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 | 4,449 | C→A | 6.2% | Q171K (CAA→AAA) | recF → | recombination protein RecF |
| RA | 35,814 | Δ1 bp | 34.9% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 36.5% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 42.6% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 41.7% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 46.3% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 23.6% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 27.0% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 59.8% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 30.6% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 31.1% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 58.7% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 28.5% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 57.0% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 29.6% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 30.0% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 30.2% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 58.9% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 54.6% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 85.3% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 51.8% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 47.9% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 32.4% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 22.9% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 35.0% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 27.4% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 11.5% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 33.8% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 53.2% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 53.5% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 49.9% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,969 | G→A | 66.0% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 6.8% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 10.4% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 27.2% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 26.1% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 10.6% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 162,116 | G→A | 8.5% | A180V (GCA→GTA) | phnB ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 195,286 | T→A | 87.1% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 215,097 | T→C | 5.2% | K164E (AAA→GAA) | argC ← | N‑acetyl‑gamma‑glutamyl‑phosphate reductase |
| RA | 396,540 | G→A | 85.9% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 405,184 | C→A | 5.5% | W61L (TGG→TTG) | ltrA ← | possible bacterial low temperature requirement protein A |
| RA | 434,310 | A→T | 7.4% | L72* (TTA→TAA) | USA300HOU_0408 ← | hypothetical protein |
| RA | 512,643 | A→G | 43.3% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 602,466 | G→T | 9.2% | intergenic (+56/‑101) | hchA → / → araB | possible hydrolase/ribulokinase |
| RA | 607,884 | G→A | 89.8% | R209* (CGA→TGA) | dck ← | deoxynucleoside kinase |
| RA | 629,681 | C→A | 71.2% | L84I (CTA→ATA) | hxlA → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 665,392 | T→G | 84.4% | L79* (TTA→TGA) | iolS → | possible acetytransferase |
| RA | 707,910 | A→G | 83.4% | intergenic (‑1/‑121) | mntB ← / → sirR | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 863,781 | A→G | 5.9% | intergenic (+310/‑30) | eno → / → USA300HOU_0807 | phosphopyruvate hydratase/hypothetical membrane protein |
| RA | 951,713 | G→T | 9.8% | intergenic (+218/‑90) | yqiG → / → rocD | flavin reductase/ornithine‑‑oxo‑acid transaminase |
| RA | 1,233,504 | T→A | 83.1% | V470D (GTT→GAT) | prkC → | non‑specific serine/threonine protein kinase |
| RA | 1,265,591 | C→T | 7.5% | intergenic (+99/‑74) | fmhC → / → dprA | FemAB family peptidoglycan biosynthesis protein/SMF family nucleotide‑binding protein |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,440,085 | G→T | 89.2% | intergenic (‑45/‑891) | cspA ← / → xpaC | cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,646,545 | G→A | 6.3% | T36T (ACC→ACT) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,362 | G→A | 92.4% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,761,889 | C→A | 78.6% | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,821,268 | C→T | 9.0% | M257I (ATG→ATA) | ald ← | alanine dehydrogenase |
| RA | 1,929,796 | T→C | 30.2% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 30.1% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 30.1% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 31.0% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 46.6% | intergenic (‑895/‑273) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,842 | Δ1 bp | 100% | intergenic (‑925/‑243) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,843 | Δ1 bp | 51.6% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 53.5% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 55.1% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 39.6% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 14.8% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 40.0% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 8.5% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 51.3% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 53.8% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 54.8% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 54.4% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 54.2% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 55.1% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 47.4% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 47.0% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 46.7% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 46.0% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 46.2% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 41.5% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 30.4% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,963,768 | C→G | 90.3% | V365L (GTA→CTA) | hemG ← | protoporphyrinogen oxidase |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,211,273 | A→G | 9.0% | M1T (ATG→ACG) † | USA300HOU_2086 ← | hypothetical protein |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,352,815 | G→A | 84.5% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,454,626 | A→T | 75.1% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,725,352 | A→T | 6.2% | intergenic (‑58/+276) | ynzC ← / ← ynzC | hypothetical protein/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 102 (1.150) | 66 (1.080) +40 bp |
48/180 | NT | 48.4% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 1998278 = | NA (NA) | intergenic (‑6/+5) | USA300HOU_t0050/rrf4 | tRNA‑Val/5S ribosomal RNA | |||||