mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 35,876 | C→T | 42.2% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 18.6% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 33.1% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 52.3% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 36.4% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 35.2% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 55.3% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 35.0% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 54.2% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 34.4% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 35.9% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 39.6% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 71.4% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 69.4% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 87.8% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 57.9% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 47.7% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 54.4% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,265 | C→T | 28.1% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 64.1% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 65.3% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 59.7% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 512,643 | A→G | 58.8% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| 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 | 1,793,181 | T→A | 28.6% | S222S (TCA→TCT) | polA ← | DNA‑directed DNA polymerase I |
| RA | 1,860,581 | A→G | 39.9% | L1198S (TTG→TCG) | sftA ← | DNA translocase |
| RA | 1,929,812 | G→A | 52.6% | 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 | 68.4% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 68.9% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 59.1% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 50.0% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 50.3% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 58.5% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 59.4% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 59.6% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 59.1% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 59.2% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 56.7% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 50.0% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 50.3% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 43.8% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 43.7% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 43.9% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 2,187,071 | C→T | 100% | R331K (AGA→AAA) | rsbU ← | sigma factor B regulator |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,373,835 | C→T | 100% | intergenic (‑60/+53) | pbuG ← / ← topB | NCS2 family nucleobase:cation symporter‑2/DNA topoisomerase TopB |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000730 | 691525 | 691587 | 63 | 2 [0] | [1] 3 | USA300HOU_0634 | hypothetical protein |
| * | * | ÷ | CP000730 | 790584 | 790601 | 18 | 2 [0] | [1] 2 | kipA/ltaS | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| * | * | ÷ | CP000730 | 964055 | 964089 | 35 | 2 [1] | [1] 2 | rexB | ATP‑dependent nuclease Rex subunit B |
| * | * | ÷ | CP000730 | 1237537 | 1237586 | 50 | 2 [1] | [1] 2 | asp | hypothetical protein |
| * | * | ÷ | CP000730 | 1242418 | 1242429 | 12 | 2 [1] | [1] 2 | fapR | hypothetical protein |
| * | * | ÷ | CP000730 | 1253719 | 1253755 | 37 | 2 [1] | [1] 2 | ftsY/yfhO | Sec family Type I general secretory pathway protein signal recognition particle protein FtsY/hypothetical membrane protein |
| * | * | ÷ | CP000730 | 1360588 | 1360621 | 34 | 2 [1] | [1] 2 | [thrB] | [thrB] |
| * | * | ÷ | CP000730 | 1461840 | 1461906 | 67 | 2 [1] | [1] 2 | [ctpA] | [ctpA] |
| * | * | ÷ | CP000730 | 1608032 | 1608089 | 58 | 2 [1] | [1] 2 | USA300HOU_1492 | possible lipoprotein |
| * | * | ÷ | CP000730 | 1639205 | 1639273 | 69 | 2 [1] | [1] 2 | argR/ispA | arginine repressor/geranyltranstransferase |
| * | * | ÷ | CP000730 | 1649069 | 1649111 | 43 | 2 [1] | [1] 2 | yqhL/gcvPB | possible rhodanese domain sulfurtransferase/glycine dehydrogenase (decarboxylating) subunit 2 |
| * | * | ÷ | CP000730 | 1780609 | 1780697 | 89 | 2 [1] | [1] 2 | tig/lysP | peptidylprolyl isomerase/APC family amino acid‑polyamine‑organocation transporter |
| * | * | ÷ | CP000730 | 1909775 | 1909843 | 69 | 2 [1] | [1] 2 | crcB | camphor resistance protein CrcB |
| * | * | ÷ | CP000730 | 2056299 | 2056304 | 6 | 2 [1] | [1] 2 | sspP | C47 family staphopain protease |
| * | * | ÷ | CP000730 | 2176705–2181145 | 2181145 | 1–4441 | 4 [0] | [1] 3 | [rrl4]–[rrs4] | [rrl4],[rrs4] |
| * | * | ÷ | CP000730 | 2726894 | 2726899 | 6 | 2 [0] | [0] 2 | USA300HOU_2581/USA300HOU_2582 | hypothetical protein/hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 6 (0.610) | 3 (0.440) +40 bp |
3/180 | NT | 30.3% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 1998278 = | 14 (1.430) | intergenic (‑6/+5) | USA300HOU_t0050/rrf4 | tRNA‑Val/5S ribosomal RNA | |||||