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 | 567,389 | 0 | A | T | 73.7% | 209.4 / 91.0 | 114 | Q98L (CAA→CTA) | ctsR | Transcriptional regulator CtsR |
| * | USA300TCH1516_ALE | 1,744,443 | 0 | C | A | 68.8% | 123.9 / 112.1 | 112 | V77F (GTT→TTT) | apt | Adenine phosphoribosyltransferase |
| * | USA300TCH1516_ALE | 2,159,426 | 0 | G | A | 60.2% | 78.4 / 132.2 | 113 | V330I (GTC→ATC) | yheS | putative ABC transporter ATP‑binding protein YheS |
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 54.0% | 55.2 / inf | 240 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 34.5% | 334.5 / 186.5 | 194 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 34.0% | 241.3 / 182.8 | 194 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 1,776,534 | 0 | C | . | 27.0% | 291.1 / 121.9 | 111 | intergenic (‑11/+140) | clpX/tig | ATP‑dependent Clp protease ATP‑binding subunit ClpX/Trigger factor |
| * | USA300TCH1516_ALE | 2,372,559 | 0 | C | T | 25.2% | 205.2 / 73.1 | 115 | C406Y (TGT→TAT) | pbuG | Guanine/hypoxanthine permease PbuG |
| * | USA300TCH1516_ALE | 722,085 | 0 | T | A | 24.6% | 265.0 / 87.3 | 126 | I19K (ATA→AAA) | fepC | Ferric enterobactin transport ATP‑binding protein FepC |
| * | USA300TCH1516_ALE | 2,227,320 | 0 | T | G | 23.2% | 229.7 / 101.7 | 144 | I40L (ATT→CTT) | atpB | ATP synthase subunit a |
| * | USA300TCH1516_ALE | 1,231,396 | 0 | G | T | 22.3% | 344.3 / 61.6 | 130 | R14I (AGA→ATA) | stp | Serine/threonine phosphatase stp |
| Marginal new junction evidence (lowest skew 10 of 102 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 1205383 = | 111 (0.860) | 41 (0.390) +25 bp |
7/228 | 13.6 | 33.1% | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 2478476 = | 91 (0.710) | intergenic (+363/‑212) | USA300HOU_RS12760/USA300HOU_RS12765 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 1205383 = | 111 (0.860) | 40 (0.380) +25 bp |
6/228 | 14.3 | 37.0% | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1426741 = | 55 (0.430) | intergenic (‑472/+500) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B | |||||
| * | ? | USA300TCH1516_ALE | = 2636366 | 141 (1.090) | 7 (0.060) | 7/256 | 14.8 | 5.2% | intergenic (‑419/+50) | fnbA_2/gntT | Fibronectin‑binding protein A/High‑affinity gluconate transporter |
| ? | USA300TCH1516_ALE | = 2636392 | 124 (1.050) | intergenic (‑445/+24) | fnbA_2/gntT | Fibronectin‑binding protein A/High‑affinity gluconate transporter | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 75 (0.580) | 194 (1.520) +T |
8/276 | 15.0 | 65.5% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 131 (1.020) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 130 (1.010) | 46 (0.360) | 8/278 | 15.1 | 27.6% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1205383 = | 111 (0.860) | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase | |||||
| * | ? | USA300TCH1516_ALE | 2041611 = | 112 (0.870) | 6 (0.050) | 6/256 | 15.5 | 5.7% | intergenic (‑694/+75) | dagK/gatB_2 | Diacylglycerol kinase/Aspartyl/glutamyl‑tRNA(Asn/Gln) amidotransferase subunit B |
| ? | USA300TCH1516_ALE | 2041657 = | 97 (0.820) | intergenic (‑740/+29) | dagK/gatB_2 | Diacylglycerol kinase/Aspartyl/glutamyl‑tRNA(Asn/Gln) amidotransferase subunit B | |||||
| * | ? | USA300TCH1516_ALE | = 1545880 | 105 (0.810) | 5 (0.040) | 5/258 | 16.3 | 4.7% | intergenic (‑183/+39) | der_1/rpsA_1 | GTPase Der/30S ribosomal protein S1 |
| ? | USA300TCH1516_ALE | = 1545890 | 104 (0.870) | intergenic (‑193/+29) | der_1/rpsA_1 | GTPase Der/30S ribosomal protein S1 | |||||
| * | ? | USA300TCH1516_ALE | 2082519 = | 118 (0.920) | 5 (0.040) | 5/260 | 16.4 | 4.5% | intergenic (+160/+164) | aspC/USA300HOU_RS10520 | Aspartate aminotransferase/65 kDa membrane protein |
| ? | USA300TCH1516_ALE | 2082566 = | 101 (0.840) | intergenic (+207/+117) | aspC/USA300HOU_RS10520 | Aspartate aminotransferase/65 kDa membrane protein | |||||
| * | ? | USA300TCH1516_ALE | 1217678 = | 97 (0.750) | 5 (0.040) | 4/246 | 16.6 | 6.0% | intergenic (+7/‑430) | USA300HOU_RS06060/USA300HOU_RS06065 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1217746 = | 72 (0.630) | intergenic (+75/‑362) | USA300HOU_RS06060/USA300HOU_RS06065 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2035543 = | 114 (0.880) | 5 (0.040) | 5/270 | 16.8 | 4.0% | intergenic (+43/‑346) | ftnA/polC_2 | Bacterial non‑heme ferritin/DNA polymerase III PolC‑type |
| ? | USA300TCH1516_ALE | 2035581 = | 127 (1.010) | intergenic (+81/‑308) | ftnA/polC_2 | Bacterial non‑heme ferritin/DNA polymerase III PolC‑type | |||||