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 |
| RA | CP000731 | 81 | N→G | 100% | intergenic (–/‑151) | – / → repA | –/replication protein A |
| JC | CP000731 | 6,552 | +28 bp | 100% | intergenic (+1069/‑419) | cadX → / → USA300HOU_pUSA300HOUMR0010 | cadmium efflux regulator/MarR family transcriptional regulator |
| RA | CP000731 | 25,663 | Δ1 bp | 100% | coding (316/333 nt) | USA300HOU_pUSA300HOUMR0031 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 40,898 | T→A | 5.4% | N79I (AAC→ATC) | pbp ← | Beta‑lactam‑inducible penicillin‑binding protein |
| JC | USA300TCH1516_ALE | 62,817 | +TCAATT | 100% | intergenic (‑284/+229) | USA300TCH1516_00053 ← / ← speG | hypothetical protein/Spermidine N(1)‑acetyltransferase |
| RA | USA300TCH1516_ALE | 110,651 | C→T | 8.9% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 13.5% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 29.9% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 33.1% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 8.1% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 216,236 | G→C | 6.9% | P191A (CCA→GCA) | rocD2_1 ← | Ornithine aminotransferase 2 |
| RA | USA300TCH1516_ALE | 405,929 | C→T | 6.6% | A9V (GCA→GTA) | USA300HOU_RS01880 → | putative acetyl‑CoA acyltransferase |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 40.7% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 622,464 | G→A | 11.2% | S1009S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,479 | T→C | 10.0% | D1014D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 683,202 | T→A | 6.0% | Y23F (TAT→TTT) | ftsL_1 ← | Cell division protein FtsL |
| RA | USA300TCH1516_ALE | 729,046 | G→T | 5.6% | M305I (ATG→ATT) | USA300HOU_RS03535 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,021,533 | T→C | 5.5% | D201G (GAT→GGT) | ugtP ← | Processive diacylglycerol beta‑glucosyltransferase |
| RA | USA300TCH1516_ALE | 1,216,836 | A→G | 6.5% | K7E (AAA→GAA) | pyrE → | Orotate phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,473,325 | C→T | 5.0% | A9567T (GCA→ACA) | 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 | 1,615,451 | T→A | 5.6% | V106V (GTA→GTT) | fur ← | Ferric uptake regulation protein |
| RA | USA300TCH1516_ALE | 1,646,189 | G→C | 100% | A155G (GCA→GGA) | ypdF ← | Aminopeptidase YpdF |
| RA | USA300TCH1516_ALE | 1,668,532 | G→T | 9.0% | Q444K (CAA→AAA) | cshB ← | DEAD‑box ATP‑dependent RNA helicase CshB |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,211,305 | A→G | 12.1% | intergenic (+298/+515) | USA300HOU_RS11275 → / ← yidC | hypothetical protein/Membrane protein insertase YidC |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,774,969 | A→G | 9.4% | D739D (GAT→GAC) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,775,041 | A→G | 6.5% | D715D (GAT→GAC) | clfB ← | Clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 96 (1.140) | 52 (0.890) +40 bp |
31/180 | NT | 44.0% | 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 | |||||
| * | ? | USA300TCH1516_ALE | = 800928 | 76 (0.900) | 8 (0.100) | 5/246 | NT | 9.5% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 80 (1.000) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||