mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| MC | CP000731 | 1 | Δ27,041 bp | 100% | repA–USA300HOU_pUSA300HOUMR0033 | 26 genes repA, USA300HOU_pUSA300HOUMR0003, USA300HOU_pUSA300HOUMR0004, USA300HOU_pUSA300HOUMR0005, USA300HOU_pUSA300HOUMR0006, cadR, cadX, USA300HOU_pUSA300HOUMR0010, blaZ, blaR, blaI, USA300HOU_pUSA300HOUMR0014, USA300HOU_pUSA300HOUMR0015, USA300HOU_pUSA300HOUMR0016, USA300HOU_pUSA300HOUMR0018, USA300HOU_pUSA300HOUMR0019, USA300HOU_pUSA300HOUMR0021, USA300HOU_pUSA300HOUMR0023, USA300HOU_pUSA300HOUMR0024, USA300HOU_pUSA300HOUMR0027, USA300HOU_pUSA300HOUMR0028, USA300HOU_pUSA300HOUMR0029, USA300HOU_pUSA300HOUMR0030, USA300HOU_pUSA300HOUMR0031, USA300HOU_pUSA300HOUMR0032, USA300HOU_pUSA300HOUMR0033 |
|
| MC | NC_012417 | 1 | Δ3,125 bp | 100% | USA300HOU_RS14890–USA300HOU_RS14900 | USA300HOU_RS14890, USA300HOU_RS15665, USA300HOU_RS14895, USA300HOU_RS14900 | |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 19.0% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 17.5% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 175,610 | T→A | 13.3% | H61Q (CAT→CAA) | ywqE_1 → | Tyrosine‑protein phosphatase YwqE |
| RA | USA300TCH1516_ALE | 367,644 | G→T | 100% | intergenic (‑96/‑62) | nanA ← / → bglK | N‑acetylneuraminate lyase/Beta‑glucoside kinase |
| RA | USA300TCH1516_ALE | 479,553 | G→A | 100% | A194T (GCA→ACA) | USA300HOU_RS02280 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 506,009 | C→A | 14.1% | P137Q (CCA→CAA) | treA → | Trehalose‑6‑phosphate hydrolase |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 65.6% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 522,999 | A→G | 14.5% | M11V (ATG→GTG) | yabA → | Initiation‑control protein YabA |
| RA | USA300TCH1516_ALE | 638,614 | G→T | 100% | T14K (ACA→AAA) | pdxK ← | Pyridoxine kinase |
| RA | USA300TCH1516_ALE | 707,879 | A→T | 100% | L11I (TTA→ATA) | znuC_1 ← | High‑affinity zinc uptake system ATP‑binding protein ZnuC |
| RA | USA300TCH1516_ALE | 790,778 | G→A | 100% | intergenic (+277/‑197) | kipA_1 → / → ltaS | KipI antagonist/Lipoteichoic acid synthase |
| RA | USA300TCH1516_ALE | 1,232,465 | G→C | 100% | A124P (GCG→CCG) | prkC → | Serine/threonine‑protein kinase PrkC |
| RA | USA300TCH1516_ALE | 1,388,143 | T→C | 16.1% | L10L (CTT→CTC) | parC → | DNA topoisomerase 4 subunit A |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA_2 ← | Cold shock protein CspA |
| RA | USA300TCH1516_ALE | 1,474,639 | C→G | 100% | A9129P (GCA→CCA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,481,355 | G→T | 100% | A6890E (GCA→GAA) | ebh_1 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 1,513,930 | A→T | 100% | L413F (TTA→TTT) | USA300HOU_RS07375 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,682,458 | A→G | 11.5% | intergenic (‑203/+101) | USA300HOU_RS08380 ← / ← USA300HOU_RS08385 | PhoH‑like protein/hypothetical protein |
| RA | USA300TCH1516_ALE | 1,744,454 | C→T | 100% | G73D (GGC→GAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,797,772 | G→C | 100% | R7G (CGC→GGC) | phoR ← | Alkaline phosphatase synthesis sensor protein PhoR |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,021,817 | C→T | 23.3% | V139I (GTT→ATT) | USA300HOU_RS10190 ← | putative acyl‑CoA thioester hydrolase |
| RA | USA300TCH1516_ALE | 2,028,233 | G→C | 19.0% | Q138E (CAA→GAA) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,108,625 | C→T | 11.3% | G454S (GGC→AGC) | USA300HOU_RS10675 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,486,221 | C→A | 14.8% | V481L (GTA→TTA) | lctP_2 ← | L‑lactate permease |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,856,087 | T→A | 100% | P80P (CCT→CCA) | rpoA_2 → | DNA‑directed RNA polymerase subunit alpha |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 15 (0.620) | 20 (1.190) +40 bp |
18/180 | NT | 65.9% | intergenic (+688/‑6075) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | 1998278 = | NA (NA) | intergenic (‑6/+3329) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala | |||||