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 | 24.1% | intergenic (+45/+63) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,817 | A→T | 24.3% | intergenic (+48/+60) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,850 | C→T | 31.0% | intergenic (+81/+27) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,858 | T→A | 32.9% | intergenic (+89/+19) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,876 | C→T | 36.8% | intergenic (+107/+1) | rlmH → / ← tpn | hypothetical protein/IS431mec transposase |
| RA | 35,913 | C→G | 20.1% | S213S (TCG→TCC) | tpn ← | IS431mec transposase |
| RA | 35,940 | G→A | 27.4% | R204R (CGC→CGT) | tpn ← | IS431mec transposase |
| RA | 35,970 | T→C | 56.4% | E194E (GAA→GAG) | tpn ← | IS431mec transposase |
| RA | 35,997 | T→C | 26.5% | T185T (ACA→ACG) | tpn ← | IS431mec transposase |
| RA | 36,015 | C→T | 24.0% | R179R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,087 | A→G | 64.2% | C155C (TGT→TGC) | tpn ← | IS431mec transposase |
| RA | 36,119 | C→T | 24.0% | V145I (GTA→ATA) | tpn ← | IS431mec transposase |
| RA | 36,124 | G→A | 62.7% | A143V (GCT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,133 | A→G | 25.3% | V140A (GTA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,161 | T→C | 27.3% | I131V (ATT→GTT) | tpn ← | IS431mec transposase |
| RA | 36,174 | T→C | 25.6% | K126K (AAA→AAG) | tpn ← | IS431mec transposase |
| RA | 36,269 | C→T | 57.1% | A95T (GCA→ACA) | tpn ← | IS431mec transposase |
| RA | 36,315 | G→A | 53.6% | Y79Y (TAC→TAT) | tpn ← | IS431mec transposase |
| RA | 36,378 | C→T | 81.4% | L58L (TTG→TTA) | tpn ← | IS431mec transposase |
| RA | 36,413 | C→T | 54.4% | V47I (GTC→ATC) | tpn ← | IS431mec transposase |
| RA | 36,444 | C→T | 53.5% | R36R (AGG→AGA) | tpn ← | IS431mec transposase |
| RA | 36,471 | A→G | 22.1% | S27S (AGT→AGC) | tpn ← | IS431mec transposase |
| RA | 36,479 | T→C | 17.1% | T25A (ACA→GCA) | tpn ← | IS431mec transposase |
| RA | 36,581 | C→T | 35.4% | intergenic (‑30/‑493) | tpn ← / → USA300HOU_0028 | IS431mec transposase/hypothetical protein |
| RA | 76,180 | C→T | 19.7% | intergenic (+238/‑896) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,265 | C→T | 22.1% | intergenic (+323/‑811) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,295 | T→C | 57.5% | intergenic (+353/‑781) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,322 | G→A | 55.0% | intergenic (+380/‑754) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 76,353 | G→A | 44.4% | intergenic (+411/‑723) | USA300HOU_0072 → / → USA300HOU_0075 | universal stress protein/lysophospholipase |
| RA | 108,148 | A→G | 11.8% | K1037R (AAA→AGA) | USA300HOU_0106 → | hypothetical protein |
| RA | 110,651 | C→T | 16.6% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 16.4% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 23.8% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 25.0% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 187,439 | G→T | 7.9% | A81S (GCA→TCA) | cap5N → | capsular polysaccharide biosynthesis protein Cap5N |
| RA | 189,365 | A→G | 16.7% | Y409C (TAT→TGT) | cap5O → | capsular polysaccharide biosynthesis protein Cap5O |
| RA | 264,793 | T→C | 8.2% | L336L (CTT→CTC) | glpQ1 → | possible glycerophosphodiester phosphodiesterase |
| RA | 265,956 | T→C | 11.4% | I51M (ATA→ATG) | USA300HOU_0237 ← | hypothetical protein |
| RA | 387,871 | G→T | 8.3% | S175I (AGT→ATT) | mepA → | MATE family multi‑antimicrobial extrusion protein |
| RA | 414,995 | T→C | 7.0% | I25T (ATA→ACA) | metC → | possible ParB family partitioning protein |
| RA | 494,590 | A→G | 9.3% | I138T (ATT→ACT) | yibF ← | hypothetical protein |
| RA | 512,643 | A→G | 48.2% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 591,934 | Δ1 bp | 5.3% | coding (2150/3624 nt) | rpoC → | DNA‑directed RNA polymerase subunit beta' |
| RA | 622,019 | T→C | 9.7% | L861S (TTG→TCG) | sdrE → | Ser‑Asp rich fibrinogen/bone sialoprotein‑binding protein SdrE |
| RA | 866,495 | G→A | 12.4% | C346Y (TGT→TAT) | vacB → | exoribonuclease R |
| RA | 915,857 | C→T | 9.0% | A5V (GCA→GTA) | sufB → | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 966,439 | A→G | 7.1% | S169S (TCA→TCG) | rexA → | ATP‑dependent nuclease Rex subunit A |
| RA | 984,788 | C→T | 10.0% | A50T (GCT→ACT) | USA300HOU_0940 ← | hypothetical protein |
| RA | 989,442 | C→A | 10.0% | Q141K (CAG→AAG) | oppC1 → | oligopeptide ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 995,747 | C→T | 9.9% | intergenic (+24/‑27) | oppA2 → / → oppD2 | oligopeptide ABC superfamily ATP binding cassette transporter, binding protein/oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,091,403 | T→C | 12.0% | S378P (TCT→CCT) | ywbD → | hypothetical protein |
| RA | 1,181,141 | T→C | 7.9% | intergenic (‑145/‑104) | ydiA ← / → USA300HOU_1111 | TDT family tellurite/dicarboxylate transporter/hypothetical protein |
| RA | 1,202,470 | G→A | 10.0% | V483I (GTT→ATT) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 1,276,099 | T→A | 8.5% | T146T (ACT→ACA) | tsf → | elongation factor EF1B |
| RA | 1,291,644 | G→A | 12.6% | G439D (GGT→GAT) | infB → | translation initiation factor IF‑2 |
| RA | 1,414,715 | T→C | 15.2% | L165S (TTG→TCG) | USA300HOU_1311 → | possible hydrolase |
| 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 | 1,540,760 | A→G | 10.3% | F146S (TTC→TCC) | gerC ← | trans‑hexaprenyltranstransferase subunit II |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | pepP ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,672,327 | A→G | 16.3% | V222V (GTT→GTC) | rpoD ← | DNA‑directed RNA polymerase sigma subunit RpoD |
| RA | 1,732,905 | T→A | 10.8% | intergenic (+91/+146) | yvbT → / ← USA300HOU_1624 | dehydrogenase/hypothetical protein |
| RA | 1,776,059 | A→G | 6.7% | D155D (GAT→GAC) | clpX ← | S14 family endopeptidase ClpX |
| RA | 1,797,152 | G→A | 17.8% | S213S (TCC→TCT) | phoR ← | sensor histidine kinase |
| RA | 1,842,707 | T→C | 6.9% | I204V (ATT→GTT) | tyrS ← | tyrosine‑‑tRNA ligase |
| RA | 1,929,796 | T→C | 41.2% | intergenic (‑879/‑289) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,797 | G→A | 41.8% | intergenic (‑880/‑288) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,799 | C→A | 41.6% | intergenic (‑882/‑286) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,804 | A→G | 48.4% | intergenic (‑887/‑281) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,812 | G→A | 52.0% | 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 | 61.3% | intergenic (‑926/‑242) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,848 | C→A | 61.0% | 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 | 53.9% | intergenic (‑945/‑223) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,864 | A→T | 10.8% | 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 | 1,929,866 | G→T | 63.7% | intergenic (‑949/‑219) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,867 | G→T | 64.4% | intergenic (‑950/‑218) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,870 | A→C | 65.2% | intergenic (‑953/‑215) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,872 | G→A | 66.2% | intergenic (‑955/‑213) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,873 | C→A | 65.0% | intergenic (‑956/‑212) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,875 | T→C | 62.5% | intergenic (‑958/‑210) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,917 | C→T | 48.0% | intergenic (‑1000/‑168) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,918 | A→G | 48.0% | intergenic (‑1001/‑167) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,925 | T→A | 44.7% | intergenic (‑1008/‑160) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,928 | T→A | 44.8% | intergenic (‑1011/‑157) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,930 | T→A | 44.8% | intergenic (‑1013/‑155) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,941 | A→T | 38.2% | intergenic (‑1024/‑144) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,929,946 | G→A | 33.2% | intergenic (‑1029/‑139) | USA300HOU_1794 ← / → USA300HOU_1796 | hypothetical protein/hypothetical protein |
| RA | 1,980,512 | G→T | 6.5% | Q83K (CAA→AAA) | USA300HOU_1839 ← | hypothetical protein |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | ygaD ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,018,582 | T→A | 9.8% | K113* (AAA→TAA) | mgt ← | transglycosylase |
| RA | 2,028,124 | G→A | 34.2% | P174L (CCG→CTG) | yvqF ← | hypothetical membrane protein |
| RA | 2,057,798 | C→A | 5.5% | R165L (CGA→CTA) | USA300HOU_1913 ← | hypothetical membrane protein |
| RA | 2,094,261 | A→G | 14.3% | T553T (ACT→ACC) | hol ← | hypothetical bacteriophage protein |
| RA | 2,101,143 | A→G | 5.5% | V268A (GTA→GCA) | USA300HOU_1959 ← | bacteriophage tail length tape measure protein |
| RA | 2,128,065 | A→G | 18.2% | K273E (AAA→GAA) | int → | bacteriophage integrase |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,358,670 | T→C | 10.0% | K83R (AAA→AGA) | rpoA ← | DNA‑directed RNA polymerase alpha subunit |
| RA | 2,372,751 | A→T | 23.1% | L342* (TTA→TAA) | pbuG ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,373,531 | G→T | 13.0% | A82E (GCG→GAG) | pbuG ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,373,714 | C→T | 33.2% | G21D (GGT→GAT) | pbuG ← | NCS2 family nucleobase:cation symporter‑2 |
| RA | 2,405,833 | A→G | 9.3% | E74G (GAA→GGA) | ureA → | urease gamma subunit |
| RA | 2,425,673 | A→G | 11.6% | F809L (TTT→CTT) | USA300HOU_2291 ← | formate dehydrogenase alpha subunit |
| RA | 2,451,070 | T→C | 9.8% | K116K (AAA→AAG) | hutU ← | urocanate hydratase |
| RA | 2,462,758 | G→A | 25.0% | A70T (GCA→ACA) | mag → | DNA‑3‑methyladenine glycosylase |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,532,665 | G→T | 10.3% | G138C (GGT→TGT) | murN → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,568,885 | T→A | 9.1% | L245* (TTA→TAA) | fmtA → | FmtA protein |
| RA | 2,615,078 | A→G | 17.0% | G919G (GGT→GGC) | USA300HOU_2480 ← | helicase |
| RA | 2,638,727 | C→T | 8.7% | D240N (GAT→AAT) | gntK ← | gluconokinase |
| RA | 2,656,802 | A→T | 6.4% | S72R (AGT→AGA) | USA300HOU_2510 ← | MarR family transcriptional regulator |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 512620 = | 39 (1.000) | 32 (1.260) +45 bp |
20/170 | NT | 52.2% | intergenic (+688/‑173) | recR/rrs1 | recombination protein RecR/16S ribosomal RNA |
| ? | CP000730 | 2176447 = | 51 (1.310) | noncoding (114/114 nt) | rrf5 | 5S ribosomal RNA | |||||
| * | ? | CP000730 | 895785 = | 48 (1.230) | 9 (0.270) | 8/226 | NT | 22.0% | coding (806/822 nt) | metQ | ABC superfamily ATP binding cassette transporter, binding protein |
| ? | CP000730 | = 909740 | 22 (0.650) | intergenic (‑663/‑371) | ear/USA300HOU_0868 | Ear protein/hypothetical protein | |||||
| * | ? | CP000730 | 2085296 = | 27 (0.690) | 7 (0.200) | 5/232 | NT | 17.7% | intergenic (‑558/‑400) | mapW2/USA300HOU_1944 | cell surface protein MapW2/hypothetical protein |
| ? | CP000730 | = 2128343 | 41 (1.180) | intergenic (+57/+1062) | int/hlgB | bacteriophage integrase/possible leukocidin subunit | |||||