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 | 110,651 | C→T | 6.5% | D170D (GAC→GAT) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 110,660 | T→A | 11.0% | I173I (ATT→ATA) | USA300HOU_RS00515 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,512 | A→G | 32.4% | S194S (TCA→TCG) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,516 | C→A | 34.5% | Q196K (CAA→AAA) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 111,560 | T→C | 7.1% | R210R (CGT→CGC) | USA300HOU_RS00520 → | putative lipoprotein |
| RA | USA300TCH1516_ALE | 512,643 | A→G | 46.9% | intergenic (+711/‑6052) | recR → / → speA_2 | Recombination protein RecR/Arginine decarboxylase |
| RA | USA300TCH1516_ALE | 613,998 | G→A | 5.8% | S770S (TCG→TCA) | sdrC → | Serine‑aspartate repeat‑containing protein C |
| RA | USA300TCH1516_ALE | 614,034 | G→A | 5.6% | S782S (TCG→TCA) | sdrC → | Serine‑aspartate repeat‑containing protein C |
| RA | USA300TCH1516_ALE | 618,588 | G→A | 5.2% | S1230S (TCG→TCA) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 618,636 | G→A | 6.6% | S1246S (TCG→TCA) | sdrD → | Serine‑aspartate repeat‑containing protein D |
| RA | USA300TCH1516_ALE | 622,359 | T→C | 5.1% | D974D (GAT→GAC) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,464 | G→A | 9.7% | S1009S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 622,536 | G→A | 5.8% | S1033S (TCG→TCA) | sdrE → | Serine‑aspartate repeat‑containing protein E |
| RA | USA300TCH1516_ALE | 848,908 | G→T | 21.5% | E12* (GAA→TAA) | USA300HOU_RS04145 → | Nucleotide‑binding protein |
| RA | USA300TCH1516_ALE | 1,141,235 | C→A | 7.4% | S285* (TCA→TAA) | USA300HOU_RS05655 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,313,831 | C→A | 7.7% | A17E (GCA→GAA) | USA300HOU_RS06490 → | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,324,247 | C→A | 6.1% | P340Q (CCA→CAA) | mutL → | DNA mismatch repair protein MutL |
| RA | USA300TCH1516_ALE | 1,416,458 | A→T | 100% | I216N (ATT→AAT) | oppD_4 ← | Oligopeptide transport ATP‑binding protein OppD |
| RA | USA300TCH1516_ALE | 1,435,071 | C→T | 11.8% | T143I (ACT→ATT) | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| RA | USA300TCH1516_ALE | 1,435,074 | G→A | 11.0% | G144D (GGT→GAT) | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| RA | USA300TCH1516_ALE | 1,435,082 | G→A | 7.9% | V147I (GTA→ATA) | dapH → | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| 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 | 1,744,302 | C→A | 9.1% | G124C (GGT→TGT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,362 | G→A | 12.1% | H104Y (CAC→TAC) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,744,607 | T→C | 34.3% | D22G (GAT→GGT) | apt ← | Adenine phosphoribosyltransferase |
| RA | USA300TCH1516_ALE | 1,857,785 | A→T | 8.4% | S197T (TCA→ACA) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 1,857,867 | C→T | 6.8% | L169L (TTG→TTA) | USA300HOU_RS09235 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,010,363 | C→T | 100% | C146Y (TGT→TAT) | USA300HOU_RS10125 ← | Putative multidrug export ATP‑binding/permease protein |
| RA | USA300TCH1516_ALE | 2,028,191 | C→A | 32.9% | A152S (GCA→TCA) | USA300HOU_RS10230 ← | hypothetical protein |
| RA | USA300TCH1516_ALE | 2,279,705 | G→A | 100% | A943V (GCA→GTA) | ebh_3 ← | Extracellular matrix‑binding protein ebh |
| RA | USA300TCH1516_ALE | 2,373,546 | G→T | 27.0% | A77D (GCT→GAT) | pbuG ← | Guanine/hypoxanthine permease PbuG |
| RA | USA300TCH1516_ALE | 2,532,298 | A→T | 100% | T15T (ACA→ACT) | femA_3 → | Aminoacyltransferase FemA |
| RA | USA300TCH1516_ALE | 2,774,858 | C→T | 6.2% | S776S (TCG→TCA) | clfB ← | Clumping factor B |
| RA | USA300TCH1516_ALE | 2,774,930 | C→T | 6.2% | S752S (TCG→TCA) | clfB ← | Clumping factor B |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 512620 = | 170 (0.760) | 110 (0.740) +40 bp |
58/166 | NT | 49.0% | 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 | |||||