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 | 53.3% | 20.5 / 104.1 | 75 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 2,845,689 | 0 | G | A | 31.6% | 23.0 / 11.6 | 19 | A77A (GCC→GCT) | USA300HOU_RS14575 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,845,707 | 0 | A | G | 30.0% | 22.6 / 12.1 | 20 | F71F (TTT→TTC) | USA300HOU_RS14575 | hypothetical protein |
| * | USA300TCH1516_ALE | 872,473 | 0 | T | C | 28.6% | 48.6 / 24.0 | 35 | N57N (AAT→AAC) | USA300HOU_RS04265 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,845,722 | 0 | A | G | 28.6% | 24.7 / 13.8 | 21 | H66H (CAT→CAC) | USA300HOU_RS14575 | hypothetical protein |
| * | USA300TCH1516_ALE | 872,520 | 0 | A | G | 27.3% | 30.8 / 10.8 | 22 | E73G (GAG→GGG) | USA300HOU_RS04265 | hypothetical protein |
| * | USA300TCH1516_ALE | 247,381 | 0 | C | A | 26.1% | 46.5 / 11.0 | 23 | I72I (ATC→ATA) | cycB | Cyclodextrin‑binding protein |
| * | USA300TCH1516_ALE | 2,845,668 | 0 | G | A | 26.1% | 35.8 / 10.9 | 23 | C84C (TGC→TGT) | USA300HOU_RS14575 | hypothetical protein |
| * | USA300TCH1516_ALE | 1,646,129 | 0 | G | A | 25.7% | 65.6 / 15.3 | 35 | A175V (GCA→GTA) | ypdF | Aminopeptidase YpdF |
| * | USA300TCH1516_ALE | 2,845,632 | 0 | T | G | 25.0% | 31.6 / 16.4 | 24 | G96G (GGA→GGC) | USA300HOU_RS14575 | hypothetical protein |
| * | USA300TCH1516_ALE | 2,845,665 | 0 | C | T | 25.0% | 40.0 / 12.1 | 24 | S85S (TCG→TCA) | USA300HOU_RS14575 | hypothetical protein |
| * | USA300TCH1516_ALE | 795,642 | 0 | A | G | 22.9% | 59.7 / 18.6 | 35 | I188V (ATC→GTC) | recQ_1 | ATP‑dependent DNA helicase RecQ |
| * | USA300TCH1516_ALE | 115,823 | 0 | C | T | 21.6% | 74.2 / 15.9 | 37 | intergenic (+90/‑61) | btr/yxeP_1 | HTH‑type transcriptional activator Btr/putative hydrolase YxeP |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 20.6% | 179.0 / 29.3 | 68 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 2,263,657 | 0 | T | C | 20.4% | 98.1 / 23.9 | 49 | N286N (AAT→AAC) | czcD_2 | Cadmium, cobalt and zinc/H(+)‑K(+) antiporter |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 20.3% | 139.0 / 35.3 | 69 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | = 1610 | 101 (0.840) | 4 (0.010) +22 bp |
3/250 | 10.5 | 0.83% | intergenic (+395/‑461) | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| ? | NC_012417 | = 1057 | 1030 (0.950) | coding (138/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | CP000731 | = 4399 | 130 (1.080) | 4 (0.010) | 3/272 | 11.1 | 0.66% | intergenic (+364/‑101) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1963 | 1077 (1.070) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 2352 | 165 (1.370) | 4 (0.010) | 3/272 | 11.1 | 0.65% | intergenic (+132/+36) | USA300HOU_pUSA300HOUMR0003/USA300HOU_pUSA300HOUMR0004 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 1963 | 1077 (1.070) | intergenic (+196/+130) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_012417 | = 1057 | 1030 (0.950) | 4 (0.000) | 4/250 | 52.6 | 0.45% | coding (138/192 nt) | USA300HOU_RS15665 | hypothetical protein |
| ? | NC_012417 | = 1103 | 879 (0.960) | coding (92/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | NC_012417 | = 1974 | 1162 (1.070) | 5 (0.000) | 4/272 | 54.7 | 0.48% | intergenic (+207/+119) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein |
| ? | NC_012417 | = 2041 | 989 (0.990) | intergenic (+274/+52) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||