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 33.9% intergenic (+45/+63) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,817 A→T 33.0% intergenic (+48/+60) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,850 C→T 40.1% 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 51.7% intergenic (+107/+1) rlmH → / ← tpn hypothetical protein/IS431mec transposase
RA 35,913 C→G 27.2% S213S (TCG→TCC tpn ← IS431mec transposase
RA 35,940 G→A 31.1% R204R (CGC→CGT tpn ← IS431mec transposase
RA 35,970 T→C 57.7% E194E (GAA→GAG tpn ← IS431mec transposase
RA 35,997 T→C 30.7% T185T (ACA→ACG tpn ← IS431mec transposase
RA 36,015 C→T 29.9% R179R (AGG→AGA tpn ← IS431mec transposase
RA 36,087 A→G 59.4% C155C (TGT→TGC tpn ← IS431mec transposase
RA 36,119 C→T 32.3% V145I (GTA→ATA)  tpn ← IS431mec transposase
RA 36,124 G→A 55.7% A143V (GCT→GTT)  tpn ← IS431mec transposase
RA 36,133 A→G 32.6% V140A (GTA→GCA)  tpn ← IS431mec transposase
RA 36,161 T→C 31.8% I131V (ATT→GTT)  tpn ← IS431mec transposase
RA 36,174 T→C 30.3% K126K (AAA→AAG tpn ← IS431mec transposase
RA 36,269 C→T 58.2% A95T (GCA→ACA)  tpn ← IS431mec transposase
RA 36,315 G→A 56.2% Y79Y (TAC→TAT tpn ← IS431mec transposase
RA 36,378 C→T 87.4% L58L (TTG→TTA tpn ← IS431mec transposase
RA 36,413 C→T 51.1% V47I (GTC→ATC)  tpn ← IS431mec transposase
RA 36,444 C→T 48.0% R36R (AGG→AGA tpn ← IS431mec transposase
RA 36,471 A→G 23.8% S27S (AGT→AGC tpn ← IS431mec transposase
RA 36,479 T→C 22.5% T25A (ACA→GCA)  tpn ← IS431mec transposase
RA 36,501 G→A 7.5% A17A (GCC→GCT tpn ← IS431mec transposase
RA 36,581 C→T 35.0% intergenic (‑30/‑493) tpn ← / → 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 460,262 G→A 5.7% intergenic (+111/‑272) hsdS1 → / → set type I site‑specific deoxyribonuclease specificity subunit/staphylococcal exotoxin
RA 491,927 T→A 9.2% L118L (CTT→CTA sle1 → 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 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)  htrA → 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)  oppD ← 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 1,580,165 G→T 7.4% S108* (TCA→TAA)  USA300HOU_1448 ← hypothetical bacteriophage protein
RA 1,646,189 G→C 100% A155G (GCA→GGA)  pepP ← 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)  nfeD ← 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 1,884,975 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 1,929,862:1 +T 54.2% intergenic (‑945/‑223) 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 1,929,870 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)  ygaD ← ABC superfamily ATP binding cassette transporter, membrane 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 pbuG ← NCS2 family nucleobase:cation symporter‑2
RA 2,420,667 G→T 9.5% intergenic (+98/‑264) ssaA → / → gyaR secretory antigen SsaA/(R)‑2‑hydroxyacid dehydrogenase
RA 2,489,727 C→A 7.4% intergenic (+76/+77) USA300HOU_2350 → / ← USA300HOU_2351 hypothetical protein/hypothetical lipoprotein
RA 2,532,298 A→T 100% T15T (ACA→ACT murN → 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)  yfkO ← FMN 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) metQ 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/hlgB bacteriophage integrase/possible leukocidin subunit