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 | 32.7% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 30.8% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 36.8% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 38.3% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 47.3% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 29.3% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 31.2% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 56.4% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 33.2% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 32.5% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 58.4% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 32.2% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 58.1% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 31.7% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 32.5% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 33.3% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 61.3% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 58.3% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 90.3% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 55.6% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 50.9% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 29.8% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 12.0% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,501 | G→A | 5.2% | A17A (GCC→GCT) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 33.6% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 37.7% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 20.3% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 30.7% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 60.6% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 60.2% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 54.6% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,889 | G→A | 9.1% | intergenic (+947/‑187) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,660 | T→A | 13.5% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,330 | C→A | 6.5% | Q134K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 30.1% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 32.0% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,560 | T→C | 9.8% | R210R (CGT→CGC) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 512,643 | A→G | 54.1% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 587,957 | G→T | 11.4% | A621S (GCG→TCG) | rpoB → | DNA‑directed RNA polymerase subunit beta |
| RA | 787,902 | G→A | 5.5% | R23H (CGC→CAC) | pabC → | possible aminodeoxychorismate lyase |
| RA | 821,301 | T→C | 5.5% | P346P (CCA→CCG) | pepT ← | M20 family peptidase T |
| RA | 937,158 | T→A | 5.3% | intergenic (+65/‑1952) | yumB → / → USA300HOU_0903 | NADH dehydrogenase/NhaC family sodium:proton (Na+:H+) antiporter |
| RA | 937,168 | G→A | 5.3% | intergenic (+75/‑1942) | yumB → / → USA300HOU_0903 | NADH dehydrogenase/NhaC family sodium:proton (Na+:H+) antiporter |
| RA | 1,035,144 | C→T | 6.1% | intergenic (‑1561/‑6145) | USA300HOU_0983 ← / → USA300HOU_0984 | competence protein/glycosyltransferase |
| RA | 1,117,630 | C→T | 8.0% | intergenic (+3416/‑104) | USA300HOU_1046 → / → typA | hypothetical protein/GTP‑binding protein TypA |
| RA | 1,141,228 | G→A | 11.3% | E283K (GAA→AAA) | USA300HOU_1066 → | hypothetical protein |
| RA | 1,231,407 | G→A | 6.5% | E18K (GAA→AAA) | prpC → | possible PP2C protein phosphatase |
| RA | 1,400,393 | C→T | 6.1% | P73L (CCA→CTA) | umuC → | ImpB/MucB/SamB family DNA‑damage repair protein |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,433,870 | A→G | 10.7% | D287G (GAC→GGC) | dapA → | dihydrodipicolinate synthase |
| RA | 1,472,896 | T→C | 7.0% | K9710E (AAG→GAG) | ebh ← | extracellular matrix binding protein |
| RA | 1,507,931 | C→T | 6.5% | intergenic (‑356/+119) | ald1 ← / ← polA | alanine dehydrogenase/5'‑3' exonuclease |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,589,223 | A→G | 7.6% | V753V (GTT→GTC) | USA300HOU_1459 ← | hypothetical bacteriophage protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,673,843 | T→C | 6.1% | K391K (AAA→AAG) | dnaG ← | DNA primase |
| RA | 1,744,443 | C→A | 16.4% | V77F (GTT→TTT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,446 | G→A | 7.6% | P76S (CCT→TCT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,744,544 | T→C | 43.8% | Y43C (TAC→TGC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,781,307 | T→C | 5.1% | K471E (AAG→GAG) | lysP ← | APC family amino acid‑polyamine‑organocation transporter |
| RA | 1,815,180 | T→C | 8.7% | E21G (GAA→GGA) | dnaE2 ← | DNA‑directed DNA polymerase III alpha subunit |
| RA | 1,929,796 | T→C | 56.6% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 56.7% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 55.3% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 56.6% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 66.7% | 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 | 70.5% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 71.6% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 73.5% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 51.1% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 21.4% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 52.7% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 13.0% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 70.7% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 72.7% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 72.9% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 72.1% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 72.3% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 72.6% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 64.2% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 63.7% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 61.7% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 61.2% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 60.7% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 50.5% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 47.5% | 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 | 2,084,760 | G→T | 8.5% | intergenic (‑22/‑936) | mapW2 ← / → USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| RA | 2,150,242 | C→G | 6.1% | H208D (CAT→GAT) | agrA → | accessory gene regulator protein A |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,305,823 | C→T | 12.2% | intergenic (‑126/‑51) | USA300HOU_2163 ← / → USA300HOU_2164 | hypothetical membrane protein/hypothetical protein |
| RA | 2,331,676 | A→G | 5.4% | Y81Y (TAT→TAC) | lacC ← | tagatose‑6‑phosphate kinase |
| RA | 2,373,506 | A→T | 15.7% | N90K (AAT→AAA) | pbuG ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,504,989 | T→C | 8.8% | intergenic (+293/+111) | USA300HOU_2365 → / ← gltT | hypothetical protein/DAACS family dicarboxylate/amino acid:sodium (Na+) or proton (H+) symporter |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,540,782 | G→A | 7.4% | E118K (GAA→AAA) | USA300HOU_2401 → | immunoglobulin G‑binding protein SBI |
| RA | 2,771,843 | C→A | 9.0% | F214L (TTC→TTA) | phoB → | alkaline phosphatase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 37094 = | 98 (1.250) | 9 (0.120) | 4/240 | NT | 10.1% | coding (21/231 nt) | USA300HOU_0028 | hypothetical protein |
| ? | CP000730 | 37188 = | 69 (0.960) | coding (115/231 nt) | USA300HOU_0028 | hypothetical protein | |||||
| * | ? | CP000730 | 512620 = | 81 (1.040) | 68 (1.260) +40 bp |
44/180 | NT | 54.9% | 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 | 1822717 = | 60 (0.770) | 3 (0.040) | 3/238 | NT | 5.5% | intergenic (+38/+208) | USA300HOU_1697/ackA | possible universal stress protein/acetate kinase |
| ? | CP000730 | 1822745 = | 49 (0.680) | intergenic (+66/+180) | USA300HOU_1697/ackA | possible universal stress protein/acetate kinase | |||||
| * | ? | CP000730 | 2085296 = | 54 (0.690) | 13 (0.190) | 12/232 | NT | 18.6% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 66 (0.950) | intergenic (+57/+1062) | int/hlgB | bacteriophage integrase/possible leukocidin subunit | |||||