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 |
| Marginal read alignment evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 49.5% | ‑4.2 / inf | 329 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 38.3% | 286.8 / 249.0 | 240 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 37.3% | 211.3 / 242.1 | 254 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 2,291,785 | 0 | A | G | 36.0% | 23.5 / 19.6 | 25 | H779R (CAC→CGC) | USA300HOU_RS11675 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,291,819 | 0 | C | T | 25.0% | 133.3 / 41.3 | 76 | D790D (GAC→GAT) | USA300HOU_RS11675 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,291,811 | 0 | C | A | 22.9% | 122.1 / 31.8 | 61 | R788R (CGA→AGA) | USA300HOU_RS11675 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,291,888 | 0 | G | A | 21.7% | 371.0 / 82.0 | 185 | K813K (AAG→AAA) | USA300HOU_RS11675 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 156 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 715303 = | 189 (1.230) | 15 (0.110) | 13/240 | 14.6 | 8.1% | intergenic (+61/+56) | tarD/dacA | Glycerol‑3‑phosphate cytidylyltransferase/D‑alanyl‑D‑alanine carboxypeptidase DacA |
| ? | USA300TCH1516_ALE | 715350 = | 170 (1.240) | intergenic (+108/+9) | tarD/dacA | Glycerol‑3‑phosphate cytidylyltransferase/D‑alanyl‑D‑alanine carboxypeptidase DacA | |||||
| * | ? | USA300TCH1516_ALE | = 515130 | NA (NA) | 16 (0.110) | 14/254 | 14.8 | NA | intergenic (+3198/‑3565) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 515141 | NA (NA) | intergenic (+3209/‑3554) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 1205383 = | 147 (0.960) | 125 (1.000) +25 bp |
10/218 | 15.1 | 57.7% | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 2478476 = | 79 (0.510) | intergenic (+363/‑212) | USA300HOU_RS12760/USA300HOU_RS12765 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1205383 = | 147 (0.960) | 115 (0.920) +25 bp |
10/218 | 15.1 | 57.8% | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1426741 = | 60 (0.390) | intergenic (‑472/+500) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B | |||||
| * | ? | USA300TCH1516_ALE | = 2753848 | 168 (1.090) | 8 (0.070) +34 bp |
8/200 | 15.3 | 6.0% | intergenic (+129/+59) | opcR/gloB | HTH‑type transcriptional repressor OpcR/Hydroxyacylglutathione hydrolase |
| ? | USA300TCH1516_ALE | 2754851 = | 169 (1.100) | intergenic (‑258/+6) | gloB/opuD_3 | Hydroxyacylglutathione hydrolase/Glycine betaine transporter OpuD | |||||
| * | ? | USA300TCH1516_ALE | = 2317464 | 177 (1.150) | 11 (0.090) +28 bp |
9/212 | 15.3 | 7.0% | intergenic (+117/‑339) | iucC_3/USA300TCH1516_02193 | Aerobactin synthase/hypothetical protein |
| ? | USA300TCH1516_ALE | 2319448 = | 194 (1.260) | intergenic (+21/+15) | USA300HOU_RS15290/USA300HOU_RS11830 | hypothetical protein/Alkaline shock protein 23 | |||||
| * | ? | USA300TCH1516_ALE | 197371 = | 150 (0.980) | 13 (0.090) | 13/254 | 15.3 | 8.4% | coding (396/975 nt) | cmpC | Bicarbonate transport ATP‑binding protein CmpC |
| ? | USA300TCH1516_ALE | = 197367 | 141 (0.970) | coding (392/975 nt) | cmpC | Bicarbonate transport ATP‑binding protein CmpC | |||||
| * | ? | USA300TCH1516_ALE | = 517640 | NA (NA) | 18 (0.120) | 13/256 | 15.4 | NA | intergenic (+5708/‑1055) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 517643 | NA (NA) | intergenic (+5711/‑1052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 2555346 = | 150 (0.980) | 12 (0.080) | 12/250 | 15.7 | 8.1% | intergenic (‑317/+552) | irtA/yfdG | Iron import ATP‑binding/permease protein IrtA/Prophage bactoprenol‑linked glucose translocase |
| ? | USA300TCH1516_ALE | 2555368 = | 134 (0.930) | intergenic (‑339/+530) | irtA/yfdG | Iron import ATP‑binding/permease protein IrtA/Prophage bactoprenol‑linked glucose translocase | |||||
| * | ? | USA300TCH1516_ALE | 1878597 = | 158 (1.030) | 13 (0.100) | 10/232 | 15.9 | 8.9% | intergenic (+56/+61) | USA300HOU_RS09320/ebh_2 | Ferredoxin‑‑NADP reductase/Extracellular matrix‑binding protein ebh |
| ? | USA300TCH1516_ALE | 1878652 = | 131 (0.990) | intergenic (+111/+6) | USA300HOU_RS09320/ebh_2 | Ferredoxin‑‑NADP reductase/Extracellular matrix‑binding protein ebh | |||||