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 506 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 | 74.9% | 851.0 / 252.2 | 409 | intergenic (+140/+135) | RPPX_13820/mscL | ferredoxin‑NADP reductase/large‑conductance mechanosensitive channel |
| * | CP009974 | 3,756,661 | 0 | T | C | 74.4% | 639.5 / 284.9 | 411 | intergenic (+543/+97) | RPPX_16775/RPPX_16780 | hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| * | CP009974 | 904,275 | 0 | C | A | 73.2% | 321.9 / 163.4 | 183 | intergenic (‑435/‑339) | RPPX_03940/RPPX_03945 | phosphoribosylformylglycinamidine synthase/murein transglycosylase |
| * | CP009974 | 769,806 | 0 | T | C | 72.8% | 155.6 / 128.7 | 195 | intergenic (‑228/+240) | RPPX_03350/RPPX_03355 | acetolactate synthase/5S ribosomal RNA |
| * | CP009974 | 1,158,290 | 0 | C | G | 72.6% | 736.0 / inf | 413 | intergenic (+1813/‑13470) | RPPX_05120/RPPX_05130 | hypothetical protein/channel protein TolC |
| * | CP009974 | 1,158,292 | 0 | T | C | 72.4% | 655.5 / 288.0 | 417 | intergenic (+1815/‑13468) | RPPX_05120/RPPX_05130 | hypothetical protein/channel protein TolC |
| * | CP009974 | 3,105,408 | 0 | A | G | 71.9% | 774.3 / 304.1 | 417 | intergenic (+129/+146) | RPPX_13820/mscL | ferredoxin‑NADP reductase/large‑conductance mechanosensitive channel |
| * | CP009974 | 769,805 | 0 | T | C | 71.5% | 144.1 / 125.5 | 195 | intergenic (‑227/+241) | RPPX_03350/RPPX_03355 | acetolactate synthase/5S ribosomal RNA |
| * | CP009974 | 3,847,581 | 0 | T | C | 71.2% | 250.4 / 189.4 | 272 | intergenic (+94/‑246) | RPPX_17150/RPPX_17155 | tRNA‑dihydrouridine synthase C/heat‑shock protein |
| * | CP009974 | 1,897,591 | 0 | T | C | 71.0% | 4694.0 / inf | 4258 | intergenic (‑5369/‑3228) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 3,756,612 | 0 | G | A | 70.0% | 626.6 / inf | 463 | intergenic (+494/+146) | RPPX_16775/RPPX_16780 | hypothetical protein/phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| * | CP009974 | 5,105,300 | 0 | A | G | 70.0% | 1.6 / 34.1 | 50 | D184D (GAT→GAC) | RPPX_22650 | benzene 1,2‑dioxygenase |
| * | CP009974 | 1,897,471 | 0 | G | C | 69.9% | 3609.3 / inf | 4428 | intergenic (‑5249/‑3348) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| * | CP009974 | 833,303 | 0 | A | G | 69.8% | 406.1 / 269.9 | 310 | Y154C (TAC→TGC) | metG | methionine‑‑tRNA ligase |
| * | CP009974 | 3,771,883 | 0 | A | . | 69.5% | 345.2 / inf | 204 | noncoding (76/76 nt) | RPPX_16845 | tRNA‑Glu |
| * | CP009974 | 2,790,883 | 1 | . | G | 69.3% | 309.4 / 164.3 | 124 | intergenic (‑90/+575) | RPPX_12370/RPPX_12380 | hypothetical protein/nicotinate phosphoribosyltransferase |
| * | CP009974 | 5,598,979 | 0 | C | T | 69.3% | 587.4 / inf | 418 | G235G (GGC→GGT) | RPPX_24920 | hypothetical protein |
| * | CP009974 | 4,147,351 | 0 | C | G | 68.8% | 12.6 / 44.0 | 48 | intergenic (+603/‑418) | RPPX_18425/RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR |
| * | CP009974 | 3,847,650 | 0 | A | G | 68.2% | 434.5 / 272.3 | 316 | intergenic (+163/‑177) | RPPX_17150/RPPX_17155 | tRNA‑dihydrouridine synthase C/heat‑shock protein |
| * | CP009974 | 1,896,121 | 0 | C | T | 67.8% | 2272.5 / inf | 4004 | intergenic (‑3899/‑4698) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 690 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | CP009974 | 1895750 = | 266 (0.810) | 417 (1.410) +GCCGGTCAGCACGTC |
161/270 | 0.5 | 17.1% | intergenic (‑3528/‑5069) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | 1897573 = | 4227 (12.850) | intergenic (‑5351/‑3246) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | = 2769966 | NA (NA) | 213 (0.650) | 141/298 | 3.2 | 60.5% | noncoding (1/2595 nt) | ISS12 | repeat region |
| ? | CP009974 | = 2770803 | 140 (0.430) | coding (604/1275 nt) | RPPX_12310 | seryl‑tRNA synthetase | |||||
| * | ? | CP009974 | 418657 = | 2 (0.010) | 126 (0.540) +AAGAAGC |
97/214 | 3.4 | 92.6% | intergenic (‑236/+415) | RPPX_01715/RPPX_01720 | hypothetical protein/lipoprotein |
| ? | CP009974 | = 4147133 | 20 (0.080) | intergenic (+385/‑636) | RPPX_18425/RPPX_18430 | enoyl‑CoA hydratase/conjugal transfer protein TraR | |||||
| * | ? | CP009974 | = 2287906 | 105 (0.320) | 157 (0.720) | 86/200 | 4.1 | 75.9% | intergenic (‑486/+207) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB |
| ? | CP009974 | = 2288016 | 30 (0.140) | intergenic (‑596/+97) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB | |||||
| * | ? | CP009974 | = 3756977 | 295 (0.900) | 163 (0.650) +35 bp |
97/230 | 4.6 | 42.8% | coding (1128/1347 nt) | RPPX_16780 | phospho‑2‑dehydro‑3‑deoxyheptonate aldolase |
| ? | CP009974 | 4030905 = | 275 (0.840) | intergenic (+47/‑737) | RPPX_17905/RPPX_17915 | 23S rRNA methyltransferase/sulfurtransferase | |||||
| * | ? | CP009974 | 2767372 = | NA (NA) | 183 (0.560) | 125/300 | 5.3 | 56.8% | noncoding (2595/2595 nt) | ISS12 | repeat region |
| ? | CP009974 | 2770795 = | 139 (0.420) | coding (596/1275 nt) | RPPX_12310 | seryl‑tRNA synthetase | |||||
| * | ? | CP009974 | 1896077 = | 3209 (9.750) | 607 (2.070) +CGCGAAAGTGGATGTC |
109/268 | 5.5 | 28.7% | intergenic (‑3855/‑4742) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein |
| ? | CP009974 | = 1898007 | 172 (0.520) | intergenic (‑5785/‑2812) | RPPX_08470/RPPX_08480 | tryptophan synthase subunit beta/hypothetical protein | |||||
| * | ? | CP009974 | 3763892 = | 116 (0.350) | 107 (0.540) | 70/182 | 5.6 | 75.3% | intergenic (‑225/+284) | RPPX_16805/RPPX_16810 | protease HtpX/aminotransferase |
| ? | CP009974 | 3764115 = | 0 (0.000) | intergenic (‑448/+61) | RPPX_16805/RPPX_16810 | protease HtpX/aminotransferase | |||||
| * | ? | CP009974 | 2287857 = | 132 (0.400) | 121 (0.550) | 78/200 | 5.6 | 68.0% | intergenic (‑437/+256) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB |
| ? | CP009974 | 2288067 = | 26 (0.120) | intergenic (‑647/+46) | RPPX_10255/RPPX_10260 | hypothetical protein/potassium transporter KefB | |||||
| * | ? | CP009974 | 1277582 = | 311 (0.950) | 224 (0.690) +C |
122/298 | 5.6 | 42.9% | intergenic (+51/+187) | RPPX_05635/RPPX_05640 | aldehyde dehydrogenase/mechanosensitive ion channel protein MscS |
| ? | CP009974 | 4286484 = | 290 (0.880) | intergenic (+340/+304) | RPPX_19070/RPPX_19075 | LacI family transcriptional regulator/hypothetical protein | |||||