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 | 50.0% | 3.9 / 276.4 | 185 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 42.2% | 159.4 / 167.2 | 149 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 41.6% | 104.5 / 173.3 | 149 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 110,660 | 0 | T | A | 21.6% | 208.9 / 62.1 | 97 | I173I (ATT→ATA) | USA300HOU_RS00515 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 365029 = | 101 (1.120) | 12 (0.150) | 11/248 | 9.8 | 11.0% | intergenic (+39/+66) | nupC_1/sglT | Nucleoside permease NupC/Sodium/glucose cotransporter |
| ? | USA300TCH1516_ALE | 365083 = | 102 (1.240) | intergenic (+93/+12) | nupC_1/sglT | Nucleoside permease NupC/Sodium/glucose cotransporter | |||||
| * | ? | USA300TCH1516_ALE | 2492466 = | 91 (1.010) | 7 (0.080) | 6/250 | 12.8 | 7.9% | intergenic (+9/+37) | yhfP/rimI_4 | Putative quinone oxidoreductase YhfP/Ribosomal‑protein‑alanine acetyltransferase |
| ? | USA300TCH1516_ALE | 2492499 = | 80 (0.970) | intergenic (+42/+4) | yhfP/rimI_4 | Putative quinone oxidoreductase YhfP/Ribosomal‑protein‑alanine acetyltransferase | |||||
| * | ? | USA300TCH1516_ALE | 329202 = | 116 (1.290) | 6 (0.070) | 6/252 | 12.9 | 5.6% | intergenic (+70/+73) | USA300HOU_RS01475/ssaA2_1 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| ? | USA300TCH1516_ALE | 329255 = | 96 (1.150) | intergenic (+123/+20) | USA300HOU_RS01475/ssaA2_1 | hypothetical protein/Staphylococcal secretory antigen ssaA2 | |||||
| * | ? | USA300TCH1516_ALE | 2537754 = | 71 (0.790) | 5 (0.060) | 5/250 | 13.5 | 6.9% | intergenic (+108/+46) | USA300TCH1516_02423/gpmA_2 | hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase |
| ? | USA300TCH1516_ALE | 2537797 = | 70 (0.850) | intergenic (+151/+3) | USA300TCH1516_02423/gpmA_2 | hypothetical protein/2,3‑bisphosphoglycerate‑dependent phosphoglycerate mutase | |||||
| * | ? | USA300TCH1516_ALE | = 782423 | 95 (1.050) | 4 (0.050) | 4/252 | 14.4 | 4.6% | intergenic (‑218/+124) | USA300HOU_RS03820/USA300HOU_RS03825 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 782442 | 78 (0.930) | intergenic (‑237/+105) | USA300HOU_RS03820/USA300HOU_RS03825 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 298069 = | 115 (1.280) | 4 (0.050) | 4/252 | 14.4 | 3.6% | intergenic (+208/‑220) | tarK/tarF_1 | Teichoic acid ribitol‑phosphate polymerase TarK/Teichoic acid glycerol‑phosphate transferase |
| ? | USA300TCH1516_ALE | 298125 = | 110 (1.320) | intergenic (+264/‑164) | tarK/tarF_1 | Teichoic acid ribitol‑phosphate polymerase TarK/Teichoic acid glycerol‑phosphate transferase | |||||
| * | ? | USA300TCH1516_ALE | 2129189 = | 75 (0.830) | 4 (0.050) | 4/258 | 14.6 | 5.2% | intergenic (+22/+216) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 |
| ? | USA300TCH1516_ALE | 2129212 = | 75 (0.880) | intergenic (+45/+193) | hlb_2/USA300HOU_RS10870 | Phospholipase C/putative leukocidin‑like protein 1 | |||||
| * | ? | USA300TCH1516_ALE | 2681949 = | 84 (0.930) | 4 (0.050) | 4/262 | 14.8 | 4.9% | coding (873/1278 nt) | mvaA | 3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase |
| ? | USA300TCH1516_ALE | 2681984 = | 73 (0.840) | coding (838/1278 nt) | mvaA | 3‑hydroxy‑3‑methylglutaryl‑coenzyme A reductase | |||||
| * | ? | USA300TCH1516_ALE | 1708636 = | 69 (0.770) | 4 (0.050) | 3/244 | 14.9 | 6.0% | intergenic (+81/+121) | USA300HOU_RS08530/entA_3 | hypothetical protein/Enterotoxin type A |
| ? | USA300TCH1516_ALE | 1708685 = | 64 (0.790) | intergenic (+130/+72) | USA300HOU_RS08530/entA_3 | hypothetical protein/Enterotoxin type A | |||||
| * | ? | USA300TCH1516_ALE | 2830190 = | 66 (0.730) | 3 (0.040) | 3/250 | 15.1 | 4.5% | intergenic (+18/+429) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 |
| ? | USA300TCH1516_ALE | 2830247 = | 67 (0.810) | intergenic (+75/+372) | icaC/lipA_2 | putative poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine export protein/Lipase 1 | |||||