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 | 72.4% | 139.2 / 67.1 | 87 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 602,466 | 0 | G | T | 28.6% | 45.2 / 11.3 | 28 | intergenic (+56/‑104) | hchA/araB | Molecular chaperone Hsp31 and glyoxalase 3/Ribulokinase |
| * | USA300TCH1516_ALE | 2,124,528 | 0 | A | G | 26.6% | 127.0 / 24.3 | 64 | D219G (GAC→GGC) ‡ | lexA_2 | LexA repressor |
| * | USA300TCH1516_ALE | 2,124,529 | 0 | C | A | 26.6% | 151.0 / 18.8 | 64 | D219E (GAC→GAA) ‡ | lexA_2 | LexA repressor |
| * | USA300TCH1516_ALE | 129,708 | 1 | . | T | 25.0% | 33.4 / 12.0 | 16 | intergenic (‑121/+300) | spa/sarS | Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS |
| * | USA300TCH1516_ALE | 2,124,513 | 0 | T | G | 22.4% | 149.5 / 18.4 | 68 | L214R (CTA→CGA) | lexA_2 | LexA repressor |
| * | USA300TCH1516_ALE | 2,124,517 | 0 | T | C | 22.4% | 161.4 / 19.8 | 68 | N215N (AAT→AAC) | lexA_2 | LexA repressor |
| * | USA300TCH1516_ALE | 2,124,527 | 0 | G | C | 21.9% | 165.7 / 23.8 | 64 | D219H (GAC→CAC) ‡ | lexA_2 | LexA repressor |
| * | USA300TCH1516_ALE | 2,124,523 | 0 | T | C | 20.9% | 152.1 / 19.2 | 68 | D217D (GAT→GAC) | lexA_2 | LexA repressor |
| * | USA300TCH1516_ALE | 2,124,503 | 0 | C | T | 20.0% | 184.8 / 25.7 | 80 | L211L (CTA→TTA) | lexA_2 | LexA repressor |
| Marginal new junction evidence (lowest skew 10 of 69 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP000731 | 4294 = | 3 (1.100) | 14 (0.040) | 9/282 | 0.1 | 2.1% | intergenic (+259/‑206) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2073 = | 1294 (1.730) | intergenic (+306/+20) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | = 1610 | 1 (0.370) | 14 (0.040) | 10/278 | 0.1 | 4.1% | intergenic (+395/‑461) | repA/USA300HOU_pUSA300HOUMR0003 | replication protein A/hypothetical protein |
| ? | NC_012417 | = 1047 | 651 (0.880) | coding (148/192 nt) | USA300HOU_RS15665 | hypothetical protein | |||||
| * | ? | CP000731 | = 4381 | 3 (1.100) | 5 (0.010) | 5/284 | 0.2 | 0.97% | intergenic (+346/‑119) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | = 1975 | 1016 (1.350) | intergenic (+208/+118) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | CP000731 | 4339 = | 4 (1.460) | 12 (0.030) | 6/286 | 0.2 | 1.9% | intergenic (+304/‑161) | USA300HOU_pUSA300HOUMR0006/cadR | hypothetical protein/cadmium binding protein |
| ? | NC_012417 | 2021 = | 1229 (1.620) | intergenic (+254/+72) | USA300HOU_RS14895/USA300HOU_RS14900 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 2687481 | 120 (1.220) | 6 (0.070) | 6/276 | 2.0 | 5.0% | intergenic (+35/+34) | clpL/USA300HOU_RS13835 | ATP‑dependent Clp protease ATP‑binding subunit ClpL/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2687499 | 117 (1.290) | intergenic (+53/+16) | clpL/USA300HOU_RS13835 | ATP‑dependent Clp protease ATP‑binding subunit ClpL/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 2508448 | 112 (1.140) | 5 (0.060) | 5/276 | 2.1 | 4.4% | intergenic (+36/+71) | USA300TCH1516_02393/narT | Acid shock protein/putative nitrate transporter NarT |
| ? | USA300TCH1516_ALE | = 2508474 | 115 (1.270) | intergenic (+62/+45) | USA300TCH1516_02393/narT | Acid shock protein/putative nitrate transporter NarT | |||||
| * | ? | USA300TCH1516_ALE | = 588673 | 206 (2.100) | 5 (0.050) | 5/282 | 2.2 | 2.5% | coding (2577/3552 nt) | rpoB | DNA‑directed RNA polymerase subunit beta |
| ? | USA300TCH1516_ALE | = 588680 | 199 (2.140) | coding (2584/3552 nt) | rpoB | DNA‑directed RNA polymerase subunit beta | |||||
| * | ? | USA300TCH1516_ALE | 82395 = | 204 (2.080) | 10 (0.100) | 5/290 | 2.2 | 4.9% | coding (500/957 nt) | nikB_1 | Nickel transport system permease protein NikB |
| ? | USA300TCH1516_ALE | 82432 = | 193 (2.020) | coding (537/957 nt) | nikB_1 | Nickel transport system permease protein NikB | |||||
| * | ? | USA300TCH1516_ALE | 2578084 = | 85 (0.870) | 4 (0.040) | 4/280 | 2.3 | 5.3% | coding (465/600 nt) | USA300HOU_RS13285 | hypothetical protein |
| ? | USA300TCH1516_ALE | 2578167 = | 62 (0.670) | coding (382/600 nt) | USA300HOU_RS13285 | hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 2378283 = | 95 (0.970) | 4 (0.040) | 4/282 | 2.3 | 4.2% | intergenic (+142/+277) | glcU_2/USA300HOU_RS12220 | putative glucose uptake protein GlcU/hypothetical protein |
| ? | USA300TCH1516_ALE | 2378322 = | 92 (0.990) | intergenic (+181/+238) | glcU_2/USA300HOU_RS12220 | putative glucose uptake protein GlcU/hypothetical protein | |||||