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 | 11,042 | A→G | 7.6% | V41V (GTA→GTG) | hutH → | histidine ammonia‑lyase |
| RA | 35,814 | Δ1 bp | 34.3% | 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 | 40.2% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 44.1% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 54.8% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 21.3% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 24.5% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 63.1% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 29.1% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 28.0% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 59.8% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 31.1% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 57.7% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 31.6% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 35.0% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 34.0% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 56.0% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 56.1% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 85.3% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 54.8% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 42.9% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 28.3% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 17.5% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 40.4% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 36.7% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,185 | G→A | 19.5% | intergenic (+243/‑891) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 31.0% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 54.0% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 53.3% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 49.2% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 110,651 | C→T | 15.7% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 27.0% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 34.4% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 31.5% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 293,940 | C→T | 25.0% | intergenic (+57/‑471) | gatD → / → ispD2 | zinc (Zn2+)‑binding dehydrogenase/2‑C‑methyl‑D‑erythritol 4‑phosphate cytidylyltransferase |
| RA | 297,176 | C→T | 6.0% | S337L (TCA→TTA) | tagB1 → | glycosyl/glycerophosphate transferase |
| RA | 478,502 | C→A | 100% | D342E (GAC→GAA) | ndhF → | NADH dehydrogenase (ubiquinone) |
| RA | 479,096 | T→C | 5.5% | F41F (TTT→TTC) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 44.4% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 538,142 | T→C | 9.6% | F151F (TTT→TTC) | mfd → | transcription‑repair coupling factor helicase |
| JC | 567,290 | Δ3 bp | 5.5% | coding (185‑187/462 nt) | ctsR → | CtsR family transcriptional regulator |
| RA | 584,121 | G→T | 100% | intergenic (+205/‑67) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 707,909 | A→T | 100% | M1M (TTG→ATG) † | mntB ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 737,162 | A→G | 7.6% | R548R (AGA→AGG) | vraE → | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 788,134 | A→T | 5.7% | K100N (AAA→AAT) | pabC → | possible aminodeoxychorismate lyase |
| RA | 873,442 | A→G | 5.1% | E116G (GAA→GGA) | clfA → | fibrinogen‑binding protein |
| RA | 973,213 | C→A | 100% | E175* (GAG→TAG) | yitU ← | possible HAD superfamily hydrolase |
| RA | 1,002,200 | T→G | 100% | M173R (ATG→AGG) | mecA2 → | competence negative regulator MecA |
| RA | 1,105,994 | T→C | 100% | T12T (ACT→ACC) | pdhD → | dihydrolipoyl dehydrogenase |
| RA | 1,135,045 | G→A | 5.3% | R55C (CGT→TGT) | ylbM ← | possible nucleotidyltransferase |
| RA | 1,196,508 | C→A | 100% | intergenic (+2563/‑1229) | ftsQ → / → ylmE | cell division protein FtsQ/hypothetical protein |
| RA | 1,333,789 | T→G | 13.7% | Y64D (TAT→GAT) | hflX → | GTP‑binding protein |
| 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 | 1,532,200 | G→A | 6.9% | R226C (CGT→TGT) | USA300HOU_1398 ← | hypothetical membrane protein |
| RA | 1,539,250 | C→G | 100% | intergenic (‑349/+37) | aroC ← / ← USA300HOU_1405 | chorismate synthase/hypothetical protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,744,473 | C→T | 100% | A67T (GCT→ACT) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,789,619 | T→A | 9.1% | intergenic (‑100/+70) | gapB ← / ← coaE | glyceraldehyde‑3‑phosphate dehydrogenase (phosphorylating)/dephospho‑CoA kinase |
| RA | 1,929,796 | T→C | 33.9% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 33.9% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 33.9% | 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 | 50.4% | 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 | 61.8% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 63.3% | intergenic (‑931/‑237) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,861 | T→C | 66.1% | intergenic (‑944/‑224) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,862:1 | +T | 47.1% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 17.3% | intergenic (‑947/‑221) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865 | A→C | 48.6% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,865:1 | +C | 10.0% | intergenic (‑948/‑220) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,866 | G→T | 64.1% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 68.1% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 67.9% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 65.4% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 66.7% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 67.6% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 58.8% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 58.2% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 59.6% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 59.8% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 59.3% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 50.3% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 43.4% | 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 | 2,024,507 | C→A | 10.1% | A37E (GCA→GAA) | USA300HOU_1878 → | hypothetical protein |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,337,959 | C→T | 100% | intergenic (‑125/‑119) | adhR ← / → USA300HOU_2196 | possible MerR family transcriptional regulator/hypothetical protein |
| RA | 2,343,438 | C→T | 48.7% | intergenic (+114/+250) | USA300HOU_2200 → / ← alsD | hypothetical protein/acetolactate decarboxylase |
| RA | 2,455,692 | Δ1 bp | 100% | coding (1210/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,455,698 | 2 bp→AT | 100% | coding (1216‑1217/1260 nt) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 84 (1.290) | 52 (1.160) +40 bp |
35/180 | NT | 47.3% | 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 | |||||