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 | 4,873 | T→A | 6.8% | I312N (ATC→AAC) | recF → | recombination protein RecF |
| RA | 35,814 | Δ1 bp | 47.1% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 47.9% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 51.7% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 56.8% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 58.4% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 25.8% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 26.2% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 63.9% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 29.0% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 28.6% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 68.6% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 26.9% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 68.0% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 26.1% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 25.8% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 26.7% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 58.3% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 58.8% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 91.1% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 54.6% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 47.1% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 30.3% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 30.4% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,501 | G→A | 10.7% | A17A (GCC→GCT) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 42.2% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 39,195 | T→C | 62.2% | K647E (AAA→GAA) | mecA ← | penicillin binding protein 2 prime |
| RA | 39,378 | C→T | 100% | D586N (GAT→AAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 39,888 | T→C | 18.5% | N416D (AAC→GAC) | mecA ← | penicillin binding protein 2 prime |
| RA | 42,835 | T→C | 28.2% | Q377Q (CAA→CAG) | USA300HOU_0034 ← | IS1272 transposase |
| RA | 51,327:1 | +G | 100% | coding (29/1092 nt) | USA300HOU_0043 → | hypothetical membrane protein |
| RA | 76,180 | C→T | 42.4% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 28.0% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 28.0% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 61.5% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 61.8% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 61.5% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,889 | G→A | 19.1% | intergenic (+947/‑187) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,907 | A→T | 15.3% | intergenic (+965/‑169) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,915 | G→A | 15.5% | intergenic (+973/‑161) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,969 | G→A | 100% | intergenic (+1027/‑107) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 93,268 | G→A | 77.5% | A73T (GCT→ACT) | yrkE → | hypothetical protein |
| RA | 111,512 | A→G | 35.5% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 37.4% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 19.6% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 129,796 | G→C | 100% | intergenic (‑173/+212) | spa ← / ← sarH1 | immunoglobulin G binding protein A/staphylococcal accessory regulator H1 |
| RA | 169,407 | G→A | 100% | intergenic (+1374/‑130) | USA300HOU_0157 → / → USA300HOU_0160 | nucleotidase/hypothetical protein |
| RA | 195,286 | T→A | 100% | intergenic (‑97/‑82) | USA300HOU_0183 ← / → USA300HOU_0184 | hypothetical protein/hypothetical protein |
| RA | 256,718 | C→T | 13.0% | E219K (GAA→AAA) | USA300HOU_0230 ← | response regulator |
| RA | 283,980 | A→G | 9.5% | intergenic (+205/+115) | ldh → / ← ptsG | L‑lactate dehydrogenase/PTS family glucose/glucoside (glc) porter component IIABC |
| RA | 396,540 | G→A | 100% | A208T (GCA→ACA) | USA300HOU_0364 → | possible lipoprotein |
| RA | 512,643 | A→G | 44.4% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 536,758 | C→T | 100% | P202L (CCA→CTA) | rplY → | ribosomal protein L25 |
| RA | 607,884 | G→A | 100% | R209* (CGA→TGA) | dck ← | deoxynucleoside kinase |
| RA | 618,567 | T→C | 19.7% | D1223D (GAT→GAC) | sdrD → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrD |
| 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 | 673,010 | T→C | 12.1% | G78G (GGT→GGC) | yvrC → | iron (Fe3+) ABC superfamily ATP binding cassette transporter, binding 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 | 744,375 | A→T | 100% | intergenic (+2212/‑714) | yetJ → / → sarX | hypothetical membrane protein/possible staphylococcal accessory protein X |
| RA | 749,249 | C→T | 100% | S59S (AGC→AGT) | USA300HOU_0696 → | MFS family major facilitator transporter, sugar:cation symporter |
| RA | 860,576 | C→T | 10.0% | S19S (AGC→AGT) | pgm → | bisphosphoglycerate mutase |
| RA | 1,017,678 | T→C | 59.6% | F391S (TTC→TCC) | USA300HOU_0971 → | AGCS family alanine or glycine:sodium (Na+) or proton (H+) symporter |
| RA | 1,063,909:1 | +C | 100% | coding (580/1218 nt) | brpA ← | LytR family transcriptional regulator |
| RA | 1,125,066 | G→C | 100% | E729Q (GAG→CAG) | pycA → | pyruvate carboxylase |
| RA | 1,233,504 | T→A | 100% | V470D (GTT→GAT) | prkC → | non‑specific serine/threonine protein kinase |
| RA | 1,298,108 | T→A | 100% | intergenic (+4/‑232) | pnp → / → rnjB | polyribonucleotide nucleotidyltransferase/beta‑lactamase |
| RA | 1,324,248 | Δ1 bp | 100% | coding (1020/2010 nt) | mutL → | DNA mismatch repair protein MutL |
| 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 | 1,448,805 | T→C | 12.8% | N153D (AAT→GAT) | USA300HOU_1346 ← | hypothetical protein |
| RA | 1,489,621 | C→A | 16.1% | A4135S (GCT→TCT) | ebh ← | extracellular matrix binding protein |
| RA | 1,499,376 | C→A | 100% | G883V (GGT→GTT) | ebh ← | extracellular matrix binding protein |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,514,843 | G→A | 13.7% | Y319Y (TAC→TAT) | ypsC ← | site‑specific DNA‑methyltransferase (adenine‑specific) |
| RA | 1,610,233 | A→G | 11.5% | S195P (TCT→CCT) | srrB ← | sensor histidine kinase SrrB |
| RA | 1,613,762 | T→C | 100% | intergenic (‑31/‑37) | scpA ← / → USA300HOU_1497 | possible segregation and condensation protein A/hypothetical protein |
| RA | 1,624,673 | T→A | 100% | K192I (AAA→ATA) | malA ← | alpha‑glucosidase |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,657,158 | C→T | 37.9% | G174S (GGT→AGT) | USA300HOU_1546 ← | competence protein ComGA |
| RA | 1,724,706 | G→T | 12.6% | P192T (CCA→ACA) | alaS ← | alanine‑‑tRNA ligase |
| 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 | 1,830,883 | C→T | 76.1% | K79K (AAG→AAA) | ezrA ← | possible septation ring formation regulator |
| RA | 1,851,260 | C→A | 100% | A115S (GCG→TCG) | acsA1 ← | acetate‑‑CoA ligase |
| RA | 1,854,250 | T→C | 12.9% | S145S (TCA→TCG) | ccpA ← | catabolite control protein A |
| RA | 1,929,796 | T→C | 40.4% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 40.2% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 39.5% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 41.2% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 54.7% | 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 | 63.5% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 63.5% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 65.2% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 46.3% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 17.6% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 48.8% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 8.8% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 63.2% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 65.7% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 65.5% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 66.5% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 66.0% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 66.9% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 66.2% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 66.3% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 64.7% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 65.7% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 65.7% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 59.1% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 52.2% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,932,853 | T→C | 100% | I799V (ATT→GTT) | USA300HOU_1798 ← | 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 | 2,018,612 | G→A | 100% | R103* (CGA→TGA) | mgt ← | transglycosylase |
| RA | 2,041,281 | T→C | 11.5% | intergenic (‑364/+219) | dagK ← / ← USA300HOU_1899 | hypothetical protein/hypothetical protein |
| RA | 2,078,566:1 | +T | 100% | coding (253/681 nt) | USA300HOU_1935 ← | hypothetical membrane protein |
| RA | 2,079,114 | T→C | 69.9% | H201R (CAC→CGC) | bcrA ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 2,186,228 | T→C | 36.0% | T129T (ACA→ACG) | rsbW ← | anti‑sigma B factor |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,352,815 | G→A | 100% | A92V (GCA→GTA) | rpsI ← | ribosomal protein S9 |
| RA | 2,454,626 | A→T | 100% | L48L (CTA→CTT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,482,693 | T→C | 22.5% | A329A (GCT→GCC) | hssS → | hemin sensor histidine kinase |
| RA | 2,502,882:1 | +A | 100% | coding (1406/2106 nt) | USA300HOU_2364 → | AraC transcriptional regulator |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,543,088 | G→A | 100% | R283K (AGA→AAA) | hlgA → | gamma‑hemolysin component A |
| RA | 2,679,455 | Δ1 bp | 100% | intergenic (+327/‑62) | USA300HOU_2535 → / → cbpD | hypothetical protein/possible secretory antigen |
| RA | 2,709,439 | Δ1 bp | 100% | coding (1488/1812 nt) | oatA ← | possible acetyltransferase |
| RA | 2,750,562 | T→C | 100% | V197V (GTA→GTG) | betA ← | choline dehydrogenase |
| RA | 2,778,338 | C→A | 12.1% | *323Y (TAG→TAT) | arcC3 ← | carbamate kinase |
| RA | 2,784,861 | C→T | 10.5% | T309T (ACG→ACA) | aur ← | M04 family aureolysin |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 37094 = | 41 (1.290) | 3 (0.100) | 3/240 | NT | 6.8% | coding (21/231 nt) | USA300HOU_0028 | hypothetical protein |
| ? | CP000730 | 37188 = | 45 (1.530) | coding (115/231 nt) | USA300HOU_0028 | hypothetical protein | |||||
| * | ? | CP000730 | 512620 = | 30 (0.940) | 26 (1.250) +45 bp |
18/170 | NT | 55.1% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 2176447 = | 35 (1.100) | noncoding (114/114 nt) | rrf5 | 5S ribosomal RNA | |||||