mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 357 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 1,383,252 | 0 | C | G | 68.8% | ‑1.3 / 10.6 | 16 | A19P (GCC→CCC) | PP_1204 | lipoprotein |
| * | NC_002947 | 1,130,191 | 0 | C | A | 64.6% | 7.1 / 47.2 | 79 | intergenic (‑240/+64) | gcvH‑I/PP_0990 | glycine cleavage system protein H/DoxX family protein |
| * | NC_002947 | 648,235 | 0 | A | C | 63.2% | ‑6.3 / 25.6 | 38 | intergenic (+1/+90) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947 | 4,350,671 | 0 | A | G | 63.0% | 85.5 / 220.6 | 209 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 1,383,258 | 0 | A | C | 62.5% | ‑3.3 / 10.4 | 17 | C17G (TGC→GGC) | PP_1204 | lipoprotein |
| * | NC_002947 | 648,240 | 0 | T | G | 62.2% | ‑2.2 / 25.9 | 38 | intergenic (+6/+85) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| * | NC_002947 | 4,160,432 | 0 | T | G | 59.6% | 3.5 / 51.3 | 104 | L159R (CTG→CGG) | PP_3661 | membrane protein |
| * | NC_002947 | 4,444,585 | 0 | A | C | 59.5% | ‑5.7 / 22.2 | 52 | intergenic (‑89/+49) | nicP‑II/nicT | porin‑like protein/metabolite transport protein NicT |
| * | NC_002947 | 4,160,437 | 0 | A | C | 59.0% | 11.8 / 45.2 | 103 | S161R (AGC→CGC) | PP_3661 | membrane protein |
| * | NC_002947 | 5,511,866 | 0 | A | C | 58.5% | 16.6 / 57.7 | 128 | Q32P (CAG→CCG) | urtB | urea ABC transporter permease |
| * | NC_002947 | 5,196,865 | 0 | G | T | 58.1% | ‑1.4 / 17.4 | 34 | intergenic (+37/+16) | PP_4574/PP_4575 | hypothetical protein/urea amidolyase‑like protein |
| * | NC_002947 | 5,922,204 | 0 | A | C | 57.7% | ‑5.3 / 11.3 | 26 | D271A (GAC→GCC) | PP_5190 | type II secretion system protein |
| * | NC_002947 | 3,449,251 | 0 | A | C | 56.6% | 30.1 / 80.7 | 176 | S18R (AGC→CGC) | PP_5556 | bacteriophage lysis protein |
| * | NC_002947 | 2,865,794 | 0 | T | G | 56.3% | 25.4 / 46.7 | 120 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947 | 1,615,720 | 0 | T | A | 55.0% | 7.4 / 16.3 | 21 | K25M (AAG→ATG) | PP_1415 | membrane protein |
| * | NC_002947 | 5,164,503 | 0 | T | C | 53.8% | ‑4.2 / 10.8 | 14 | intergenic (+56/+145) | PP_4544/PP_4545 | hypothetical protein/beta‑ketodecanoyl‑ACP synthase |
| * | NC_002947 | 3,325,568 | 0 | T | G | 53.4% | ‑0.0 / 27.5 | 65 | D97A (GAC→GCC) | PP_2923 | hypothetical protein |
| * | NC_002947 | 5,559,904 | 0 | C | G | 52.9% | ‑0.4 / 11.7 | 17 | intergenic (‑302/+29) | PP_4888/purA | methyl‑accepting chemotaxis transducer/adenylosuccinate synthetase |
| * | NC_002947 | 3,154,248 | 0 | G | C | 52.6% | ‑3.4 / 10.2 | 19 | T146T (ACG→ACC) | PP_2768 | branched‑chain amino acid ABC transporter permease |
| * | NC_002947 | 648,250 | 0 | A | C | 51.5% | ‑2.4 / 18.3 | 34 | intergenic (+16/+75) | acoR/accC | acetoin catabolism regulatory protein/acetyl‑CoA carboxylase biotin carboxylase subunit |
| Marginal new junction evidence (lowest skew 10 of 26 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | = 5990749 | 233 (1.280) | 18 (0.100) | 16/248 | 2.4 | 9.3% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5990941 = | 134 (0.780) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5990735 | 232 (1.270) | 19 (0.110) | 16/248 | 2.4 | 9.6% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5990957 = | 138 (0.800) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 1780108 | 40 (0.220) | 14 (0.080) | 11/250 | 3.0 | 26.0% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947 | 1780171 = | 42 (0.240) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947 | = 1419584 | 24 (0.130) | 26 (0.190) | 8/200 | 3.1 | 43.6% | intergenic (‑67/+70) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947 | = 1419614 | 49 (0.350) | intergenic (‑97/+40) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947 | = 2474080 | 51 (0.280) | 11 (0.060) | 8/250 | 3.5 | 12.3% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947 | 2474278 = | 108 (0.620) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947 | = 5990646 | 260 (1.420) | 7 (0.040) | 7/250 | 3.8 | 3.6% | coding (1750/1788 nt) | kefB‑III | glutathione‑regulated potassium/H+ antiporter |
| ? | NC_002947 | 5990934 = | 128 (0.740) | intergenic (+250/‑296) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 2872669 | 74 (0.410) | 40 (0.220) | 7/258 | 3.8 | 25.9% | intergenic (+11/‑519) | PP_2522/PP_2524 | transposase/HD domain‑containing protein |
| ? | NC_002947 | 4911750 = | 156 (0.870) | intergenic (+176/+303) | PP_4318/PP_4319 | transposase/hypothetical protein | |||||
| * | ? | NC_002947 | = 2872669 | 74 (0.410) | 39 (0.220) | 6/258 | 4.1 | 31.8% | intergenic (+11/‑519) | PP_2522/PP_2524 | transposase/HD domain‑containing protein |
| ? | NC_002947 | 4024607 = | 95 (0.530) | intergenic (‑336/+332) | PP_3547/emrB | NAD(P)‑binding oxidoreductase/multidrug transporter permease | |||||
| * | ? | NC_002947 | = 2416434 | 115 (0.630) | 26 (0.150) | 6/258 | 4.1 | 16.2% | intergenic (+11/‑334) | PP_2114/PP_2115 | transposase/hypothetical protein |
| ? | NC_002947 | 4911750 = | 156 (0.870) | intergenic (+176/+303) | PP_4318/PP_4319 | transposase/hypothetical protein | |||||
| * | ? | NC_002947 | = 2959045 | 105 (0.570) | 5 (0.030) | 5/254 | 4.3 | 4.0% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947 | 2959130 = | 141 (0.800) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||