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 | 33.9% | intergenic (+45/+63) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 33.0% | intergenic (+48/+60) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 40.1% | intergenic (+81/+27) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 43.6% | intergenic (+89/+19) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 51.7% | intergenic (+107/+1) | USA300HOU_0025 → / ← USA300HOU_0026 | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 27.2% | S213S (TCG→TCC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,940 | G→A | 31.1% | R204R (CGC→CGT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,970 | T→C | 57.7% | E194E (GAA→GAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 35,997 | T→C | 30.7% | T185T (ACA→ACG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,015 | C→T | 29.9% | R179R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,087 | A→G | 59.4% | C155C (TGT→TGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,119 | C→T | 32.3% | V145I (GTA→ATA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,124 | G→A | 55.7% | A143V (GCT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,133 | A→G | 32.6% | V140A (GTA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,161 | T→C | 31.8% | I131V (ATT→GTT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,174 | T→C | 30.3% | K126K (AAA→AAG) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,269 | C→T | 58.2% | A95T (GCA→ACA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,315 | G→A | 56.2% | Y79Y (TAC→TAT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,378 | C→T | 87.4% | L58L (TTG→TTA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,413 | C→T | 51.1% | V47I (GTC→ATC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,444 | C→T | 48.0% | R36R (AGG→AGA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,471 | A→G | 23.8% | S27S (AGT→AGC) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,479 | T→C | 22.5% | T25A (ACA→GCA) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,501 | G→A | 7.5% | A17A (GCC→GCT) | USA300HOU_0026 ← | IS431mec transposase |
| RA | 36,581 | C→T | 35.0% | intergenic (‑30/‑493) | USA300HOU_0026 ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 26.0% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 16.0% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 28.4% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 57.8% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 57.6% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 53.8% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 15.2% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 20.4% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 31.3% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 31.3% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 10.8% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 398,446 | A→G | 4.4% | N156S (AAC→AGC) | USA300HOU_0366 → | OFeT family oxidase‑dependent iron (Fe2+) transporter |
| RA | 428,178 | A→T | 3.6% | V371V (GTT→GTA) | ahpF ← | peroxiredoxin subunit F |
| RA | 460,262 | G→A | 5.7% | intergenic (+111/‑272) | hsdS1 → / → set | type I site‑specific deoxyribonuclease specificity subunit/staphylococcal exotoxin |
| RA | 466,487 | T→A | 3.9% | S163R (AGT→AGA) | lpl7 → | hypothetical protein |
| RA | 491,927 | T→A | 9.2% | L118L (CTT→CTA) | USA300HOU_0465 → | possible LysM family autolysin |
| RA | 512,643 | A→G | 45.2% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 620,399 | T→A | 9.0% | V321D (GTC→GAC) | sdrE → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrE |
| RA | 656,852 | T→C | 5.8% | T31T (ACT→ACC) | USA300HOU_0595 → | hypothetical protein |
| RA | 785,677 | G→T | 7.3% | A27E (GCA→GAA) | exsB ← | ExsB family post‑transcriptional regulator |
| RA | 824,661 | Δ1 bp | 4.6% | coding (231/1071 nt) | USA300HOU_0773 ← | diguanylate cyclase GGDEF domain protein |
| RA | 969,195 | C→A | 8.0% | A1088E (GCG→GAG) | rexA → | ATP‑dependent nuclease Rex subunit A |
| RA | 1,029,311 | G→A | 5.4% | D707N (GAC→AAC) | USA300HOU_0980 → | S1C family peptidase |
| RA | 1,323,313 | A→G | 6.2% | K29E (AAA→GAA) | mutL → | DNA mismatch repair protein MutL |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,453,382 | G→T | 9.5% | N180K (AAC→AAA) | sucA ← | oxoglutarate dehydrogenase (succinyl‑transferring) E1 |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,574,491 | A→T | 4.5% | L1009H (CTC→CAC) | USA300HOU_1441 ← | possible bacteriophage tail protein |
| RA | 1,580,165 | G→T | 7.4% | S108* (TCA→TAA) | USA300HOU_1448 ← | hypothetical bacteriophage protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,653,690 | G→T | 10.5% | Q97K (CAA→AAA) | aroK ← | shikimate kinase |
| RA | 1,684,834 | G→T | 7.0% | S52Y (TCT→TAT) | USA300HOU_1575 ← | hypothetical membrane protein |
| RA | 1,689,325 | T→C | 5.6% | T181A (ACA→GCA) | dnaJ ← | chaperone DnaJ |
| RA | 1,697,768 | G→A | 6.5% | intergenic (+24/+21) | rpsT → / ← holA | ribosomal protein S20/possible DNA‑directed DNA polymerase III delta subunit |
| RA | 1,708,278 | A→G | 7.0% | intergenic (‑99/‑8) | USA300HOU_1601 ← / → USA300HOU_1602 | hypothetical protein/hypothetical membrane protein |
| RA | 1,742,872 | A→G | 5.0% | V292A (GTG→GCG) | relA2 ← | GTP pyrophosphokinase |
| RA | 1,744,424 | A→G | 11.0% | L83S (TTA→TCA) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,544 | T→C | 58.7% | Y43C (TAC→TGC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,837,421 | T→C | 4.8% | E259G (GAA→GGA) | USA300HOU_1714 ← | hypothetical protein |
| RA | 1,884,975 | T→A | 5.9% | N82Y (AAT→TAT) | fmtB1 ← | cell surface anchored protein |
| RA | 1,899,742 | A→G | 11.0% | N421N (AAT→AAC) | USA300HOU_1761 ← | hypothetical protein |
| RA | 1,926,533 | A→G | 5.6% | K114E (AAA→GAA) | USA300HOU_1789 → | hypothetical protein |
| RA | 1,929,796 | T→C | 48.9% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 49.0% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 52.4% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 51.6% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 65.5% | 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 | 70.3% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 71.7% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 72.1% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,863:1 | +T | 54.2% | intergenic (‑946/‑222) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 16.1% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 54.6% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 10.4% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 67.0% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 69.4% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,868:1 | +T | 3.4% | intergenic (‑951/‑217) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 68.4% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 67.9% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 68.0% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 68.8% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 60.6% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 59.9% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 56.4% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 56.9% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 56.1% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 49.2% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 38.3% | 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 | 2,091,501 | G→T | 4.8% | Q34K (CAA→AAA) | USA300HOU_1954 ← | hypothetical bacteriophage protein |
| RA | 2,113,299 | G→T | 6.4% | D38E (GAC→GAA) | USA300HOU_1981 ← | hypothetical protein |
| RA | 2,113,304 | G→T | 7.2% | H37N (CAT→AAT) | USA300HOU_1981 ← | hypothetical protein |
| RA | 2,113,305 | G→T | 7.1% | D36E (GAC→GAA) | USA300HOU_1981 ← | hypothetical protein |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,359,473 | G→T | 7.0% | Q100K (CAA→AAA) | rpsM ← | ribosomal protein S13 |
| RA | 2,373,506 | A→T | 7.3% | N90K (AAT→AAA) | USA300HOU_2234 ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,420,667 | G→T | 9.5% | intergenic (+98/‑264) | ssaA → / → USA300HOU_2286 | secretory antigen SsaA/(R)‑2‑hydroxyacid dehydrogenase |
| RA | 2,464,772 | A→T | 4.6% | L344M (TTG→ATG) | USA300HOU_2327 ← | isopentenyl‑diphosphate delta‑isomerase |
| RA | 2,489,727 | C→A | 7.4% | intergenic (+76/+77) | USA300HOU_2350 → / ← USA300HOU_2351 | hypothetical protein/hypothetical lipoprotein |
| RA | 2,519,798 | T→A | 3.5% | S278S (TCA→TCT) | narG ← | nitrate reductase alpha subunit |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,575,960 | C→T | 6.0% | V33I (GTT→ATT) | USA300HOU_2436 ← | glycine betaine/choline ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,658,932 | G→A | 5.1% | A119V (GCA→GTA) | USA300HOU_2512 ← | FMN reductase |
| RA | 2,682,216 | T→C | 4.0% | Q202Q (CAA→CAG) | USA300HOU_2539 ← | hydroxymethylglutaryl‑CoA reductase |
| RA | 2,827,998 | T→C | 5.0% | S14P (TCA→CCA) | icaD → | intercellular adhesion protein D |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 52495 = | 83 (0.900) | 123 (1.350) +T |
7/258 | NT | 59.6% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 85 (0.930) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 512620 = | 112 (1.220) | 69 (1.090) +40 bp |
37/180 | NT | 47.2% | 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 | 895785 = | 62 (0.680) | 27 (0.340) | 15/226 | NT | 32.6% | coding (806/822 nt) | USA300HOU_0849 | ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | = 909740 | 58 (0.730) | intergenic (‑663/‑371) | ear/USA300HOU_0868 | Ear protein/hypothetical protein | |||||
| * | ? | CP000730 | 1697752 = | 75 (0.820) | 5 (0.060) | 5/228 | NT | 7.8% | intergenic (+8/+37) | rpsT/holA | ribosomal protein S20/possible DNA‑directed DNA polymerase III delta subunit |
| ? | CP000730 | 1697788 = | 52 (0.650) | intergenic (+44/+1) | rpsT/holA | ribosomal protein S20/possible DNA‑directed DNA polymerase III delta subunit | |||||
| * | ? | CP000730 | 2085296 = | 62 (0.680) | 63 (0.770) | 48/232 | NT | 48.0% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 81 (0.990) | intergenic (+57/+1062) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||
| * | ? | CP000730 | = 2085309 | 69 (0.750) | 3 (0.040) | 3/232 | NT | 4.0% | intergenic (‑571/‑387) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | 2128358 = | 81 (0.990) | intergenic (+72/+1047) | int/USA300HOU_2011 | bacteriophage integrase/possible leukocidin subunit | |||||
| * | ? | CP000730 | 2660570 = | 108 (1.180) | 3 (0.040) | 3/236 | NT | 3.0% | intergenic (+12/+237) | ddh/USA300HOU_2514 | D‑lactate dehydrogenase/HAD superfamily hydrolase |
| ? | CP000730 | 2660603 = | 97 (1.160) | intergenic (+45/+204) | ddh/USA300HOU_2514 | D‑lactate dehydrogenase/HAD superfamily hydrolase | |||||