mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 26 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947_CJ‑RC | 697,114 | 0 | T | G | 62.5% | ‑4.5 / 11.6 | 20 | intergenic (+41/‑710) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,100 | 0 | T | G | 61.9% | ‑6.7 / 14.0 | 21 | intergenic (+27/‑724) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 61.1% | ‑2.3 / 11.9 | 21 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 58.0% | ‑3.9 / 146.6 | 119 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 52.8% | ‑1.9 / 16.1 | 37 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 697,128 | 0 | T | G | 52.6% | 8.1 / 22.7 | 21 | intergenic (+55/‑696) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,921,550 | 0 | T | A | 50.0% | ‑2.9 / 24.1 | 20 | intergenic (+25/+36) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 49.5% | 32.2 / 166.6 | 114 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 48.8% | 12.4 / 113.1 | 80 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,921,549 | 0 | T | A | 45.0% | ‑4.9 / 21.4 | 20 | intergenic (+24/+37) | PP_1720/PP_1721 | alcohol dehydrogenase/phosphoserine phosphatase |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 43.2% | 19.1 / 16.8 | 45 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 117,248 | 0 | C | A | 32.7% | 85.3 / 13.5 | 52 | intergenic (+28/+66) | PP_0111/metQ | electron transport protein SCO1/SenC/methionine ABC transporter substrate‑binding protein |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 28.8% | 59.9 / 12.0 | 52 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,754,561 | 0 | A | C | 26.7% | 49.8 / 10.5 | 32 | intergenic (‑184/‑287) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 2,282,770 | 0 | T | G | 26.5% | 46.4 / 21.1 | 34 | intergenic (‑162/+67) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| * | NC_002947_CJ‑RC | 2,813,122 | 0 | A | C | 25.4% | 104.6 / 11.1 | 55 | T103P (ACC→CCC) | pheS | phenylalanine‑‑tRNA ligase subunit alpha |
| * | NC_002947_CJ‑RC | 418,289 | 0 | C | A | 25.0% | 207.2 / 12.5 | 80 | F24L (TTC→TTA) | PP_0345 | heptose kinase WapP |
| * | NC_002947_CJ‑RC | 4,044,569 | 0 | A | C | 24.6% | 116.1 / 18.3 | 61 | V380G (GTG→GGG) | PP_3566 | MFS transporter |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 23.5% | 88.1 / 24.6 | 35 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 2,282,779 | 0 | C | A | 23.3% | 57.8 / 12.7 | 31 | intergenic (‑171/+58) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| Marginal new junction evidence (lowest skew 10 of 28 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 14 (0.200) +CGGG |
14/282 | 6.1 | 100% | intergenic (‑133/+71) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein |
| ? | NC_002947_CJ‑RC | 5684231 = | 0 (0.000) | intergenic (‑134/+70) | PP_4986/PP_4987 | hemolysin III family channel protein/putative Chemotaxis protein | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 1 (0.010) | 16 (0.250) | 11/266 | 6.8 | 40.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 46 (0.710) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 42 (0.600) | 13 (0.190) | 12/280 | 6.8 | 23.3% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 45 (0.660) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 12 (0.170) +GCC |
10/284 | 7.7 | 86.0% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 2 (0.030) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 5384135 | 42 (0.600) | 6 (0.110) | 6/220 | 7.8 | 17.4% | intergenic (+52/+81) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR |
| ? | NC_002947_CJ‑RC | = 5384163 | 25 (0.470) | intergenic (+80/+53) | smpB/pdhR | SsrA‑binding protein/DNA‑binding transcriptional regulator LldR | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 1 (0.010) | 9 (0.150) | 5/250 | 9.3 | 29.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 42 (0.690) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 52 (0.740) | 5 (0.080) | 5/274 | 10.0 | 9.6% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 45 (0.680) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1970739 | 22 (0.310) | 5 (0.080) | 4/250 | 10.0 | 20.4% | intergenic (+33/‑233) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region |
| ? | NC_002947_CJ‑RC | = 1970801 | 20 (0.330) | intergenic (+95/‑171) | mtnA/PP_mr25 | methylthioribose‑1‑phosphate isomerase/gyrA regulatory region | |||||
| * | ? | NC_002947_CJ‑RC | 1419549 = | 30 (0.430) | 3 (0.050) | 3/232 | 10.2 | 14.0% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | 1419637 = | 13 (0.230) | intergenic (‑126/+10) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 2034168 | 70 (0.990) | 3 (0.050) +24 bp |
3/242 | 10.5 | 7.7% | coding (1649/1665 nt) | pgi‑I | glucose 6‑phosphate isomerase |
| ? | NC_002947_CJ‑RC | = 5346222 | 16 (0.230) | intergenic (+94/‑84) | pgi‑II/acsA‑II | glucose 6‑phosphate isomerase/acetyl‑CoA synthetase | |||||