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 31.8% intergenic (+45/+63) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,817 A→T 35.2% intergenic (+48/+60) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,850 C→T 38.9% intergenic (+81/+27) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,858 T→A 41.9% intergenic (+89/+19) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,876 C→T 49.3% intergenic (+107/+1) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,913 C→G 23.9% S213S (TCG→TCC tpn ← IS431mec transposase
RA 35,940 G→A 27.8% R204R (CGC→CGT tpn ← IS431mec transposase
RA 35,970 T→C 62.5% E194E (GAA→GAG tpn ← IS431mec transposase
RA 35,997 T→C 29.1% T185T (ACA→ACG tpn ← IS431mec transposase
RA 36,015 C→T 28.8% R179R (AGG→AGA tpn ← IS431mec transposase
RA 36,087 A→G 61.6% C155C (TGT→TGC tpn ← IS431mec transposase
RA 36,119 C→T 32.1% V145I (GTA→ATA)  tpn ← IS431mec transposase
RA 36,124 G→A 59.8% A143V (GCT→GTT)  tpn ← IS431mec transposase
RA 36,133 A→G 30.5% V140A (GTA→GCA)  tpn ← IS431mec transposase
RA 36,161 T→C 29.0% I131V (ATT→GTT)  tpn ← IS431mec transposase
RA 36,174 T→C 28.7% K126K (AAA→AAG tpn ← IS431mec transposase
RA 36,269 C→T 58.3% A95T (GCA→ACA)  tpn ← IS431mec transposase
RA 36,315 G→A 59.1% Y79Y (TAC→TAT tpn ← IS431mec transposase
RA 36,378 C→T 88.2% L58L (TTG→TTA tpn ← IS431mec transposase
RA 36,413 C→T 54.9% V47I (GTC→ATC)  tpn ← IS431mec transposase
RA 36,444 C→T 50.2% R36R (AGG→AGA tpn ← IS431mec transposase
RA 36,471 A→G 18.3% S27S (AGT→AGC tpn ← IS431mec transposase
RA 36,479 T→C 12.6% T25A (ACA→GCA)  tpn ← IS431mec transposase
RA 36,581 C→T 27.3% intergenic (‑30/‑493) tpn ← / → USA300HOU_0028 IS431mec transposase/hypothetical protein
RA 76,180 C→T 24.6% intergenic (+238/‑896) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 76,185 G→A 9.9% intergenic (+243/‑891) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 76,265 C→T 30.9% intergenic (+323/‑811) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 76,295 T→C 60.9% intergenic (+353/‑781) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 76,322 G→A 59.7% intergenic (+380/‑754) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 76,353 G→A 58.7% intergenic (+411/‑723) USA300HOU_0072 → / → USA300HOU_0075 universal stress protein/lysophospholipase
RA 110,651 C→T 6.8% D170D (GAC→GAT USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 110,660 T→A 8.4% I173I (ATT→ATA USA300HOU_0109 → staphylococcal tandem lipoprotein
RA 111,512 A→G 28.8% S194S (TCA→TCG USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,516 C→A 27.2% Q196K (CAA→AAA)  USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 111,560 T→C 9.6% R210R (CGT→CGC USA300HOU_0110 → possible staphylococcal tandem lipoprotein
RA 455,181 C→A 11.2% intergenic (+181/‑199) set23 → / → set24 staphylococcal exotoxin/staphylococcal exotoxin
RA 512,643 A→G 52.9% intergenic (+711/‑150) recR → / → rrs1 recombination protein RecR/16S ribosomal RNA
RA 873,632 A→T 6.0% S179S (TCA→TCT clfA → fibrinogen‑binding protein
RA 984,359 A→G 5.9% K101E (AAA→GAA)  eap → possible extracellular adherence protein Eap
RA 1,056,257 C→A 12.8% intergenic (‑1758/+1909) sspA ← / ← atl S01 family glutamyl endopeptidase/bifunctional N‑acetylmuramoyl‑L‑alanine amidase/mannosyl‑glycoprotein endo‑beta‑N‑acetylglucosaminidase
RA 1,081,153 T→C 6.6% N295N (AAT→AAC purM → phosphoribosylformylglycinamidine cyclo‑ligase
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 1,646,189 G→C 100% A155G (GCA→GGA)  pepP ← M24B family Xaa‑Pro dipeptidase
RA 1,744,362 G→A 11.1% H104Y (CAC→TAC)  apt ← adenine phosphoribosyltransferase
RA 1,744,424 A→G 11.6% L83S (TTA→TCA)  apt ← adenine phosphoribosyltransferase
RA 1,744,473 C→T 7.7% A67T (GCT→ACT)  apt ← adenine phosphoribosyltransferase
RA 1,744,644 C→A 22.8% V10F (GTT→TTT)  apt ← adenine phosphoribosyltransferase
RA 1,857,839 T→C 6.6% I179V (ATT→GTT)  USA300HOU_1728 ← hypothetical protein
RA 1,857,867 C→T 7.6% L169L (TTG→TTA USA300HOU_1728 ← hypothetical protein
RA 1,929,796 T→C 35.9% intergenic (‑879/‑289) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,797 G→A 34.1% intergenic (‑880/‑288) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,799 C→A 35.2% intergenic (‑882/‑286) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,804 A→G 36.1% intergenic (‑887/‑281) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,812 G→A 50.9% 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 58.6% intergenic (‑926/‑242) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,848 C→A 59.6% intergenic (‑931/‑237) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,861 T→C 61.9% intergenic (‑944/‑224) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,862:1 +T 43.2% intergenic (‑945/‑223) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,864 A→T 19.0% intergenic (‑947/‑221) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,865 A→C 43.5% intergenic (‑948/‑220) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,865:1 +C 12.5% intergenic (‑948/‑220) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,866 G→T 58.4% intergenic (‑949/‑219) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,867 G→T 61.0% intergenic (‑950/‑218) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,870 A→C 61.3% intergenic (‑953/‑215) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,872 G→A 59.9% intergenic (‑955/‑213) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,873 C→A 60.4% intergenic (‑956/‑212) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,875 T→C 61.0% intergenic (‑958/‑210) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,917 C→T 52.9% intergenic (‑1000/‑168) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,918 A→G 52.4% intergenic (‑1001/‑167) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,925 T→A 51.0% intergenic (‑1008/‑160) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,928 T→A 50.2% intergenic (‑1011/‑157) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,930 T→A 50.7% intergenic (‑1013/‑155) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,941 A→T 38.9% intergenic (‑1024/‑144) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 1,929,946 G→A 34.6% intergenic (‑1029/‑139) USA300HOU_1794 ← / → USA300HOU_1796 hypothetical protein/hypothetical protein
RA 2,010,363 C→T 100% C146Y (TGT→TAT)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane protein
RA 2,233,544 T→C 6.4% E174G (GAA→GGA)  prmC ← HemK family methyltransferase
RA 2,279,705 G→A 100% intergenic (+1373/+6659) mtlD → / ← glmM mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase
RA 2,386,969 A→T 6.9% K117* (AAA→TAA)  marR → MarR family transcriptional regulator
RA 2,390,270 T→C 7.2% E54G (GAA→GGA)  moaA ← molybdenum (Mo2+) cofactor biosynthesis protein A
RA 2,519,951 T→G 6.5% P227P (CCA→CCC narG ← nitrate reductase alpha subunit
RA 2,532,298 A→T 100% T15T (ACA→ACT murN → FemAB family peptidoglycan biosynthesis protein
RA 2,680,105 T→A 6.5% intergenic (+157/+375) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,680,132 A→G 8.1% intergenic (+184/+348) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,680,184 T→A 6.3% intergenic (+236/+296) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,680,185:1 +T 6.6% intergenic (+237/+295) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,680,197:1 +A 6.2% intergenic (+249/+283) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,680,198 C→T 7.5% intergenic (+250/+282) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,680,214 T→C 6.8% intergenic (+266/+266) cbpD → / ← USA300HOU_2537 possible secretory antigen/hypothetical protein
RA 2,774,969 A→G 10.1% D739D (GAT→GAC clfB ← clumping factor B
RA 2,774,981 A→G 10.1% D735D (GAT→GAC clfB ← clumping factor B

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? CP000730 = 26029450 (0.780)3 (0.050) 3/238 NT 6.0% intergenic (‑408/‑165) USA300HOU_0232/pfl iron (Fe3+) ABC superfamily ATP binding cassette transporter, membrane/binding protein/formate C‑acetyltransferase
?CP000730 = 260312 49 (0.830)intergenic (‑426/‑147) USA300HOU_0232/pfl iron (Fe3+) ABC superfamily ATP binding cassette transporter, membrane/binding protein/formate C‑acetyltransferase
* ? CP000730 512620 =61 (0.950)54 (1.220)
+40 bp
45/180 NT 56.2% 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 = 120532363 (0.980)3 (0.050)
+AGCGAA
3/248 NT 6.2% intergenic (+459/‑365) yfiE/lspA possible lactoylglutathione lyase/A8 family signal peptidase II
?CP000730 = 1893309 33 (0.510)intergenic (‑1303/+177) rot/USA300HOU_1755 repressor of toxins Rot/lysophospholipase
* ? CP000730 2001491 =8 (0.120)6 (0.100) 4/246 NT 44.2% intergenic (‑100/+116) rrl3/USA300HOU_t0051 23S ribosomal RNA/tRNA‑Ala
?CP000730 2179606 = NA (NA)intergenic (‑50/+262) rrl4/rrs4 23S ribosomal RNA/16S ribosomal RNA