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 | 32.8% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 33.4% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 39.5% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 43.6% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 54.2% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 23.2% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 26.7% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 60.2% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 30.1% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 29.4% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 62.0% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 28.8% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 62.0% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 28.2% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 29.4% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 30.2% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 57.9% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 55.7% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 92.6% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 55.4% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 52.6% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 34.5% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 26.2% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 37.5% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 39,378 | C→A | 100% | D586Y (GAT→TAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 76,180 | C→T | 36.4% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 23.4% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 32.0% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 56.6% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 55.4% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 52.9% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,889 | G→A | 21.2% | intergenic (+947/‑187) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,915 | G→A | 12.8% | intergenic (+973/‑161) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 12.2% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 19.9% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 29.0% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 29.4% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 10.3% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 462,218 | A→T | 11.7% | K329I (AAA→ATA) | USA300HOU_0436 → | hypothetical protein |
| RA | 499,857 | C→T | 16.5% | A854V (GCG→GTG) | gltB1 → | glutamate synthase (NADPH), large subunit |
| RA | 512,643 | A→G | 43.6% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 531,519 | G→A | 17.0% | intergenic (+1090/‑4635) | veg → / → rplY | hypothetical protein/ribosomal protein L25 |
| RA | 531,520 | C→A | 18.7% | intergenic (+1091/‑4634) | veg → / → rplY | hypothetical protein/ribosomal protein L25 |
| RA | 567,389 | A→T | 60.8% | Q95L (CAA→CTA) | ctsR → | CtsR family transcriptional regulator |
| RA | 587,957 | G→T | 58.6% | A621S (GCG→TCG) | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | 667,603 | G→A | 8.6% | intergenic (+635/‑413) | ywfO → / → adh | phosphohydrolase/alcohol dehydrogenase |
| RA | 677,166 | T→G | 13.8% | Y24D (TAC→GAC) | USA300HOU_0620 → | hypothetical protein |
| RA | 945,717 | C→T | 6.4% | A776T (GCA→ACA) | mnhA2 ← | CPA3 family monovalent cation:proton (H+) antiporter‑3 subunit A |
| RA | 964,580 | T→C | 9.0% | F709L (TTT→CTT) | rexB → | ATP‑dependent nuclease Rex subunit B |
| RA | 982,331 | T→C | 5.5% | D67D (GAT→GAC) | USA300HOU_0938 → | hypothetical membrane protein |
| RA | 1,000,948 | C→T | 63.3% | T11I (ACA→ATA) | spxA → | possible glutaredoxin |
| RA | 1,083,479 | T→C | 6.5% | G33G (GGT→GGC) | purD → | phosphoribosylamine‑‑glycine ligase |
| RA | 1,231,396 | G→T | 19.6% | R14I (AGA→ATA) | prpC → | possible PP2C protein phosphatase |
| RA | 1,231,407 | G→A | 50.8% | E18K (GAA→AAA) | prpC → | possible PP2C protein phosphatase |
| RA | 1,231,720 | G→A | 12.3% | R122K (AGA→AAA) | prpC → | possible PP2C protein phosphatase |
| 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 | 1,516,802 | A→T | 8.7% | intergenic (‑8/+6) | gpsB ← / ← ypsA | hypothetical protein/hypothetical protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,693,509 | A→G | 5.3% | L10S (TTA→TCA) | hrcA ← | heat shock transcriptional repressor HrcA |
| RA | 1,716,758 | C→T | 10.8% | E77K (GAA→AAA) | kipI ← | possible allophanate hydrolase subunit 1 |
| RA | 1,744,443 | C→A | 59.3% | V77F (GTT→TTT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,759,201 | T→A | 20.9% | L31F (TTA→TTT) | USA300HOU_1650 ← | hypothetical protein |
| RA | 1,817,305 | G→A | 9.6% | A153V (GCG→GTG) | ytoI ← | hypothetical protein |
| RA | 1,929,796 | T→C | 53.5% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 52.8% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 54.0% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 56.9% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 64.6% | 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 | 69.9% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 69.6% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 70.8% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 49.2% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 20.5% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 49.8% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 13.7% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 68.1% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 69.1% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 70.3% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 70.0% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 70.1% | 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 | 57.8% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 56.2% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 53.6% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 53.7% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 53.0% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 47.4% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 39.5% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,996,160 | G→A | 11.2% | noncoding (55/75 nt) | USA300HOU_t0027 ← | tRNA‑Gly |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,227,320 | T→G | 23.1% | I40L (ATT→CTT) | atpB ← | F‑ATPase superfamily proton(H+)‑ or sodium (Na+)‑translocating F‑type ATPase subunit A |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,372,559 | C→T | 5.5% | C406Y (TGT→TAT) | pbuG ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,373,506 | A→T | 30.0% | N90K (AAT→AAA) | pbuG ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,436,416 | A→G | 10.2% | L28P (CTT→CCT) | yifK ← | APC family amino acid‑polyamine‑organocation transporter |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,610,072:1 | +T | 100% | coding (454/795 nt) | USA300HOU_2473 ← | lipoprotein |
| RA | 2,701,061 | C→T | 8.5% | M266I (ATG→ATA) | mtnE ← | aminotransferase |
| RA | 2,704,755 | C→T | 11.9% | G363S (GGT→AGT) | crtQ ← | glycosyltransferase |
| RA | 2,774,873 | A→G | 7.4% | D771D (GAT→GAC) | clfB ← | clumping factor B |
| RA | 2,797,361 | T→C | 6.1% | S503S (TCT→TCC) | acmB → | possible N‑acetylmuramoyl‑L‑alanine amidase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | = 450716 | 25 (0.380) | 33 (0.580) | 27/226 | NT | 63.0% | intergenic (+83/‑266) | set19/set20 | staphylococcal exotoxin/staphylococcal exotoxin |
| ? | CP000730 | 451778 = | 17 (0.300) | intergenic (+77/‑369) | set20/set21 | staphylococcal exotoxin/staphylococcal exotoxin | |||||
| * | ? | CP000730 | 512620 = | 86 (1.320) | 50 (1.110) +40 bp |
35/180 | NT | 45.7% | 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 | 895785 = | 59 (0.910) | 4 (0.070) | 4/226 | NT | 7.8% | coding (806/822 nt) | metQ | ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | = 909740 | 44 (0.780) | intergenic (‑663/‑371) | ear/USA300HOU_0868 | Ear protein/hypothetical protein | |||||
| * | ? | CP000730 | 2085296 = | 71 (1.090) | 13 (0.220) | 10/232 | NT | 19.5% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 44 (0.760) | intergenic (+57/+1062) | int/hlgB | bacteriophage integrase/possible leukocidin subunit | |||||