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 | 35,814 | Δ1 bp | 21.7% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 22.2% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 23.3% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 27.7% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 34.1% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 23.4% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 27.1% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 58.6% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 30.2% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 26.1% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 60.1% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 24.0% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 58.9% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 24.8% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 28.4% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 26.5% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 63.7% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 58.9% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 82.3% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 48.8% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 39.3% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 14.4% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 76,180 | C→T | 16.7% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 14.2% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 24.2% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 50.6% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 48.6% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 43.8% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,969 | G→A | 79.2% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,904 | G→T | 7.7% | D255Y (GAT→TAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 33.2% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 33.5% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 20.7% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 134,761 | A→T | 12.9% | K135M (AAG→ATG) | sbnA → | possible pyridoxal‑phosphate dependent enzyme |
| RA | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 217,036 | T→A | 15.4% | intergenic (‑203/+23) | argD ← / ← brnQ | ornithine‑‑oxo‑acid transaminase/possible LIVCS family branched chain amino acid:cation symporter |
| RA | 253,973 | C→T | 11.8% | intergenic (+186/‑2) | USA300HOU_0226 → / → USA300HOU_0227 | hypothetical protein/hypothetical protein |
| RA | 396,540 | G→A | 86.7% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 512,643 | A→G | 57.4% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 593,430 | T→A | 12.2% | intergenic (+22/‑58) | rpoC → / → USA300HOU_0538 | DNA‑directed RNA polymerase subunit beta'/possible RNA‑binding ribosomal protein |
| RA | 607,884 | G→A | 87.2% | R209* (CGA→TGA) | dck ← | deoxynucleoside kinase |
| RA | 629,681 | C→A | 100% | L84I (CTA→ATA) | hxlA → | possible 3‑hexulose‑6‑phosphate synthase |
| RA | 665,392 | T→G | 100% | L79* (TTA→TGA) | iolS → | possible acetytransferase |
| RA | 693,258 | T→A | 11.1% | I65F (ATT→TTT) | USA300HOU_0636 ← | hypothetical protein |
| RA | 707,910 | A→G | 100% | intergenic (‑1/‑121) | mntB ← / → sirR | ABC superfamily ATP binding cassette transporter, ABC protein/possible metal‑dependent transcriptional regulator |
| RA | 1,105,994 | T→C | 16.9% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | prkC → | non‑specific serine/threonine protein kinase |
| 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 | 100% | 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 | 1,539,250 | C→G | 22.6% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,579,073 | T→C | 12.7% | D85G (GAT→GGT) | USA300HOU_1445 ← | major tail protein |
| RA | 1,608,818 | G→A | 14.3% | T20M (ACG→ATG) | USA300HOU_1492 ← | possible lipoprotein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,715,153 | T→C | 10.5% | D33G (GAC→GGC) | accB ← | acetyl‑CoA carboxylase biotin carboxyl carrier subunit |
| RA | 1,744,362 | G→A | 100% | H104Y (CAC→TAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,761,889 | C→A | 100% | D388Y (GAT→TAT) | folC ← | tetrahydrofolate synthase |
| RA | 1,929,796 | T→C | 22.7% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 22.3% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 22.3% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 22.2% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 35.6% | 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 | 51.0% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 48.8% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 48.0% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 37.0% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 11.0% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 37.1% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 47.5% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 47.1% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 47.2% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 46.1% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 46.0% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 47.5% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 38.7% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 36.3% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 40.9% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 40.8% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 39.4% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 32.3% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 31.2% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,963,768 | C→G | 100% | 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 | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,337,959 | C→T | 13.2% | intergenic (‑125/‑119) | adhR ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,352,815 | G→A | 85.1% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,372,419 | C→T | 15.1% | intergenic (‑5536/+22) | rpmC ← / ← pbuG | ribosomal protein L29/NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,394,308 | G→A | 9.5% | A85V (GCA→GTA) | moaB ← | molybdopterin cofactor biosynthesis protein MoaB |
| RA | 2,454,626 | A→T | 91.8% | 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 | 2,670,935 | G→A | 14.8% | A60V (GCG→GTG) | USA300HOU_2525 ← | esterase |
| RA | 2,732,937 | C→G | 9.3% | R311R (CGC→CGG) | USA300HOU_2590 → | possible S15 family peptidase |
| RA | 2,845,036 | T→G | 8.6% | K93Q (AAA→CAA) | USA300HOU_2686 ← | ABC superfamily ATP‑binding cassette transporter, membrane protein |
| RA | 2,855,054 | G→T | 11.8% | T190T (ACC→ACA) | rarD ← | DMT superfamily drug/metabolite transporter |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 26 (0.940) | 30 (1.580) +40 bp |
27/178 | NT | 62.7% | 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 | |||||
| * | ? | CP000730 | 760026 = | 41 (1.490) | 3 (0.120) | 3/230 | NT | 7.6% | coding (1674/1674 nt) | cydC | ABC superfamily ATP binding cassette transporter, ABC protein |
| ? | CP000730 | 760070 = | 36 (1.470) | intergenic (+44/+83) | cydC/USA300HOU_0709 | ABC superfamily ATP binding cassette transporter, ABC protein/possible MarR family transcriptional regulator | |||||
| * | ? | CP000730 | = 802757 | 19 (0.690) | 3 (0.120) | 3/244 | NT | 15.0% | coding (544/918 nt) | dgkA1 | possible diacylglycerol kinase |
| ? | CP000730 | = 802799 | 16 (0.610) | coding (502/918 nt) | dgkA1 | possible diacylglycerol kinase | |||||
| * | ? | CP000730 | = 1045832 | 29 (1.050) | 5 (0.190) | 3/248 | NT | 15.2% | intergenic (+9/+43) | USA300HOU_0988/menA | hypothetical protein/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase |
| ? | CP000730 | = 1045855 | 28 (1.060) | intergenic (+32/+20) | USA300HOU_0988/menA | hypothetical protein/1,4‑dihydroxy‑2‑naphthoate octaprenyltransferase | |||||
| * | ? | CP000730 | 1131036 = | 29 (1.050) | 3 (0.130) | 3/224 | NT | 12.2% | coding (435/435 nt) | ylbF | hypothetical protein |
| ? | CP000730 | 1131101 = | 18 (0.750) | intergenic (+65/‑1163) | ylbF/USA300HOU_1059 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000730 | = 1373642 | 32 (1.160) | 4 (0.160) | 4/236 | NT | 11.7% | intergenic (+663/‑1232) | yneF/sbcC | hypothetical protein/exodeoxyribonuclease SbcC |
| ? | CP000730 | = 1373669 | 31 (1.230) | intergenic (+690/‑1205) | yneF/sbcC | hypothetical protein/exodeoxyribonuclease SbcC | |||||
| * | ? | CP000730 | = 2066558 | 30 (1.090) | 3 (0.110) | 3/248 | NT | 9.3% | coding (214/561 nt) | pncA | nicotinamidase |
| ? | CP000730 | = 2066576 | 30 (1.130) | coding (232/561 nt) | pncA | nicotinamidase | |||||
| * | ? | CP000730 | = 2440052 | 26 (0.940) | 3 (0.120) | 3/234 | NT | 11.4% | intergenic (+13/+53) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC |
| ? | CP000730 | = 2440086 | 23 (0.920) | intergenic (+47/+19) | USA300HOU_2302/glvC | hypothetical protein/PTS family arbutin‑salicin‑cellobiose (ASC) porter component IIBC | |||||
| * | ? | CP000730 | = 2746384 | 25 (0.910) | 5 (0.190) | 5/242 | NT | 17.4% | intergenic (+7/+53) | USA300HOU_2601/acsA2 | hypothetical protein/acetate‑‑CoA ligase |
| ? | CP000730 | = 2746433 | 24 (0.930) | intergenic (+56/+4) | USA300HOU_2601/acsA2 | hypothetical protein/acetate‑‑CoA ligase | |||||