mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 483 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP009974 | 3,105,419 | 0 | G | A | 74.8% | 708.2 / 211.2 | 349 | intergenic (+140/+135) | RPPX_13820/mscL | ferredoxin‑NADP reductase/large‑conductance mechanosensitive channel |
| * | CP009974 | 4,132,231 | 0 | A | C | 74.0% | 440.3 / 163.5 | 238 | intergenic (+147/+82) | RPPX_18375/RPPX_18380 | membrane protein/phosphonoacetaldehyde hydrolase |
| * | CP009974 | 3,756,386 | 0 | T | C | 72.8% | 877.2 / inf | 553 | intergenic (+268/+372) | RPPX_16775/RPPX_16780 | hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| * | CP009974 | 1,155,634 | 0 | T | C | 72.8% | 602.4 / 246.8 | 366 | G778G (GGT→GGC) | RPPX_05115 | hypothetical protein |
| * | CP009974 | 1,277,620 | 0 | G | C | 72.6% | 443.3 / 189.7 | 307 | intergenic (+89/+149) | RPPX_05635/RPPX_05640 | aldehyde dehydrogenase/mechanosensitive ion channel protein MscS |
| * | CP009974 | 3,837,713 | 0 | C | . | 72.1% | 16.2 / 58.6 | 43 | intergenic (+264/‑287) | RPPX_17095/RPPX_17100 | proteophosphoglycan precursor/cupin |
| * | CP009974 | 3,105,408 | 0 | A | G | 71.7% | 647.8 / 261.9 | 352 | intergenic (+129/+146) | RPPX_13820/mscL | ferredoxin‑NADP reductase/large‑conductance mechanosensitive channel |
| * | CP009974 | 5,598,967 | 0 | C | T | 70.8% | 510.1 / 274.3 | 358 | P231P (CCC→CCT) | RPPX_24920 | hypothetical protein |
| * | CP009974 | 1,896,184 | 0 | A | G | 70.6% | 2348.1 / inf | 3354 | intergenic (‑3962/‑4635) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 3,771,883 | 0 | A | . | 69.9% | 326.3 / 281.3 | 174 | noncoding (76/76 nt) | RPPX_16845 | tRNA‑Glu |
| * | CP009974 | 3,847,581 | 0 | T | C | 69.9% | 163.9 / 182.3 | 229 | intergenic (+94/‑246) | RPPX_17150/RPPX_17155 | tRNA‑dihydrouridine synthase C/heat‑shock protein |
| * | CP009974 | 542,115 | 0 | C | T | 69.8% | 40.2 / 28.9 | 43 | intergenic (‑376/+153) | argD/RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| * | CP009974 | 542,116 | 0 | A | G | 69.8% | 39.7 / 26.0 | 43 | intergenic (‑377/+152) | argD/RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| * | CP009974 | 1,895,734 | 0 | C | G | 69.5% | 569.1 / 284.3 | 302 | intergenic (‑3512/‑5085) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 1,897,471 | 0 | G | C | 69.3% | 3696.9 / inf | 4645 | intergenic (‑5249/‑3348) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 3,837,717 | 0 | G | . | 68.9% | 30.5 / 74.5 | 46 | intergenic (+268/‑283) | RPPX_17095/RPPX_17100 | proteophosphoglycan precursor/cupin |
| * | CP009974 | 5,105,300 | 0 | A | G | 68.8% | ‑4.0 / 22.4 | 32 | D184D (GAT→GAC) | RPPX_22650 | benzene 1,2‑dioxygenase |
| * | CP009974 | 1,897,351 | 0 | C | T | 68.1% | 2784.4 / inf | 1828 | intergenic (‑5129/‑3468) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 1,897,591 | 0 | T | C | 68.0% | 4093.6 / inf | 4604 | intergenic (‑5369/‑3228) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 1,897,124 | 0 | C | G | 67.7% | 41.5 / 63.2 | 65 | intergenic (‑4902/‑3695) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 716 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009974 | 1895750 = | 305 (1.120) | 436 (1.780) +GCCGGTCAGCACGTC |
171/270 | 0.0 | 17.6% | intergenic (‑3528/‑5069) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | 1897573 = | 4220 (15.500) | intergenic (‑5351/‑3246) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 1897055 = | 23 (0.080) | 184 (0.830) +28 bp |
98/244 | 2.7 | 9.7% | intergenic (‑4833/‑3764) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | 1897574 = | 4194 (15.400) | intergenic (‑5352/‑3245) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 2287857 = | 95 (0.350) | 122 (0.670) | 75/200 | 3.2 | 76.2% | intergenic (‑437/+256) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB |
| ? | CP009974 | 2288067 = | 13 (0.070) | intergenic (‑647/+46) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB | |||||
| * | ? | CP009974 | = 1896675 | 0 (0.000) | 168 (0.740) +25 bp |
95/250 | 3.3 | 100% | intergenic (‑4453/‑4144) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | 1897988 = | NA (NA) | intergenic (‑5766/‑2831) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 1897988 = | NA (NA) | 174 (0.770) +25 bp |
94/250 | 3.4 | 78.3% | intergenic (‑5766/‑2831) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | = 1898637 | 58 (0.210) | intergenic (‑6415/‑2182) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | = 1511356 | NA (NA) | 155 (0.570) | 115/300 | 3.4 | 41.4% | noncoding (2595/2595 nt) | ISS12 | repeat region |
| ? | CP009974 | 1538760 = | 219 (0.800) | intergenic (‑152/+12) | RPPX_06815/RPPX_06820 | bacterioferritin/catalase | |||||
| * | ? | CP009974 | 1277572 = | 276 (1.010) | 160 (0.680) | 96/258 | 3.6 | 39.6% | intergenic (+41/+197) | RPPX_05635/RPPX_05640 | aldehyde dehydrogenase/mechanosensitive ion channel protein MscS |
| ? | CP009974 | = 1277722 | 251 (1.070) | intergenic (+191/+47) | RPPX_05635/RPPX_05640 | aldehyde dehydrogenase/mechanosensitive ion channel protein MscS | |||||
| * | ? | CP009974 | = 2287906 | 101 (0.370) | 112 (0.620) | 72/200 | 3.7 | 73.2% | intergenic (‑486/+207) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB |
| ? | CP009974 | = 2288016 | 15 (0.080) | intergenic (‑596/+97) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB | |||||
| * | ? | CP009974 | 541996 = | NA (NA) | 164 (0.620) +ACGCA |
108/290 | 3.7 | 58.8% | intergenic (‑257/+272) | argD/RPPX_02300 | acetylornithine aminotransferase/AraC family transcriptional regulator |
| ? | CP009974 | 2545982 = | 119 (0.440) | intergenic (+88/‑177) | RPPX_11350/RPPX_11355 | hypothetical protein/urocanate hydratase | |||||
| * | ? | CP009974 | = 1095752 | 273 (1.000) | 117 (0.650) +50 bp |
68/200 | 4.3 | 39.7% | intergenic (+179/+17) | RPPX_04810/RPPX_04815 | flavodoxin/carbon‑nitrogen hydrolase |
| ? | CP009974 | = 4363596 | 261 (0.960) | intergenic (+252/‑63) | RPPX_19410/RPPX_19415 | alkyl hydroperoxide reductase/hypothetical protein | |||||