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 | 2,314,215 | 0 | C | T | 69.9% | 137.1 / 88.4 | 116 | S352N (AGT→AAT) | ndhE | NAD(P)H‑quinone oxidoreductase subunit 4L, chloroplastic |
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 49.5% | 25.1 / inf | 283 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 41.0% | 173.9 / 225.1 | 219 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 39.7% | 165.1 / 237.6 | 221 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,560 | 0 | T | C | 22.3% | 256.4 / 63.4 | 132 | R210R (CGT→CGC) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 2,679,265 | 0 | A | T | 20.0% | 298.5 / 25.4 | 140 | intergenic (+137/‑252) | USA300HOU_RS13790/ssaA2_4 | hypothetical protein/Staphylococcal secretory antigen ssaA2 |
| Marginal new junction evidence (lowest skew 10 of 35 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 52489 = | 126 (1.040) | 33 (0.310) | 7/250 | 6.7 | 25.0% | intergenic (+99/‑574) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52983 | 86 (0.800) | intergenic (+593/‑80) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 52495 = | 115 (0.950) | 146 (1.220) +T |
7/278 | 7.3 | 57.9% | intergenic (+105/‑568) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 52988 | 99 (0.820) | intergenic (+598/‑75) | USA300HOU_RS00215/USA300HOU_RS00220 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 848580 | 114 (0.940) | 6 (0.050) +CTGAAAAAAAAAA |
5/254 | 7.8 | 5.2% | intergenic (+585/‑295) | trxB/USA300HOU_RS04145 | Thioredoxin reductase/Nucleotide‑binding protein |
| ? | USA300TCH1516_ALE | 2866847 = | 127 (1.050) | intergenic (‑246/+207) | USA300HOU_RS14695/noc_2 | hypothetical protein/Nucleoid occlusion protein | |||||
| * | ? | USA300TCH1516_ALE | = 848580 | 114 (0.940) | 5 (0.050) +CTGAAAAAAAAAAA |
3/252 | 8.9 | 3.6% | intergenic (+585/‑295) | trxB/USA300HOU_RS04145 | Thioredoxin reductase/Nucleotide‑binding protein |
| ? | USA300TCH1516_ALE | 2665075 = | 182 (1.500) | intergenic (+310/+128) | pitA_2/USA300TCH1516_02535 | L‑methionine sulfoximine/L‑methionine sulfone acetyltransferase/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 72990 = | 134 (1.110) | 7 (0.060) | 3/254 | 9.0 | 5.6% | intergenic (‑17/+69) | arcD_1/arcA_1 | Arginine/ornithine antiporter/Arginine deiminase |
| ? | USA300TCH1516_ALE | 73054 = | 115 (1.050) | intergenic (‑81/+5) | arcD_1/arcA_1 | Arginine/ornithine antiporter/Arginine deiminase | |||||
| * | ? | USA300TCH1516_ALE | = 2618806 | 162 (1.340) | 4 (0.040) | 3/264 | 9.2 | 2.5% | coding (291/1638 nt) | pgcA | Phosphoglucomutase |
| ? | USA300TCH1516_ALE | = 2618808 | 153 (1.340) | coding (293/1638 nt) | pgcA | Phosphoglucomutase | |||||
| * | ? | USA300TCH1516_ALE | = 842626 | 95 (0.790) | 3 (0.030) | 3/264 | 9.2 | 3.1% | intergenic (+12/‑650) | uvrA/hprK | UvrABC system protein A/HPr kinase/phosphorylase |
| ? | USA300TCH1516_ALE | = 842653 | 99 (0.870) | intergenic (+39/‑623) | uvrA/hprK | UvrABC system protein A/HPr kinase/phosphorylase | |||||
| * | ? | USA300TCH1516_ALE | 2699163 = | 123 (1.020) | 45 (0.390) +TAGTGT |
3/268 | 9.3 | 26.4% | intergenic (+67/‑224) | copA/copZ | Copper‑exporting P‑type ATPase A/Copper chaperone CopZ |
| ? | USA300TCH1516_ALE | = 2699363 | 139 (1.150) | intergenic (+267/‑24) | copA/copZ | Copper‑exporting P‑type ATPase A/Copper chaperone CopZ | |||||
| * | ? | USA300TCH1516_ALE | 2406948 = | 167 (1.380) | 8 (0.070) | 3/266 | 9.3 | 5.0% | coding (613/1716 nt) | ureC | Urease subunit alpha |
| ? | USA300TCH1516_ALE | 2406995 = | 144 (1.250) | coding (660/1716 nt) | ureC | Urease subunit alpha | |||||
| * | ? | USA300TCH1516_ALE | = 1999809 | NA (NA) | 7 (0.060) | 3/268 | 9.3 | NA | intergenic (‑1537/+1798) | USA300TCH1516_01882/USA300TCH1516_01883 | tRNA‑Val/tRNA‑Ala |
| ? | USA300TCH1516_ALE | = 2177978 | NA (NA) | intergenic (+1740/+3555) | ilvA/USA300TCH1516_02069 | L‑threonine dehydratase biosynthetic IlvA/tRNA‑Gly | |||||