‑nucleoside phosphorylase |
| RA | 2,214,528 | G→T | 8.7% | Q57K (CAA→AAA) | nth ← | endonuclease III |
| RA | 2,408,718 | G→C | 7.8% | P330A (CCG→GCG) | spoIIIAE ← | stage III sporulation protein AE |
| RA | 2,502,254 | G→T | 9.3% | Q270K (CAA→AAA) | hrcA ← | heat‑inducible transcriptional repressor HrcA |
| RA | 2,589,693 | T→G | 8.1% | intergenic (‑52/+339) | EO946_RS13405 ← / ← EO946_RS13410 | YrzI family small protein/formate/nitrite transporter family protein |
| RA | 2,709,410 | T→C | 5.1% | L22L (TTA→CTA) | EO946_RS13995 → | YsnF/AvaK domain‑containing protein |
| RA | 2,978,137 | A→T | 12.9% | noncoding (2664/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,150 | G→A | 15.4% | noncoding (2651/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,153 | A→G | 15.5% | noncoding (2648/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,155 | G→A | 16.7% | noncoding (2646/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,186 | G→A | 14.6% | noncoding (2615/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,204 | G→A | 16.0% | noncoding (2597/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,211 | T→A | 14.7% | noncoding (2590/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,212 | G→T | 14.4% | noncoding (2589/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,978,224 | C→A | 14.8% | noncoding (2577/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,979,248 | T→C | 37.7% | noncoding (1553/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,979,628 | T→A | 15.4% | noncoding (1173/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,231 | G→C | 14.3% | noncoding (570/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,233 | C→T | 15.4% | noncoding (568/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,247 | A→T | 14.7% | noncoding (554/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,263:1 | +C | 11.3% | noncoding (538/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,264 | T→G | 15.4% | noncoding (537/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 2,980,272 | G→T | 12.7% | noncoding (529/2928 nt) | EO946_RS15430 ← | 23S ribosomal RNA |
| RA | 3,247,065 | C→T | 100% | intergenic (‑11/+110) | bdbD ← / ← cadA | disulfide bond formation protein BdbD/cadmium‑translocating P‑type ATPase |
| RA | 3,280,341 | C→A | 9.8% | E127* (GAG→TAG) | EO946_RS16965 ← | lantibiotic dehydratase |
| RA | 3,285,567 | C→T | 35.1% | L278L (CTG→CTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,575 | T→G | 36.0% | N276H (AAT→CAT) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,580 | A→G | 38.6% | I274T (ATA→ACA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,647 | C→A | 41.7% | V252L (GTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,285,713 | G→A | 34.0% | L230L (CTA→TTA) | EO946_RS16995 ← | IS3 family transposase |
| RA | 3,349,666 | T→G | 7.4% | intergenic (+1/+26) | EO946_RS17305 → / ← padC | hypothetical protein/phenolic acid decarboxylase |
| RA | 3,362,393 | G→C | 11.0% | L99L (CTG→CTC) | EO946_RS17380 → | MazG‑like family protein |
| RA | 3,362,413 | C→A | 5.9% | A106E (GCA→GAA) | EO946_RS17380 → | MazG‑like family protein |
| RA | 3,394,434 | T→G | 6.6% | S156R (AGC→CGC) | ppaX ← | pyrophosphatase PpaX |
| RA | 3,446,955 | T→G | 5.8% | N211H (AAC→CAC) | degU ← | two‑component system response regulator DegU |
| RA | 3,446,995 | C→A | 5.1% | V197V (GTG→GTT) | degU ← | two‑component system response regulator DegU |
| RA | 3,447,038 | T→G | 12.6% | N183T (AAC→ACC) | degU ← | two‑component system response regulator DegU |
| RA | 3,496,387 | G→T | 8.8% | S347R (AGC→AGA) | EO946_RS17995 ← | glucosaminidase domain‑containing protein |
| RA | 3,496,395 | A→T | 5.1% | S345T (TCA→ACA) | EO946_RS17995 ← | glucosaminidase domain‑containing protein |
| RA | 3,498,677 | G→T | 5.1% | intergenic (‑172/‑95) | manA ← / → EO946_RS18005 | mannose‑6‑phosphate isomerase, class I/spore germination protein |
| RA | 3,562,015 | A→C | 12.7% | intergenic (‑661/‑137) | EO946_RS18300 ← / → EO946_RS21105 | response regulator/HAMP domain‑containing histidine kinase |
| RA | 3,769,576 | T→G | 8.7% | I281S (ATT→AGT) | sacX → | SacY negative regulator SacX |
| RA | 3,796,125 | C→A | 8.1% | L8F (TTG→TTT) | EO946_RS19550 ← | ABC transporter permease subunit |
| RA | 3,851,220 | G→T | 7.4% | T52K (ACG→AAG) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,234 | C→A | 5.3% | M47I (ATG→ATT) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,237 | G→T | 7.7% | I46I (ATC→ATA) ‡ | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,238 | A→T | 5.2% | I46N (ATC→AAC) ‡ | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,254 | G→C | 7.4% | L41V (CTT→GTT) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,851,262 | C→A | 11.7% | W38L (TGG→TTG) | EO946_RS19820 ← | hypothetical protein |
| RA | 3,976,149 | G→T | 5.3% | G19G (GGC→GGA) | rlmH ← | 23S rRNA (pseudouridine(1915)‑N(3))‑methyltransferase RlmH |
| RA | 3,996,857 | C→A | 5.9% | intergenic (‑163/+43) | purA ← / ← EO946_RS20530 | adenylosuccinate synthase/VOC family protein |
| RA | 3,996,910 | G→T | 7.5% | S137* (TCA→TAA) | EO946_RS20530 ← | VOC family protein |
| RA | 4,000,117 | G→T | 7.6% | L121F (TTG→TTT) | EO946_RS20555 → | MFS transporter |
| RA | 4,022,645 | G→C | 5.2% | A623P (GCA→CCA) | EO946_RS20675 → | thioredoxin domain‑containing protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NZ_CP034943 | = 91969 | NA (NA) | 13 (0.040) | 9/250 | 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 | |||||