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 | 39.7% | intergenic (+45/+63) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 40.9% | intergenic (+48/+60) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 46.8% | intergenic (+81/+27) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 47.9% | intergenic (+89/+19) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 60.1% | intergenic (+107/+1) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 24.8% | S213S (TCG→TCC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,940 | G→A | 27.3% | R204R (CGC→CGT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,970 | T→C | 56.7% | E194E (GAA→GAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,997 | T→C | 31.9% | T185T (ACA→ACG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,015 | C→T | 30.7% | R179R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,087 | A→G | 60.9% | C155C (TGT→TGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,119 | C→T | 31.0% | V145I (GTA→ATA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,124 | G→A | 62.8% | A143V (GCT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,133 | A→G | 28.3% | V140A (GTA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,161 | T→C | 30.0% | I131V (ATT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,174 | T→C | 29.6% | K126K (AAA→AAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,269 | C→T | 56.1% | A95T (GCA→ACA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,315 | G→A | 54.1% | Y79Y (TAC→TAT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,378 | C→T | 85.5% | L58L (TTG→TTA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,413 | C→T | 51.5% | V47I (GTC→ATC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,444 | C→T | 44.2% | R36R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,471 | A→G | 24.5% | S27S (AGT→AGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,479 | T→C | 15.2% | T25A (ACA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,581 | C→T | 41.1% | intergenic (‑30/‑493) | USA300HOU_0026 ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 34.6% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 20.5% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 27.3% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 59.9% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 59.3% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 57.8% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 12.7% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 14.3% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 28.0% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 28.0% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 148,138 | A→G | 8.2% | intergenic (+30/‑40) | USA300HOU_0139 → / → galE | hypothetical protein/UDP‑glucose 4‑epimerase |
| RA | 293,940 | C→T | 19.5% | intergenic (+57/‑471) | USA300HOU_0261 → / → ispD2 | zinc (Zn2+)‑binding dehydrogenase/2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 478,502 | C→A | 100% | D342E (GAC→GAA) | USA300HOU_0457 → | NADH dehydrogenase (ubiquinone) |
| RA | 512,643 | A→G | 57.5% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 526,744 | C→T | 8.4% | R355C (CGT→TGT) | metS → | methionine‑‑tRNA ligase |
| RA | 529,100 | A→G | 7.8% | K159E (AAA→GAA) | USA300HOU_0492 → | hypothetical protein |
| RA | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 707,909 | A→T | 100% | M1M (TTG→ATG) † | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 736,763 | A→G | 9.1% | I415M (ATA→ATG) | vraE → | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 973,213 | C→A | 100% | E175* (GAG→TAG) | USA300HOU_0930 ← | possible HAD superfamily hydrolase |
| RA | 990,792 | A→G | 11.4% | A228A (GCA→GCG) | oppD1 → | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,076,774 | T→C | 19.2% | W51R (TGG→CGG) | purL → | phosphoribosylformylglycinamidine synthase subunit II |
| RA | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,194,918 | A→G | 11.7% | intergenic (+973/‑2819) | ftsQ → / → USA300HOU_1125 | cell division protein FtsQ/hypothetical protein |
| RA | 1,196,508 | C→A | 100% | intergenic (+2563/‑1229) | ftsQ → / → USA300HOU_1125 | cell division protein FtsQ/hypothetical 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 | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,680,793 | A→G | 11.5% | I15I (ATT→ATC) | dgkA2 ← | diacylglycerol kinase |
| RA | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,929,796 | T→C | 39.7% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 39.5% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 41.5% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 40.8% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 52.4% | 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 | 58.0% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 61.8% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 65.6% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,863:1 | +T | 43.4% | intergenic (‑946/‑222) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 21.7% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 42.5% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 10.5% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 61.2% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 63.3% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 63.2% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 62.7% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 62.8% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 65.4% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 65.9% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 67.0% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 58.0% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 58.0% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 58.9% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 48.3% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 42.0% | 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 | 2,153,482 | T→C | 10.5% | K254K (AAA→AAG) | scrR ← | sucrose operon repressor |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,113 | T→C | 14.4% | Q126R (CAA→CGA) | USA300HOU_2153 ← | hypothetical membrane protein |
| 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 | 40.1% | intergenic (+114/+250) | USA300HOU_2200 → / ← alsD | hypothetical protein/acetolactate decarboxylase |
| 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 | 2,463,475 | T→C | 14.9% | intergenic (+316/‑21) | USA300HOU_2325 → / → USA300HOU_2326 | DNA‑3‑methyladenine glycosylase/ESS family glutamate:sodium (Na+) symporter |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | CP000730 | 2176701–2181115 | 2181115 | 1–4415 | 7 [6] | [6] 7 | [rrl4]–[rrs4] | [rrl4], [rrs4] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 25 (0.840) | 25 (1.220) +40 bp |
19/180 | NT | 59.2% | 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 | = 800928 | 27 (0.910) | 3 (0.110) | 3/246 | NT | 8.0% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 43 (1.530) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | 2085296 = | 19 (0.640) | 4 (0.150) | 4/232 | NT | 17.4% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 21 (0.790) | intergenic (+57/+1062) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||