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 | 2,343,438 | 0 | C | T | 40.2% | 124.5 / 206.3 | 174 | intergenic (+114/+250) | USA300HOU_RS11955/aldC_1 | 65 kDa membrane protein/Alpha‑acetolactate decarboxylase |
| * | USA300TCH1516_ALE | 111,512 | 0 | A | G | 29.5% | 332.5 / 184.8 | 220 | S194S (TCA→TCG) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 111,516 | 0 | C | A | 27.7% | 443.2 / 196.3 | 217 | Q196K (CAA→AAA) | USA300HOU_RS00520 | putative lipoprotein |
| * | USA300TCH1516_ALE | 217,036 | 0 | T | A | 26.3% | 411.2 / 165.8 | 209 | intergenic (‑230/+23) | rocD2_1/brnQ_1 | Ornithine aminotransferase 2/Branched‑chain amino acid transport system 2 carrier protein |
| * | USA300TCH1516_ALE | 937,158 | 0 | T | A | 23.9% | 372.2 / 120.2 | 180 | intergenic (+65/‑66) | USA300HOU_RS04665/pepA_1 | NADH dehydrogenase‑like protein/Cytosol aminopeptidase |
| * | USA300TCH1516_ALE | 2,372,413 | 0 | C | G | 23.5% | 509.5 / 153.1 | 223 | intergenic (+164/+28) | USA300TCH1516_02262/pbuG | hypothetical protein/Guanine/hypoxanthine permease PbuG |
| * | USA300TCH1516_ALE | 2,744,213 | 0 | T | A | 22.8% | 503.7 / 139.1 | 206 | intergenic (+150/+43) | fda/mqo2 | Fructose‑bisphosphate aldolase class 1/putative malate:quinone oxidoreductase 2 |
| * | USA300TCH1516_ALE | 512,643 | 0 | A | G | 22.5% | 379.5 / 109.5 | 191 | intergenic (+711/‑6052) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| * | USA300TCH1516_ALE | 293,940 | 0 | C | T | 21.4% | 334.1 / 84.3 | 159 | intergenic (+57/‑471) | gatD/tarI' | Galactitol‑1‑phosphate 5‑dehydrogenase/Ribitol‑5‑phosphate cytidylyltransferase 2 |
| * | USA300TCH1516_ALE | 2,372,419 | 0 | C | T | 21.3% | 492.3 / 123.6 | 231 | intergenic (+170/+22) | USA300TCH1516_02262/pbuG | hypothetical protein/Guanine/hypoxanthine permease PbuG |
| * | USA300TCH1516_ALE | 2,744,205 | 0 | A | G | 21.0% | 444.8 / 105.4 | 200 | intergenic (+142/+51) | fda/mqo2 | Fructose‑bisphosphate aldolase class 1/putative malate:quinone oxidoreductase 2 |
| * | USA300TCH1516_ALE | 2,744,221 | 0 | C | T | 20.4% | 488.1 / 105.5 | 211 | intergenic (+158/+35) | fda/mqo2 | Fructose‑bisphosphate aldolase class 1/putative malate:quinone oxidoreductase 2 |
| * | USA300TCH1516_ALE | 9,716 | 0 | T | C | 20.1% | 382.4 / 95.2 | 184 | intergenic (+21/+66) | gyrA/nnrD | DNA gyrase subunit A/ADP‑dependent (S)‑NAD(P)H‑hydrate dehydratase |
| * | USA300TCH1516_ALE | 1,931,599 | 0 | A | T | 20.1% | 599.1 / 148.8 | 249 | L1217I (TTA→ATA) | USA300HOU_RS09605 | hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 676 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | USA300TCH1516_ALE | 1910672 = | 192 (1.090) | 224 (1.470) | 30/156 | 7.9 | 57.4% | intergenic (+205/‑350) | crcB_2/USA300TCH1516_01771 | Putative fluoride ion transporter CrcB/hypothetical protein |
| ? | USA300TCH1516_ALE | 1910712 = | NA (NA) | intergenic (+245/‑310) | crcB_2/USA300TCH1516_01771 | Putative fluoride ion transporter CrcB/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | 932460 = | 183 (1.040) | 21 (0.140) | 18/156 | 12.3 | 11.3% | intergenic (+6/+257) | USA300HOU_RS04635/nfuA | hypothetical protein/Fe/S biogenesis protein NfuA |
| ? | USA300TCH1516_ALE | 932506 = | 172 (1.130) | intergenic (+52/+211) | USA300HOU_RS04635/nfuA | hypothetical protein/Fe/S biogenesis protein NfuA | |||||
| * | ? | USA300TCH1516_ALE | = 514606 | NA (NA) | 72 (0.440) | 20/166 | 12.3 | NA | intergenic (+2674/‑4089) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase |
| ? | USA300TCH1516_ALE | = 514610 | NA (NA) | intergenic (+2678/‑4085) | recR/speA_2 | Recombination protein RecR/Arginine decarboxylase | |||||
| * | ? | USA300TCH1516_ALE | 2661788 = | 196 (1.110) | 26 (0.180) | 16/148 | 12.6 | 14.1% | intergenic (‑181/‑140) | ybiV/yydI | Sugar phosphatase YbiV/putative peptide export ATP‑binding protein YydI |
| ? | USA300TCH1516_ALE | 2661832 = | 157 (1.090) | intergenic (‑225/‑96) | ybiV/yydI | Sugar phosphatase YbiV/putative peptide export ATP‑binding protein YydI | |||||
| * | ? | USA300TCH1516_ALE | = 2090980 | 183 (1.040) | 14 (0.130) +35 bp |
9/110 | 12.7 | 12.0% | intergenic (‑214/+324) | USA300HOU_RS10575/USA300HOU_RS10590 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2265579 | 155 (0.880) | intergenic (+442/+587) | USA300HOU_RS11590/hin_3 | hypothetical protein/DNA‑invertase hin | |||||
| * | ? | USA300TCH1516_ALE | 1662000 = | 183 (1.040) | 28 (0.180) | 17/156 | 12.8 | 15.1% | intergenic (‑87/+68) | USA300HOU_RS08275/rpmG2_2 | 5‑formyltetrahydrofolate cyclo‑ligase/50S ribosomal protein L33 2 |
| ? | USA300TCH1516_ALE | 1662039 = | 157 (1.030) | intergenic (‑126/+29) | USA300HOU_RS08275/rpmG2_2 | 5‑formyltetrahydrofolate cyclo‑ligase/50S ribosomal protein L33 2 | |||||
| * | ? | USA300TCH1516_ALE | 75971 = | 231 (1.310) | 27 (0.190) | 15/148 | 13.0 | 12.8% | intergenic (+29/‑244) | USA300HOU_RS00335/USA300HOU_RS00140 | hypothetical protein/hypothetical protein |
| ? | USA300TCH1516_ALE | 76020 = | 177 (1.230) | intergenic (+78/‑195) | USA300HOU_RS00335/USA300HOU_RS00140 | hypothetical protein/hypothetical protein | |||||
| * | ? | USA300TCH1516_ALE | = 1662011 | 191 (1.090) | 26 (0.170) | 16/156 | 13.2 | 13.8% | intergenic (‑98/+57) | USA300HOU_RS08275/rpmG2_2 | 5‑formyltetrahydrofolate cyclo‑ligase/50S ribosomal protein L33 2 |
| ? | USA300TCH1516_ALE | = 1662026 | 159 (1.040) | intergenic (‑113/+42) | USA300HOU_RS08275/rpmG2_2 | 5‑formyltetrahydrofolate cyclo‑ligase/50S ribosomal protein L33 2 | |||||
| * | ? | USA300TCH1516_ALE | 2696548 = | 162 (0.920) | 29 (0.190) | 16/160 | 13.6 | 16.8% | intergenic (+100/‑140) | USA300HOU_RS13875/copA | hypothetical protein/Copper‑exporting P‑type ATPase A |
| ? | USA300TCH1516_ALE | 2696587 = | 143 (0.920) | intergenic (+139/‑101) | USA300HOU_RS13875/copA | hypothetical protein/Copper‑exporting P‑type ATPase A | |||||
| * | ? | USA300TCH1516_ALE | = 2442821 | 201 (1.140) | 26 (0.180) | 14/148 | 13.6 | 13.7% | intergenic (+18/+40) | glvR/USA300HOU_RS12585 | HTH‑type transcriptional regulator GlvR/hypothetical protein |
| ? | USA300TCH1516_ALE | = 2442838 | 164 (1.140) | intergenic (+35/+23) | glvR/USA300HOU_RS12585 | HTH‑type transcriptional regulator GlvR/hypothetical protein | |||||