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 34 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 | 1,070,246 | 2 | . | A | 68.8% | 54.3 / 32.5 | 33 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,070,246 | 1 | . | G | 65.5% | 44.0 / 31.5 | 33 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 57.5% | ‑4.0 / 141.5 | 113 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 170,833 | 0 | A | G | 57.1% | ‑6.0 / 11.5 | 16 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,412,533 | 0 | A | C | 52.1% | 26.6 / 146.7 | 96 | intergenic (+14/‑44) | PP_3896/PP_3897 | Cro/CI family transcriptional regulator/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 51.9% | 15.8 / 178.6 | 132 | 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 | 45.3% | 40.8 / 126.1 | 95 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 4,353,309 | 0 | A | C | 42.9% | 4.5 / 11.7 | 14 | T110P (ACG→CCG) | yrpB | 2‑nitropropane dioxygenase |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 42.5% | 85.7 / 138.0 | 125 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,923,026 | 0 | A | C | 42.5% | 39.9 / 15.0 | 41 | K266T (AAG→ACG) | PP_5190 | type II secretion system protein |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 33.3% | 39.2 / 27.9 | 36 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 32.1% | 55.8 / 10.8 | 62 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 28.6% | 188.7 / 66.2 | 94 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 197,590 | 0 | T | C | 28.5% | 218.8 / 108.4 | 146 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 25.9% | 251.0 / 97.8 | 132 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 25.7% | 165.4 / 67.1 | 101 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 1,438,934 | 0 | C | A | 25.3% | 181.1 / 31.8 | 75 | A246S (GCC→TCC) | yveA | aspartate‑proton symporter |
| * | NC_002947_CJ‑RC | 197,572 | 0 | G | A | 24.8% | 296.9 / 98.5 | 162 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 647,266 | 0 | G | T | 24.6% | 178.4 / 13.1 | 69 | G297C (GGC→TGC) | acoR | acetoin catabolism regulatory protein |
| * | NC_002947_CJ‑RC | 1,751,059 | 0 | A | G | 24.6% | 98.4 / 13.5 | 62 | T140A (ACC→GCC) | PP_1551 | replication protein O |
| Marginal new junction evidence (lowest skew 10 of 47 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 2 (0.020) | 31 (0.390) | 22/264 | 5.0 | 56.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 46 (0.580) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.080) | 16 (0.240) | 13/218 | 6.4 | 35.0% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 54 (0.830) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 50 (0.580) | 16 (0.190) | 14/278 | 8.0 | 24.8% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 49 (0.590) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 50 (0.580) | 11 (0.130) | 11/272 | 9.1 | 15.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 73 (0.890) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 2 (0.020) | 12 (0.160) | 9/248 | 9.2 | 26.5% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 65 (0.870) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | 1499507 = | 11 (0.130) | 10 (0.130) | 9/264 | 9.8 | 23.2% | intergenic (+84/‑80) | trpS/zapE | tryptophan‑‑tRNA ligase/nucleoside triphosphate hydrolase domain‑containing protein |
| ? | NC_002947_CJ‑RC | = 6063320 | 56 (0.710) | intergenic (+141/+40) | PP_5311/PP_5312 | signal transduction protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | 5479905 = | 37 (0.430) | 5 (0.080) | 5/206 | 10.0 | 21.1% | intergenic (+3/+109) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein |
| ? | NC_002947_CJ‑RC | 5480004 = | 11 (0.180) | intergenic (+102/+10) | PP_4813/PP_4814 | PAP2 family protein/DedA family protein/ATP‑dependent protease La domain‑containing protein | |||||
| * | ? | NC_002947_CJ‑RC | = 499202 | 16 (0.190) | 13 (0.160) | 7/270 | 11.1 | 43.3% | intergenic (+46/‑250) | uhpA/PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | = 499271 | 19 (0.230) | intergenic (+115/‑181) | uhpA/PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1967177 | 32 (0.370) | 4 (0.060) | 4/222 | 11.3 | 14.9% | intergenic (+47/+72) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947_CJ‑RC | = 1967207 | 21 (0.320) | intergenic (+77/+42) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | 5762219 = | 35 (0.400) | 4 (0.060) | 4/224 | 11.4 | 15.3% | intergenic (+13/+143) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB |
| ? | NC_002947_CJ‑RC | 5762311 = | 17 (0.250) | intergenic (+105/+51) | trmL/secB | tRNA (cytosine(34)‑2'‑O)‑methyltransferase TrmL/protein‑export protein SecB | |||||