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 33 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 | 63.9% | 69.1 / 43.3 | 37 | 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 | 62.9% | 71.3 / 41.7 | 37 | intergenic (+46/+96) | aroP‑I/PP_0928 | aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein |
| * | NC_002947_CJ‑RC | 5,923,026 | 0 | A | C | 52.4% | 7.6 / 21.9 | 22 | K266T (AAG→ACG) | PP_5190 | type II secretion system protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 50.5% | ‑2.4 / 155.3 | 109 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 49.6% | 59.9 / 198.4 | 139 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 648,232 | 0 | A | C | 48.3% | 11.1 / 10.6 | 29 | intergenic (+1/+90) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 48.0% | 30.1 / 128.0 | 103 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 43.5% | 76.3 / 144.0 | 116 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 648,237 | 0 | T | G | 40.5% | 20.2 / 14.5 | 37 | intergenic (+6/+85) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 40.5% | 22.7 / 14.2 | 46 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 5,512,711 | 0 | A | C | 39.5% | 31.4 / 12.8 | 45 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 195,559 | 0 | C | A | 31.3% | 103.3 / 51.3 | 67 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 6,135,378 | 0 | A | T | 31.2% | 56.7 / 11.3 | 49 | H430Q (CAT→CAA) | copA‑II | copper resistance protein A |
| * | NC_002947_CJ‑RC | 245,412 | 0 | A | G | 31.1% | 68.6 / 14.5 | 45 | S121P (TCC→CCC) | PP_0195 | hypothetical protein |
| * | NC_002947_CJ‑RC | 1,731,228 | 0 | T | G | 30.3% | 52.6 / 11.4 | 33 | intergenic (‑141/+50) | dapE/PP_1526 | succinyl‑diaminopimelate desuccinylase/beta‑(1‑3)‑glucosyl transferase |
| * | NC_002947_CJ‑RC | 5,905,980 | 0 | A | C | 30.0% | 22.4 / 10.6 | 21 | intergenic (‑129/‑139) | PP_5175/PP_5176 | HlyD family secretion protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 4,433,580 | 0 | G | C | 29.5% | 111.1 / 19.5 | 61 | intergenic (‑29/‑89) | PP_5648/PP_3928 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 196,879 | 0 | G | A | 29.2% | 28.2 / 13.2 | 24 | V795V (GTG→GTA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 6,135,416 | 0 | T | C | 28.9% | 51.2 / 13.2 | 48 | T418A (ACC→GCC) | copA‑II | copper resistance protein A |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 27.2% | 113.1 / 56.7 | 83 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 2 (0.030) | 14 (0.190) +GCC |
12/284 | 7.0 | 87.7% | 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 | = 4809882 | 2 (0.030) | 12 (0.180) | 10/266 | 7.3 | 33.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 46 (0.680) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 41 (0.550) | 11 (0.150) | 11/280 | 7.3 | 21.2% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 42 (0.590) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 499202 | 13 (0.180) | 12 (0.170) | 10/272 | 7.5 | 52.0% | intergenic (+46/‑250) | uhpA/PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein |
| ? | NC_002947_CJ‑RC | = 499271 | 10 (0.140) | intergenic (+115/‑181) | uhpA/PP_0411 | two‑component system response regulator UhpA/polyamine ABC transporter ATP‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 49 (0.660) | 8 (0.110) | 8/274 | 8.4 | 13.9% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 53 (0.760) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 1311718 | 18 (0.240) | 8 (0.110) | 8/280 | 8.6 | 24.1% | intergenic (‑186/+92) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA |
| ? | NC_002947_CJ‑RC | 1311803 = | 33 (0.460) | intergenic (‑271/+7) | PP_1144/rapA | membrane protein/RNA polymerase‑associated protein RapA | |||||
| * | ? | NC_002947_CJ‑RC | = 5684230 | 0 (0.000) | 9 (0.120) +CGGG |
8/282 | 8.7 | 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 | = 2472115 | 32 (0.430) | 6 (0.090) | 6/276 | 9.6 | 13.4% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 47 (0.670) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | 4586141 = | 18 (0.240) | 4 (0.060) | 4/246 | 10.0 | 25.6% | intergenic (+117/+98) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase |
| ? | NC_002947_CJ‑RC | 4586212 = | 8 (0.130) | intergenic (+188/+27) | PP_4061/PP_4063 | hypothetical protein/long‑chain fatty acid‑‑CoA ligase | |||||
| * | ? | NC_002947_CJ‑RC | 1487006 = | 38 (0.510) | 3 (0.050) | 3/230 | 10.2 | 13.3% | intergenic (+22/+108) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | 1487096 = | 9 (0.150) | intergenic (+112/+18) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||