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 24 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 | 170,833 | 0 | A | G | 56.2% | ‑2.4 / 14.2 | 16 | intergenic (+14/‑556) | PP_0159/PP_16SA | family III CoA‑transferase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 5,558,407 | 0 | G | T | 56.2% | 10.4 / 20.4 | 16 | intergenic (‑68/+103) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| * | NC_002947_CJ‑RC | 4,158,466 | 0 | T | G | 53.8% | ‑6.4 / 13.4 | 27 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,338,608 | 0 | G | T | 53.6% | 10.6 / 27.3 | 29 | intergenic (+121/+21) | PP_3812/PP_5632 | lipase/allo‑isoleucine metabolism protein |
| * | NC_002947_CJ‑RC | 4,158,471 | 0 | A | C | 46.9% | 9.0 / 12.4 | 32 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947_CJ‑RC | 4,348,812 | 0 | A | G | 45.7% | 67.3 / 177.5 | 129 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 3,447,291 | 0 | T | G | 44.4% | 26.0 / 14.9 | 39 | A19A (GCT→GCG) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 43.9% | 61.4 / 170.0 | 132 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 43.7% | 115.5 / 191.4 | 158 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 6,000,018 | 0 | C | G | 42.4% | 39.6 / 10.2 | 33 | intergenic (‑172/+28) | PP_5252/PP_5253 | hypothetical protein/arylesterase |
| * | NC_002947_CJ‑RC | 5,512,720 | 0 | T | G | 38.1% | 29.7 / 11.6 | 44 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,754,529 | 0 | C | A | 37.5% | 58.0 / 11.5 | 32 | intergenic (‑152/‑319) | thiI/glnA | tRNA sulfurtransferase/glutamine synthetase |
| * | NC_002947_CJ‑RC | 441,326 | 0 | G | . | 37.0% | 98.9 / 62.7 | 48 | coding (207/1173 nt) | bioF | 8‑amino‑7‑oxononanoate synthase |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 37.0% | 33.6 / 10.4 | 46 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 697,094 | 0 | A | G | 35.7% | 25.0 / 12.7 | 32 | intergenic (+21/‑730) | mmsA‑I/PP_16SD | methylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA |
| * | NC_002947_CJ‑RC | 3,447,286 | 0 | A | C | 32.4% | 22.1 / 10.0 | 39 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947_CJ‑RC | 1,130,199 | 0 | G | T | 32.0% | 88.6 / 10.3 | 50 | intergenic (‑254/+50) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947_CJ‑RC | 5,211,931 | 0 | A | G | 30.6% | 52.8 / 10.9 | 38 | intergenic (‑94/+84) | rnd/PP_4592 | ribonuclease D/metal dependent hydrolase |
| * | NC_002947_CJ‑RC | 5,181,205 | 0 | C | G | 25.9% | 130.0 / 12.4 | 54 | intergenic (‑179/+13) | PP_4556/PP_4557 | hypothetical protein/hypothetical protein |
| * | NC_002947_CJ‑RC | 197,632 | 0 | T | C | 24.7% | 161.9 / 55.8 | 89 | T1046T (ACT→ACC) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 39 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 652782 | 65 (0.830) | 17 (0.250) | 15/252 | 5.6 | 37.8% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947_CJ‑RC | = 4809862 | 0 (0.000) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 17 (0.240) | 16/268 | 5.7 | 39.2% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | 5991580 = | 49 (0.690) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 40 (0.510) | 18 (0.240) | 15/282 | 6.4 | 31.4% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 40 (0.530) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 3 (0.040) | 15 (0.200) +GCC |
15/286 | 6.6 | 83.6% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 3 (0.040) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | 4809877 = | 7 (0.090) | 12 (0.200) | 9/222 | 7.0 | 37.3% | intergenic (‑283/‑272) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991750 | 35 (0.590) | intergenic (+229/‑317) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 4809882 | 4 (0.050) | 12 (0.180) | 11/252 | 7.1 | 33.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947_CJ‑RC | = 5991764 | 44 (0.660) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 51 (0.650) | 8 (0.110) | 8/276 | 9.2 | 14.5% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 46 (0.620) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 30 (0.390) | 7 (0.090) | 7/278 | 9.8 | 11.9% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 75 (1.010) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 2282748 | 18 (0.230) | 7 (0.090) | 7/280 | 9.8 | 24.4% | intergenic (‑140/+89) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein |
| ? | NC_002947_CJ‑RC | 2282815 = | 26 (0.350) | intergenic (‑207/+22) | PP_2010/PP_2011 | cytochrome b561/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 3968879 | NA (NA) | 6 (0.080) | 6/278 | 10.3 | 11.6% | coding (1007/1179 nt) | PP_3498 | transposase |
| ? | NC_002947_CJ‑RC | 3968942 = | 48 (0.620) | coding (1070/1179 nt) | PP_3498 | transposase | |||||