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 | 46.3% | 33.3 / 226.2 | 176 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 28.6% | 165.0 / 73.7 | 119 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 28.6% | 171.7 / 70.3 | 119 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (lowest skew 10 of 13 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 1961511 = | 129 (1.420) | 99 (1.140) +TATTTT |
4/268 | 9.1 | 47.2% | noncoding (74/74 nt) | USA300TCH1516_01819 | tRNA‑Glu |
| ? | USA300TCH1516_ALE | = 1998272 | 102 (1.120) | noncoding (1/76 nt) | USA300TCH1516_01882 | tRNA‑Val | |||||
| * | ? | USA300TCH1516_ALE | 1179979 = | 89 (0.980) | 6 (0.070) | 3/252 | 9.4 | 6.9% | intergenic (+235/+70) | USA300HOU_RS05875/USA300HOU_RS05880 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 1180015 = | 83 (1.020) | intergenic (+271/+34) | USA300HOU_RS05875/USA300HOU_RS05880 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 580739 = | 104 (1.150) | 4 (0.050) | 3/250 | 9.4 | 4.1% | intergenic (+33/‑48) | USA300HOU_RS02805/sigH | hypothetical protein/RNA polymerase sigma‑H factor |
| ? | USA300TCH1516_ALE | 580788 = | 95 (1.170) | coding (2/570 nt) | sigH | RNA polymerase sigma‑H factor | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 76 (0.840) | 103 (1.140) +T |
4/278 | 9.4 | 58.9% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 69 (0.760) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 300188 = | 96 (1.060) | 4 (0.050) | 3/260 | 9.6 | 4.0% | coding (455/717 nt) | tarI | Ribitol‑5‑phosphate cytidylyltransferase 1 |
| ? | USA300TCH1516_ALE | 300250 = | 104 (1.230) | coding (517/717 nt) | tarI | Ribitol‑5‑phosphate cytidylyltransferase 1 | |||||
| * | ? | USA300TCH1516_ALE | 2699163 = | 72 (0.790) | 22 (0.250) +TAGTGT |
3/268 | 9.8 | 24.2% | intergenic (+67/‑224) | copA/copZ | Copper‑exporting P‑type ATPase A/Copper chaperone CopZ |
| ? | USA300TCH1516_ALE | = 2699363 | 72 (0.790) | intergenic (+267/‑24) | copA/copZ | Copper‑exporting P‑type ATPase A/Copper chaperone CopZ | |||||
| * | ? | NC_012417 | = 1974 | 2079 (1.090) | 7 (0.000) | 6/258 | 69.1 | 0.37% | intergenic (+207/+119) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 2041 | 1830 (1.040) | intergenic (+274/+52) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 4399 | 6 (3.780) | 6 (0.010) | 5/258 | 70.3 | 0.63% | intergenic (+364/‑101) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1963 | 1902 (1.080) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 2352 | 1 (0.630) | 6 (0.010) | 5/258 | 70.3 | 0.63% | intergenic (+132/+36) | USA300HOU_pUSA300HOUMR0003/USA300HOU_pUSA300HOUMR0004 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 1963 | 1902 (1.080) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_012417 | = 1575 | 1589 (0.830) | 5 (0.000) | 5/268 | 71.5 | 0.33% | intergenic (‑381/‑4) | USA300HOU_RS15665/USA300HOU_RS14895 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 1586 | 1515 (0.830) | coding (8/189 nt) | USA300HOU_RS14895 | hypothetical protein | |||||