mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.32.1 revision 5f2cb669173e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 39,378 | C→A | 100% | D586Y (GAT→TAT) | mecA ← | penicillin binding protein 2 prime |
| RA | 110,651 | C→T | 18.3% | D170D (GAC→GAT) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 110,660 | T→A | 16.5% | I173I (ATT→ATA) | USA300HOU_0109 → | staphylococcal tandem lipoprotein |
| RA | 111,512 | A→G | 32.1% | S194S (TCA→TCG) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 111,516 | C→A | 32.8% | Q196K (CAA→AAA) | USA300HOU_0110 → | possible staphylococcal tandem lipoprotein |
| RA | 188,567 | A→T | 5.0% | D143V (GAT→GTT) | cap5O → | capsular polysaccharide biosynthesis protein Cap5O |
| RA | 221,865 | C→A | 7.4% | G475V (GGC→GTC) | USA300HOU_0203 ← | PTS family glucose/glucoside (glc) porter component IIABC |
| RA | 367,644 | G→T | 100% | intergenic (‑96/‑20) | nanA ← / → USA300HOU_0336 | N‑acetylneuraminate lyase/possible transcriptional regulator |
| RA | 423,247 | A→G | 100% | V112V (GTA→GTG) | USA300HOU_0394 → | hypothetical protein |
| RA | 454,656 | G→A | 100% | V119I (GTT→ATT) | set23 → | staphylococcal exotoxin |
| RA | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_0458 → | hypothetical protein |
| RA | 512,643 | A→G | 49.3% | intergenic (+711/‑150) | recR → / → rrs1 | recombination protein RecR/16S ribosomal RNA |
| RA | 583,939 | G→A | 6.9% | intergenic (+23/‑249) | rplA → / → rplJ | ribosomal protein L1/ribosomal protein L10 |
| RA | 638,614 | G→T | 100% | T14K (ACA→AAA) | thiD ← | phosphomethylpyrimidine kinase |
| RA | 693,258 | T→A | 8.3% | I65F (ATT→TTT) | USA300HOU_0636 ← | hypothetical protein |
| RA | 707,879 | A→T | 100% | L11I (TTA→ATA) | USA300HOU_0653 ← | ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 790,778 | G→A | 100% | intergenic (+277/‑197) | USA300HOU_0741 → / → USA300HOU_0742 | possible allophanate hydrolase subunit 2/possible phosphatidylglycerol‑‑membrane‑oligosaccharide glycerophosphotransferase |
| RA | 911,610 | G→A | 100% | intergenic (‑221/‑107) | USA300HOU_0869 ← / → USA300HOU_0870 | hypothetical membrane protein/ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,199,222 | C→A | 10.7% | F80L (TTC→TTA) | USA300HOU_1127 → | hypothetical protein |
| RA | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | USA300HOU_1157 → | non‑specific serine/threonine protein kinase |
| MC JC | 1,302,967 | Δ4 bp | 100% | coding (325‑328/714 nt) | USA300HOU_1209 → | possible GntR family transcriptional regulator |
| RA | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | USA300HOU_1314 ← | oligopeptide ABC superfamily ATP binding cassette transporter, ABC protein |
| RA | 1,419,527 | G→T | 100% | P7T (CCT→ACT) | USA300HOU_1317 ← | hypothetical membrane protein |
| RA | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA ← | cold shock protein CspA |
| RA | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh ← | extracellular matrix binding protein |
| RA | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh ← | extracellular matrix binding protein |
| RA | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_1379 → | hypothetical membrane protein |
| RA | 1,551,783 | A→G | 7.4% | S231P (TCA→CCA) | ebpS ← | elastin‑binding protein |
| RA | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | USA300HOU_1531 ← | M24B family Xaa‑Pro dipeptidase |
| RA | 1,672,434 | C→T | 72.4% | A187T (GCA→ACA) | rpoD ← | DNA‑directed RNA polymerase sigma subunit RpoD |
| RA | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | adenine phosphoribosyltransferase |
| RA | 1,784,962 | C→T | 5.0% | G40D (GGC→GAC) | thrS ← | threonine‑‑tRNA ligase |
| RA | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | USA300HOU_1679 ← | sensor histidine kinase |
| RA | 1,802,628 | A→T | 7.8% | K321M (AAG→ATG) | USA300HOU_1683 → | APC family amino acid‑polyamine‑organocation transporter |
| RA | 1,809,898 | A→G | 6.5% | F91F (TTT→TTC) | accD ← | acetyl‑CoA carboxylase beta subunit |
| RA | 1,944,670 | G→A | 100% | intergenic (‑251/‑713) | splA ← / → USA300HOU_1807 | S1B family serine protease SplA/hypothetical protein |
| RA | 1,946,057 | G→A | 8.9% | intergenic (+108/+366) | USA300HOU_1807 → / ← epiG | hypothetical protein/lantibiotic epidermin immunity protein F |
| RA | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_1861 ← | ABC superfamily ATP binding cassette transporter, membrane protein |
| RA | 2,026,655 | C→T | 100% | E87K (GAA→AAA) | vraR ← | response regulator VraR |
| RA | 2,261,772 | T→C | 5.6% | V185V (GTA→GTG) | USA300HOU_2133 ← | hypothetical protein |
| RA | 2,279,705 | G→A | 100% | intergenic (+1373/+6659) | mtlD → / ← glmM | mannitol‑1‑phosphate 5‑dehydrogenase/phosphoglucosamine mutase |
| RA | 2,289,325 | C→A | 100% | Q55H (CAG→CAT) | USA300HOU_2153 ← | hypothetical membrane protein |
| RA | 2,386,119 | G→A | 62.5% | P114L (CCG→CTG) | USA300HOU_2245 ← | hypothetical protein |
| RA | 2,454,551 | G→T | 4.3% | M23I (ATG→ATT) | USA300HOU_2315 → | hypothetical membrane protein |
| RA | 2,502,141 | C→A | 100% | A222D (GCC→GAC) | USA300HOU_2364 → | AraC transcriptional regulator |
| RA | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | USA300HOU_2392 → | FemAB family peptidoglycan biosynthesis protein |
| RA | 2,679,462 | (A)8→7 | 100% | intergenic (+334/‑55) | USA300HOU_2535 → / → USA300HOU_2536 | hypothetical protein/possible secretory antigen |
| RA | 2,710,898 | (T)6→5 | 100% | coding (29/1812 nt) | USA300HOU_2562 ← | possible acetyltransferase |
| RA | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | USA300HOU_2698 → | hypothetical protein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000730 | 34173 = | 72 (1.140) | 5 (0.080) | 5/246 | NT | 7.0% | coding (462/480 nt) | orfX | hypothetical protein OrfX |
| ? | CP000730 | = 57858 | 64 (1.070) | intergenic (+304/+613) | USA300HOU_0048/USA300HOU_0049 | hypothetical membrane protein/hypothetical protein | |||||
| * | ? | CP000730 | 52495 = | 62 (0.990) | 111 (1.780) +T |
3/256 | NT | 63.3% | intergenic (+105/‑568) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator |
| ? | CP000730 | = 52988 | 68 (1.080) | intergenic (+598/‑75) | USA300HOU_0043/USA300HOU_0044 | hypothetical membrane protein/possible transcriptional regulator | |||||
| * | ? | CP000730 | 512620 = | 84 (1.330) | 47 (1.090) +40 bp |
34/178 | NT | 44.9% | 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 | = 800928 | 63 (1.000) | 4 (0.070) | 4/244 | NT | 5.0% | intergenic (+62/‑289) | hisC1/USA300HOU_0748 | histidinol‑phosphate transaminase/hypothetical protein |
| ? | CP000730 | 801948 = | 94 (1.580) | intergenic (+189/+435) | USA300HOU_0748/dgkA1 | hypothetical protein/possible diacylglycerol kinase | |||||
| * | ? | CP000730 | 2001491 = | 11 (0.170) | 3 (0.050) | 3/244 | NT | 22.4% | 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 | |||||
| * | ? | CP000730 | = 2674542 | 69 (1.100) | 6 (0.100) | 3/238 | NT | 8.2% | intergenic (‑21/+247) | ptsG/ilvB2 | PTS family glucose/glucoside (glc) porter component IIABC/pyruvate oxidase |
| ? | CP000730 | = 2674577 | 71 (1.220) | intergenic (‑56/+212) | ptsG/ilvB2 | PTS family glucose/glucoside (glc) porter component IIABC/pyruvate oxidase | |||||
| * | ? | CP000730 | = 2777745 | 41 (0.650) | 3 (0.050) | 3/244 | NT | 6.9% | coding (495/705 nt) | USA300HOU_2631 | transcriptional regulator |
| ? | CP000730 | = 2777785 | 42 (0.710) | coding (455/705 nt) | USA300HOU_2631 | transcriptional regulator | |||||