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 | 37,542 | 0 | T | C | 52.0% | ‑0.7 / 20.6 | 26 | intergenic (+566/‑271) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 46.6% | 40.7 / 210.6 | 175 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 37,539 | 0 | C | A | 46.4% | 15.5 / 32.2 | 28 | intergenic (+563/‑274) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| * | USA300TCH1516_ALE | 37,540 | 0 | A | G | 46.4% | 14.6 / 30.5 | 28 | intergenic (+564/‑273) | USA300HOU_RS14915/ugpQ_1 | hypothetical protein/Glycerophosphodiester phosphodiesterase, cytoplasmic |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 37.1% | 107.2 / 90.7 | 105 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 34.2% | 110.3 / 92.4 | 111 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 1,435,071 | 0 | C | T | 24.7% | 158.1 / 12.7 | 81 | T143I (ACT→ATT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| * | USA300TCH1516_ALE | 1,435,065 | 0 | C | G | 23.5% | 188.3 / 11.8 | 86 | A141G (GCT→GGT) | dapH | 2,3,4,5‑tetrahydropyridine‑2,6‑dicarboxylate N‑acetyltransferase |
| Marginal new junction evidence (lowest skew 10 of 19 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 4399 | 8 (3.840) | 11 (0.010) | 7/258 | 0.2 | 1.1% | intergenic (+364/‑101) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1963 | 1951 (1.100) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4311 = | 9 (4.320) | 10 (0.010) | 5/258 | 0.2 | 1.1% | intergenic (+276/‑189) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2053 = | 1866 (1.050) | intergenic (+286/+40) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 800928 | 69 (0.770) | 5 (0.060) | 5/266 | 9.6 | 7.0% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 801948 = | 68 (0.800) | intergenic (+189/+435) | USA300HOU_RS03915/USA300HOU_RS03920 | Putative 5'(3')‑deoxyribonucleotidase/Putative lipid kinase | |||||
| * | ? | USA300TCH1516_ALE | 2400537 = | 107 (1.200) | 4 (0.050) | 4/256 | 10.0 | 3.8% | intergenic (‑43/+78) | bioY/rihB | Biotin transporter BioY/Pyrimidine‑specific ribonucleoside hydrolase RihB |
| ? | USA300TCH1516_ALE | 2400570 = | 105 (1.290) | intergenic (‑76/+45) | bioY/rihB | Biotin transporter BioY/Pyrimidine‑specific ribonucleoside hydrolase RihB | |||||
| * | ? | USA300TCH1516_ALE | = 800928 | 69 (0.770) | 5 (0.060) | 4/266 | 10.3 | 5.6% | intergenic (+62/‑289) | hisC_1/USA300HOU_RS03915 | Histidinol‑phosphate aminotransferase/Putative 5'(3')‑deoxyribonucleotidase |
| ? | USA300TCH1516_ALE | 2220679 = | 103 (1.210) | intergenic (‑330/+232) | USA300HOU_RS11345/atpC | hypothetical protein/ATP synthase epsilon chain | |||||
| * | ? | USA300TCH1516_ALE | 2388283 = | 114 (1.280) | 3 (0.040) | 3/246 | 10.4 | 3.1% | intergenic (+18/+84) | ribZ_1/sarV | Riboflavin transporter RibZ/HTH‑type transcriptional regulator SarV |
| ? | USA300TCH1516_ALE | 2388362 = | 85 (1.080) | intergenic (+97/+5) | ribZ_1/sarV | Riboflavin transporter RibZ/HTH‑type transcriptional regulator SarV | |||||
| * | ? | USA300TCH1516_ALE | 1114090 = | 73 (0.820) | 4 (0.050) | 3/246 | 10.4 | 6.1% | intergenic (+19/+63) | USA300HOU_RS05510/mntH_1 | hypothetical protein/Divalent metal cation transporter MntH |
| ? | USA300TCH1516_ALE | 1114149 = | 60 (0.770) | intergenic (+78/+4) | USA300HOU_RS05510/mntH_1 | hypothetical protein/Divalent metal cation transporter MntH | |||||
| * | ? | USA300TCH1516_ALE | = 1205323 | 83 (0.930) | 43 (0.480) | 4/280 | 10.6 | 32.7% | intergenic (‑204/‑365) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase |
| ? | USA300TCH1516_ALE | 1205383 = | 94 (1.050) | intergenic (‑264/‑305) | USA300HOU_RS15290/lspA | hypothetical protein/Lipoprotein signal peptidase | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 77 (0.860) | 67 (0.760) +T |
4/278 | 10.6 | 45.0% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 88 (0.990) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1183556 | 72 (0.810) | 3 (0.040) | 3/260 | 10.8 | 4.3% | intergenic (+67/+42) | yfnB/USA300HOU_RS05910 | Putative HAD‑hydrolase YfnB/putative N‑acetyltransferase |
| ? | USA300TCH1516_ALE | = 1183574 | 66 (0.800) | intergenic (+85/+24) | yfnB/USA300HOU_RS05910 | Putative HAD‑hydrolase YfnB/putative N‑acetyltransferase | |||||