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 247 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 4,160,437 | 0 | A | C | 72.2% | 31.8 / 10.7 | 58 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947 | 1,130,191 | 0 | C | A | 62.2% | ‑2.6 / 35.2 | 46 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947 | 4,160,432 | 0 | T | G | 61.7% | 25.8 / 14.9 | 58 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947 | 5,511,866 | 0 | A | C | 61.4% | 10.3 / 32.5 | 78 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947 | 5,511,875 | 0 | T | G | 58.0% | 15.4 / 26.9 | 77 | L35R (CTG→CGG) | urtB | urea ABC transporter permease |
| * | NC_002947 | 3,011,559 | 0 | A | C | 57.9% | ‑4.8 / 21.0 | 38 | intergenic (‑500/‑1168) | PP_2628/PP_2631 | ABC transporter ATP‑binding protein/cellulose biosynthesis protein BcsF/YhjT |
| * | NC_002947 | 3,617,420 | 0 | G | T | 57.1% | ‑4.2 / 10.3 | 22 | intergenic (+18/‑211) | PP_3186/codB | transcriptional regulator/cytosine transporter |
| * | NC_002947 | 3,449,251 | 0 | A | C | 55.4% | 14.6 / 18.7 | 60 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947 | 1,440,040 | 0 | A | C | 55.0% | 5.6 / 20.7 | 20 | intergenic (‑364/‑295) | yveA/PP_1260 | aspartate‑proton symporter/transposase |
| * | NC_002947 | 3,011,545 | 0 | C | G | 54.0% | ‑2.3 / 18.9 | 37 | intergenic (‑486/‑1182) | PP_2628/PP_2631 | ABC transporter ATP‑binding protein/cellulose biosynthesis protein BcsF/YhjT |
| * | NC_002947 | 1,148,793 | 0 | A | C | 53.3% | ‑5.8 / 17.1 | 31 | V153G (GTC→GGC) | PP_1007 | transmembrane sensor |
| * | NC_002947 | 3,325,568 | 0 | T | G | 53.3% | 0.1 / 11.9 | 33 | D97A (GAC→GCC) | PP_2923 | hypothetical protein |
| * | NC_002947 | 5,461,530 | 0 | T | G | 50.9% | 3.7 / 21.3 | 62 | intergenic (+18/‑22) | PP_4795/holA | lipoprotein/DNA polymerase III subunit delta |
| * | NC_002947 | 1,148,800 | 0 | T | G | 50.0% | ‑5.3 / 13.6 | 33 | T151P (ACG→CCG) | PP_1007 | transmembrane sensor |
| * | NC_002947 | 2,951,766 | 0 | T | G | 50.0% | ‑3.8 / 10.3 | 28 | intergenic (+66/+47) | PP_2583/oguA | acetyltransferase/8‑oxoguanine deaminase |
| * | NC_002947 | 2,865,794 | 0 | T | G | 49.1% | ‑4.7 / 24.5 | 56 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947 | 699,725 | 0 | A | G | 49.0% | 4.8 / 73.1 | 49 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 3,449,271 | 0 | A | C | 47.5% | 38.6 / 23.9 | 59 | A24A (GCA→GCC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947 | 1,544,446 | 0 | T | G | 47.2% | 28.1 / 11.3 | 36 | V403G (GTG→GGG) | mdfA | multidrug MFS transporter |
| * | NC_002947 | 5,511,878 | 0 | T | G | 46.5% | 15.1 / 32.8 | 77 | L36R (CTC→CGC) | urtB | urea ABC transporter permease |
| Marginal new junction evidence (lowest skew 10 of 40 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 652785 | 121 (0.990) | 30 (0.290) | 16/224 | 3.2 | 36.2% | coding (1961/1962 nt) | ctpL | methyl‑accepting chemotaxis protein CtpL |
| ? | NC_002947 | = 4810126 | 3 (0.030) | intergenic (‑268/‑287) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 | |||||
| * | ? | NC_002947 | = 4810146 | 3 (0.020) | 27 (0.240) | 15/240 | 3.7 | 24.6% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | 5990743 = | 163 (1.460) | intergenic (+59/‑487) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | 699535 = | 43 (0.350) | 15 (0.180) +42 bp |
10/180 | 3.8 | 35.3% | noncoding (1/76 nt) | PP_t06 | tRNA‑Ala |
| ? | NC_002947 | = 2552338 | 38 (0.310) | noncoding (77/77 nt) | PP_t35 | tRNA‑Ile | |||||
| * | ? | NC_002947 | = 2552338 | 38 (0.310) | 10 (0.120) +42 bp |
9/180 | 4.1 | 22.9% | noncoding (77/77 nt) | PP_t35 | tRNA‑Ile |
| ? | NC_002947 | = 5312869 | 61 (0.500) | noncoding (1/76 nt) | PP_t51 | tRNA‑Ala | |||||
| * | ? | NC_002947 | = 2552338 | 38 (0.310) | 11 (0.130) +42 bp |
9/180 | 4.1 | 29.1% | noncoding (77/77 nt) | PP_t35 | tRNA‑Ile |
| ? | NC_002947 | 2552363 = | 41 (0.330) | noncoding (1/76 nt) | PP_t36 | tRNA‑Ala | |||||
| * | ? | NC_002947 | = 699510 | 23 (0.190) | 10 (0.120) +42 bp |
9/180 | 4.1 | 25.9% | noncoding (77/77 nt) | PP_t05 | tRNA‑Ile |
| ? | NC_002947 | = 5312869 | 61 (0.500) | noncoding (1/76 nt) | PP_t51 | tRNA‑Ala | |||||
| * | ? | NC_002947 | = 699510 | 23 (0.190) | 11 (0.130) +42 bp |
9/180 | 4.1 | 33.6% | noncoding (77/77 nt) | PP_t05 | tRNA‑Ile |
| ? | NC_002947 | 2552363 = | 41 (0.330) | noncoding (1/76 nt) | PP_t36 | tRNA‑Ala | |||||
| * | ? | NC_002947 | = 699510 | 23 (0.190) | 11 (0.130) +42 bp |
9/180 | 4.1 | 32.9% | noncoding (77/77 nt) | PP_t05 | tRNA‑Ile |
| ? | NC_002947 | 699535 = | 43 (0.350) | noncoding (1/76 nt) | PP_t06 | tRNA‑Ala | |||||
| * | ? | NC_002947 | = 4810146 | 3 (0.020) | 18 (0.170) | 11/224 | 4.4 | 23.4% | intergenic (‑288/‑267) | PP_4234/dsbD‑II | bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2 |
| ? | NC_002947 | = 5990927 | 115 (1.100) | intergenic (+243/‑303) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5990735 | 172 (1.400) | 13 (0.110) | 11/248 | 4.9 | 8.1% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5990957 = | 135 (1.170) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||