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 (highest frequency 20 of 220 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | REL606 | 720,466 | 0 | G | C | 55.0% | ‑3.9 / 18.4 | 20 | A23P (GCC→CCC) | phrB | deoxyribodipyrimidine photolyase, FAD‑binding |
| * | REL606 | 720,464 | 0 | C | G | 51.8% | 5.1 / 41.8 | 27 | A22G (GCC→GGC) | phrB | deoxyribodipyrimidine photolyase, FAD‑binding |
| * | REL606 | 1,118,209 | 0 | G | T | 44.7% | ‑1.3 / 42.9 | 38 | intergenic (‑444/‑311) | csgD/csgB | DNA‑binding transcriptional activator in two‑component regulatory system/curlin nucleator protein, minor subunit in curli complex |
| * | REL606 | 4,392,556 | 0 | C | T | 44.2% | 126.3 / 116.5 | 154 | L43L (CTA→TTA) | aidB | isovaleryl CoA dehydrogenase |
| * | REL606 | 2,735,608 | 0 | G | C | 42.3% | 20.4 / 13.8 | 26 | A409P (GCC→CCC) | ascF | fused cellobiose/arbutin/salicin‑specific PTS enzymes: IIB component/IC component |
| * | REL606 | 2,376,348 | 0 | T | G | 41.7% | 238.7 / 45.6 | 156 | T63P (ACC→CCC) | folC | bifunctional folylpolyglutamate synthase/ dihydrofolate synthase |
| * | REL606 | 2,515,909 | 0 | A | C | 40.5% | 122.3 / 22.4 | 74 | V260G (GTG→GGG) | ypfI | predicted hydrolase |
| * | REL606 | 4,180,249 | 0 | T | G | 40.2% | 180.4 / 35.5 | 107 | G24G (GGT→GGG) | yjaH | hypothetical protein |
| * | REL606 | 1,485,450 | 0 | A | G | 40.0% | 296.5 / 167.8 | 210 | G193G (GGA→GGG) | ydcV | predicted spermidine/putrescine transporter subunit |
| * | REL606 | 2,320,038 | 0 | A | C | 38.6% | 344.3 / 41.6 | 163 | V5G (GTC→GGC) | pmrD | polymyxin resistance protein B |
| * | REL606 | 1,854,401 | 0 | A | C | 38.5% | 152.3 / 40.0 | 104 | K88N (AAA→AAC) | yeaO | hypothetical protein |
| * | REL606 | 433 | 0 | T | G | 37.1% | 110.7 / 28.7 | 70 | V33G (GTG→GGG) | thrA | bifunctional aspartokinase I/homeserine dehydrogenase I |
| * | REL606 | 2,437,406 | 0 | G | T | 37.1% | 66.7 / 16.2 | 35 | D435E (GAC→GAA) | ypdD | fused predicted PTS enzymes: Hpr component/enzyme I component/enzyme IIA component |
| * | REL606 | 414,056 | 0 | T | G | 36.2% | 253.1 / 54.7 | 138 | T345P (ACC→CCC) | yajR | predicted transporter |
| * | REL606 | 4,032,450 | 0 | T | G | 36.1% | 184.2 / 51.6 | 108 | T363P (ACC→CCC) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL: response regulator/sigma54 interaction protein |
| * | REL606 | 4,474,971 | 0 | T | G | 35.5% | 373.4 / 29.4 | 166 | N261T (AAC→ACC) | idnT | L‑idonate and D‑gluconate transporter |
| * | REL606 | 3,774,914 | 0 | C | G | 35.4% | 303.0 / 124.9 | 164 | A20P (GCC→CCC) | yicJ | predicted transporter |
| * | REL606 | 239,163 | 0 | T | G | 34.3% | 387.5 / 111.5 | 198 | V58G (GTG→GGG) | dnaQ | DNA polymerase III subunit epsilon |
| * | REL606 | 406,958 | 0 | T | G | 34.0% | 335.9 / 56.6 | 156 | T548P (ACC→CCC) | dxs | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| * | REL606 | 254,043 | 0 | T | G | 34.0% | 84.9 / 17.5 | 53 | pseudogene (588/1710 nt) | fhiA | b0229; flagellar system protein |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | REL606 | 2802968 = | 225 (1.020) | 3 (0.020) | 3/132 | 20.3 | 1.6% | coding (961/1302 nt) | rumA | 23S rRNA (uracil‑5‑)‑methyltransferase |
| ? | REL606 | = 4211851 | 171 (0.890) | coding (314/1350 nt) | lysC | aspartate kinase III | |||||
| * | ? | REL606 | = 2039707 | 91 (0.410) | 4 (0.020) | 4/144 | 20.3 | 3.7% | coding (422/438 nt) | vioB | VioB, involved in dTDP‑N‑acetylviosamine synthesis |
| ? | REL606 | = 2040225 | 121 (0.570) | intergenic (‑97/+46) | vioB/vioA | VioB, involved in dTDP‑N‑acetylviosamine synthesis/VioA, involved in dTDP‑N‑acetylviosamine synthesis | |||||
| * | ? | REL606 | = 2680757 | 221 (1.010) | 3 (0.010) | 3/138 | 20.8 | 1.8% | coding (283/897 nt) | ECB_02511 | ParB family protein |
| ? | REL606 | = 2681225 | 116 (0.570) | coding (751/897 nt) | ECB_02511 | ParB family protein | |||||
| * | ? | REL606 | = 1556432 | 247 (1.120) | 3 (0.010) | 3/138 | 20.8 | 1.3% | coding (44/1683 nt) | ydeN | hypothetical protein |
| ? | REL606 | = 1556925 | 221 (1.100) | coding (714/762 nt) | ydeO | predicted DNA‑binding transcriptional acfivator | |||||
| * | ? | REL606 | = 2040186 | 126 (0.570) | 3 (0.010) | 3/140 | 20.9 | 2.8% | intergenic (‑58/+85) | vioB/vioA | VioB, involved in dTDP‑N‑acetylviosamine synthesis/VioA, involved in dTDP‑N‑acetylviosamine synthesis |
| ? | REL606 | = 2040466 | 94 (0.460) | coding (918/1113 nt) | vioA | VioA, involved in dTDP‑N‑acetylviosamine synthesis | |||||
| * | ? | REL606 | = 3737261 | 180 (0.820) | 3 (0.010) | 3/142 | 21.0 | 2.1% | coding (566/1254 nt) | waaL | Lipid A‑core, surface polymer ligase |
| ? | REL606 | = 3737695 | 112 (0.540) | coding (132/1254 nt) | waaL | Lipid A‑core, surface polymer ligase | |||||
| * | ? | REL606 | 2583007 = | 344 (1.570) | 73 (0.350) | 3/144 | 21.2 | 18.2% | intergenic (‑177/+275) | iscR/yfhQ | DNA‑binding transcriptional repressor/predicted methyltransferase |
| ? | REL606 | = 2583279 | 327 (1.550) | intergenic (‑449/+3) | iscR/yfhQ | DNA‑binding transcriptional repressor/predicted methyltransferase | |||||
| * | ? | REL606 | = 1530048 | 271 (1.230) | 3 (0.010) | 3/144 | 21.2 | 1.0% | coding (171/216 nt) | bdm | biofilm‑dependent modulation protein |
| ? | REL606 | 3790384 = | 311 (1.480) | coding (2144/3498 nt) | ECB_03531 | hypothetical protein | |||||
| * | ? | REL606 | = 2589475 | 199 (0.910) | 3 (0.010) | 3/148 | 21.4 | 1.5% | coding (121/891 nt) | hcaR | DNA‑binding transcriptional activator of 3‑phenylpropionic acid catabolism |
| ? | REL606 | 4277048 = | 190 (0.880) | coding (1141/2148 nt) | fdhF | formate dehydrogenase‑H, selenopolypeptide subunit | |||||
| * | ? | REL606 | = 2948453 | 198 (0.900) | 3 (0.010) | 3/150 | 21.6 | 1.3% | coding (1853/2145 nt) | sbm | methylmalonyl‑CoA mutase |
| ? | REL606 | 3953252 = | 262 (1.190) | coding (270/2547 nt) | cyaA | adenylate cyclase | |||||