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 | 52.2% | 58.3 / 313.4 | 247 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 35.0% | 234.5 / 186.6 | 200 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 33.5% | 272.7 / 165.2 | 195 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 1,435,065 | 0 | C | G | 24.5% | 244.3 / 25.1 | 107 | A141G (GCT→GGT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,074 | 0 | G | A | 23.4% | 246.6 / 19.8 | 111 | G144D (GGT→GAT) ‡ | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,075 | 0 | T | A | 22.5% | 255.7 / 17.5 | 111 | G144G (GGT→GGA) ‡ | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,069 | 0 | A | C | 22.4% | 215.7 / 12.0 | 108 | T142T (ACA→ACC) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,081 | 0 | T | A | 22.4% | 236.2 / 21.3 | 110 | N146K (AAT→AAA) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,073 | 0 | G | A | 22.0% | 237.4 / 22.6 | 111 | G144S (GGT→AGT) ‡ | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,063 | 0 | T | C | 21.3% | 214.5 / 28.8 | 109 | R140R (CGT→CGC) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,064 | 0 | G | C | 20.6% | 264.2 / 20.7 | 107 | A141P (GCT→CCT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,071 | 0 | C | T | 20.0% | 247.4 / 14.3 | 111 | T143I (ACT→ATT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 53 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | = 1205323 | 102 (0.780) | 25 (0.260) +38 bp |
8/218 | 6.1 | 21.8% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 2478252 = | 141 (1.080) | intergenic (+139/‑436) | USA300HOU_RS12760/USA300HOU_RS12765 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 102 (0.780) | 25 (0.260) +38 bp |
8/218 | 6.1 | 25.4% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | = 2072043 | 96 (0.740) | intergenic (+538/+35) | USA300HOU_RS10445/USA300HOU_RS10450 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 102 (0.780) | 25 (0.260) +38 bp |
8/218 | 6.1 | 24.9% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | = 1443739 | NA (NA) | intergenic (‑312/+41) | USA300TCH1516_01342/brnQ_3 | hypothetical protein/Branched‑chain amino acid transport system 2 carrier protein | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 102 (0.780) | 25 (0.260) +38 bp |
8/218 | 6.1 | 27.0% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1426517 = | 81 (0.620) | intergenic (‑248/+724) | pstS/cvfB | Phosphate‑binding protein PstS/Conserved virulence factor B | |||||
| * | ? | USA300TCH1516_ALE | = 516939 | NA (NA) | 8 (0.060) | 7/282 | 7.9 | NA | intergenic (+5007/‑1756) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 516944 | NA (NA) | intergenic (+5012/‑1751) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 633406 = | 116 (0.890) | 6 (0.050) | 6/282 | 8.3 | 4.8% | intergenic (+130/‑414) | proP/yhfT | Proline/betaine transporter/putative acyl‑‑CoA ligase YhfT |
| ? | USA300TCH1516_ALE | 633436 = | 128 (1.030) | intergenic (+160/‑384) | proP/yhfT | Proline/betaine transporter/putative acyl‑‑CoA ligase YhfT | |||||
| * | ? | USA300TCH1516_ALE | 1454018 = | 96 (0.740) | 8 (0.070) | 5/270 | 8.6 | 8.1% | intergenic (‑97/+187) | odhA/arlS | 2‑oxoglutarate dehydrogenase E1 component/Signal transduction histidine‑protein kinase ArlS |
| ? | USA300TCH1516_ALE | 1454048 = | 94 (0.790) | intergenic (‑127/+157) | odhA/arlS | 2‑oxoglutarate dehydrogenase E1 component/Signal transduction histidine‑protein kinase ArlS | |||||
| * | ? | USA300TCH1516_ALE | 2440041 = | 105 (0.810) | 4 (0.030) | 4/270 | 9.1 | 3.8% | intergenic (+2/+64) | USA300HOU_RS12570/malP | hypothetical protein/PTS system maltose‑specific EIICB component |
| ? | USA300TCH1516_ALE | 2440099 = | 106 (0.890) | intergenic (+60/+6) | USA300HOU_RS12570/malP | hypothetical protein/PTS system maltose‑specific EIICB component | |||||
| * | ? | USA300TCH1516_ALE | 399691 = | 119 (0.910) | 5 (0.040) | 4/272 | 9.1 | 4.4% | coding (1712/1713 nt) | efeU | Ferrous iron permease EfeU |
| ? | USA300TCH1516_ALE | 399718 = | 108 (0.900) | intergenic (+26/+66) | efeU/tatC2 | Ferrous iron permease EfeU/Sec‑independent protein translocase protein TatCy | |||||
| * | ? | USA300TCH1516_ALE | = 800928 | 158 (1.210) | 5 (0.040) | 4/280 | 9.3 | 3.4% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 134 (1.080) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||