mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.32.1 revision 5f2cb669173e
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 | 33.3% | intergenic (+45/+63) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 33.6% | intergenic (+48/+60) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 39.8% | intergenic (+81/+27) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 42.6% | intergenic (+89/+19) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 51.6% | intergenic (+107/+1) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 25.4% | S213S (TCG→TCC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,940 | G→A | 28.0% | R204R (CGC→CGT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,970 | T→C | 58.1% | E194E (GAA→GAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,997 | T→C | 29.8% | T185T (ACA→ACG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,015 | C→T | 28.3% | R179R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,087 | A→G | 62.4% | C155C (TGT→TGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,119 | C→T | 30.7% | V145I (GTA→ATA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,124 | G→A | 60.8% | A143V (GCT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,133 | A→G | 30.3% | V140A (GTA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,161 | T→C | 30.8% | I131V (ATT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,174 | T→C | 30.2% | K126K (AAA→AAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,269 | C→T | 59.4% | A95T (GCA→ACA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,315 | G→A | 58.4% | Y79Y (TAC→TAT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,378 | C→T | 86.4% | L58L (TTG→TTA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,413 | C→T | 53.4% | V47I (GTC→ATC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,444 | C→T | 45.6% | R36R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,471 | A→G | 24.1% | S27S (AGT→AGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,479 | T→C | 24.1% | T25A (ACA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,501 | G→A | 6.5% | A17A (GCC→GCT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,581 | C→T | 30.9% | intergenic (‑30/‑493) | USA300HOU_0026 ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 38,405 | C→G | 3.6% | T198S (ACT→AGT) | ugpQ1 → | glycerophosphodiester phosphodiesterase |
| JC | 68,674 | (AAT)7→6 | 5.4% | coding (790‑792/852 nt) | USA300HOU_0065 → | transposase |
| RA | 75,007 | C→T | 7.7% | M1M (ATG→ATA) † | argR1 ← | arginine repressor |
| RA | 76,180 | C→T | 24.6% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 13.1% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 30.5% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 57.5% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 58.2% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 55.5% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,889 | G→A | 14.4% | intergenic (+947/‑187) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 17.9% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 21.6% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 25.1% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 24.6% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 201,369 | A→G | 3.7% | T292A (ACG→GCG) | fdh → | formate dehydrogenase |
| RA | 235,092 | C→T | 6.3% | D490N (GAT→AAT) | USA300HOU_0212 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 286,781 | Δ1 bp | 4.6% | coding (796/936 nt) | USA300HOU_0253 → | purine nucleosidase |
| RA | 293,940 | C→T | 19.6% | intergenic (+57/‑471) | USA300HOU_0261 → / → ispD2 | zinc (Zn2+)‑binding dehydrogenase/2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 317,291 | A→G | 5.2% | M192T (ATG→ACG) | USA300HOU_0283 ← | ribose operon repressor |
| RA | 478,502 | C→A | 100% | D342E (GAC→GAA) | USA300HOU_0457 → | NADH dehydrogenase (ubiquinone) |
| RA | 512,643 | A→G | 45.9% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 622,479 | T→C | 9.5% | D1014D (GAT→GAC) | sdrE → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrE |
| RA | 628,618 | T→A | 6.9% | S8T (TCG→ACG) | nagB → | glucosamine‑6‑phosphate deaminase |
| RA | 677,733 | A→G | 5.9% | I213V (ATT→GTT) | USA300HOU_0620 → | hypothetical protein |
| RA | 685,779 | T→C | 8.7% | L127L (TTA→TTG) | USA300HOU_0629 ← | hypothetical membrane protein |
| RA | 707,909 | A→T | 100% | M1M (TTG→ATG) † | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 973,213 | C→A | 100% | E175* (GAG→TAG) | USA300HOU_0930 ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,133,417 | T→A | 5.6% | V146V (GTT→GTA) | USA300HOU_1061 → | site‑specific DNA‑methyltransferase (adenine‑specific) |
| RA | 1,196,508 | C→A | 100% | intergenic (+2563/‑1229) | ftsQ → / → USA300HOU_1125 | cell division protein FtsQ/hypothetical protein |
| RA | 1,249,530 | G→A | 5.7% | A956T (GCG→ACG) | smc → | SMC superfamily ATP‑binding chromosome segregation protein |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | 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 | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,617,132 | C→T | 5.6% | L212L (CTC→CTT) | USA300HOU_1501 → | dehydrogenase |
| RA | 1,620,134 | C→T | 8.1% | A163A (GCG→GCA) | USA300HOU_1505 ← | ribonuclease Z |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,830,450 | T→C | 7.1% | T224A (ACT→GCT) | ezrA ← | possible septation ring formation regulator |
| RA | 1,929,796 | T→C | 43.7% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 43.4% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 44.0% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 42.9% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 53.4% | 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 | 63.0% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 64.0% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 64.9% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,863:1 | +T | 46.0% | intergenic (‑946/‑222) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 18.0% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 46.7% | 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 | 61.5% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866:1 | +T | 5.8% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 63.8% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,868:1 | +T | 3.1% | intergenic (‑951/‑217) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 64.4% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 63.3% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 64.2% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 64.7% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 55.6% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 55.9% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 50.2% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 50.4% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 51.4% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 44.2% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 37.5% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,184,114 | A→G | 5.3% | R281R (CGT→CGC) | USA300HOU_2058 ← | S1 domain RNA‑binding protein |
| RA | 2,274,436 | A→G | 5.0% | T454T (ACA→ACG) | mtlF → | PTS family fructose/mannitol (fru) porter component IIBC |
| 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 | 100% | intergenic (‑125/‑119) | USA300HOU_2195 ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,343,438 | C→T | 32.9% | intergenic (+114/+250) | USA300HOU_2200 → / ← alsD | hypothetical protein/acetolactate decarboxylase |
| RA | 2,386,339 | T→C | 4.7% | K41E (AAA→GAA) | USA300HOU_2245 ← | hypothetical protein |
| RA | 2,411,914 | G→T | 7.5% | P13Q (CCA→CAA) | USA300HOU_2277 ← | hypothetical protein |
| RA | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,468,887 | A→T | 5.5% | intergenic (‑76/‑132) | USA300HOU_2331 ← / → USA300HOU_2332 | possible esterase/hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,680,194 | T→C | 7.3% | intergenic (+246/+286) | USA300HOU_2536 → / ← USA300HOU_2537 | possible secretory antigen/hypothetical protein |
| RA | 2,771,347 | C→A | 5.9% | P49Q (CCA→CAA) | USA300HOU_2626 → | alkaline phosphatase |
| RA | 2,774,969 | A→G | 6.6% | D739D (GAT→GAC) | clfB ← | clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 105 (1.370) | 59 (1.120) +40 bp |
32/180 | NT | 44.9% | 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 | 895785 = | 51 (0.670) | 10 (0.150) | 8/226 | NT | 18.1% | coding (806/822 nt) | USA300HOU_0849 | ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | = 909740 | 46 (0.690) | intergenic (‑663/‑371) | ear/USA300HOU_0868 | Ear protein/hypothetical protein | |||||
| * | ? | CP000730 | 2085296 = | 50 (0.650) | 19 (0.280) | 14/232 | NT | 25.9% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 64 (0.940) | intergenic (+57/+1062) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||
| * | ? | CP000730 | = 2419897 | 90 (1.180) | 5 (0.070) | 4/228 | NT | 5.5% | intergenic (+65/‑172) | USA300HOU_2284/ssaA | hypothetical membrane protein/secretory antigen SsaA |
| ? | CP000730 | = 2419903 | 93 (1.390) | intergenic (+71/‑166) | USA300HOU_2284/ssaA | hypothetical membrane protein/secretory antigen SsaA | |||||
| * | ? | CP000730 | = 2660581 | 91 (1.190) | 3 (0.040) | 3/236 | NT | 3.3% | intergenic (+23/+226) | ddh/USA300HOU_2514 | D‑lactate dehydrogenase/HAD superfamily hydrolase |
| ? | CP000730 | = 2660590 | 92 (1.330) | intergenic (+32/+217) | ddh/USA300HOU_2514 | D‑lactate dehydrogenase/HAD superfamily hydrolase | |||||