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 38 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 | 4,348,812 | 0 | A | G | 49.6% | 31.8 / 170.4 | 115 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947_CJ‑RC | 1,327,121 | 0 | C | T | 47.7% | 74.0 / 178.9 | 133 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 699,722 | 0 | A | G | 44.4% | 41.9 / 139.9 | 108 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947_CJ‑RC | 1,296,567 | 0 | G | T | 38.5% | 31.3 / 12.2 | 28 | intergenic (‑320/‑246) | nhaA‑I/PP_1133 | Na(+)/H(+) antiporter NhaA/transposase |
| * | NC_002947_CJ‑RC | 2,863,829 | 0 | T | G | 36.6% | 38.2 / 10.0 | 41 | S297A (TCG→GCG) | gllR | HTH‑type transcriptional regulator GalR |
| * | NC_002947_CJ‑RC | 1,013,249 | 0 | T | G | 36.4% | 9.8 / 10.2 | 11 | intergenic (+77/+54) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 195,634 | 0 | C | T | 32.5% | 91.9 / 59.2 | 81 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 337,836 | 0 | C | T | 31.8% | 26.2 / 13.2 | 22 | intergenic (‑86/+43) | PP_0279/PP_0280 | hypothetical protein/amino acid ABC transporter permease |
| * | NC_002947_CJ‑RC | 5,743,285 | 0 | A | T | 31.6% | 15.3 / 12.8 | 19 | intergenic (+35/+36) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 5,743,286 | 0 | A | T | 31.6% | 12.9 / 13.2 | 19 | intergenic (+36/+35) | hutF/PP_5037 | formiminoglutamate deiminase/lipocalin family lipoprotein |
| * | NC_002947_CJ‑RC | 1,013,241 | 0 | G | C | 31.2% | 24.0 / 12.8 | 16 | intergenic (+69/+62) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 1,013,242 | 0 | G | C | 31.2% | 24.2 / 12.8 | 16 | intergenic (+70/+61) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 196,390 | 0 | T | C | 31.2% | 91.4 / 61.9 | 78 | D632D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947_CJ‑RC | 4,648,341 | 0 | A | C | 30.8% | 59.7 / 10.0 | 39 | V302G (GTG→GGG) | PP_4112 | sulfate transporter |
| * | NC_002947_CJ‑RC | 1,013,234 | 0 | C | A | 29.4% | 31.2 / 11.4 | 17 | intergenic (+62/+69) | prfC/potF‑I | peptide chain release factor 3/putrescine‑binding protein |
| * | NC_002947_CJ‑RC | 418,289 | 0 | C | A | 29.0% | 154.2 / 10.7 | 69 | F24L (TTC→TTA) | PP_0345 | heptose kinase WapP |
| * | NC_002947_CJ‑RC | 1,544,494 | 0 | C | G | 27.8% | 32.2 / 12.4 | 18 | intergenic (+53/+61) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,499 | 0 | C | G | 27.8% | 32.7 / 10.3 | 18 | intergenic (+58/+56) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 1,544,501 | 0 | G | C | 27.8% | 28.7 / 12.1 | 18 | intergenic (+60/+54) | mdfA/ampG | multidrug MFS transporter/muropeptide permease AmpG |
| * | NC_002947_CJ‑RC | 196,351 | 0 | C | G | 26.8% | 164.6 / 80.1 | 97 | T619T (ACC→ACG) | PP_0168 | putative surface adhesion protein |
| Marginal new junction evidence (lowest skew 10 of 32 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947_CJ‑RC | = 1780066 | 21 (0.310) | 16 (0.250) | 16/278 | 4.6 | 49.2% | intergenic (+25/+81) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| ? | NC_002947_CJ‑RC | 1780129 = | 13 (0.200) | intergenic (+88/+18) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 2472115 | 27 (0.400) | 10 (0.160) | 10/278 | 6.6 | 20.1% | intergenic (+19/+130) | PP_2166/PP_2167 | anti‑anti‑sigma factor/PhoD‑like phosphatase |
| ? | NC_002947_CJ‑RC | 2472313 = | 54 (0.840) | coding (1783/1851 nt) | PP_2167 | PhoD‑like phosphatase | |||||
| * | ? | NC_002947_CJ‑RC | = 4898101 | 14 (0.210) | 7 (0.120) | 7/250 | 7.2 | 37.9% | intergenic (+31/‑177) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein |
| ? | NC_002947_CJ‑RC | = 4898148 | 11 (0.190) | intergenic (+78/‑130) | PP_4304/sbp‑I | VIC family cation transporter/sulfate ABC transporter substrate‑binding protein | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 12 (0.180) | 11 (0.170) | 9/286 | 7.2 | 41.7% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1419636 | 19 (0.290) | intergenic (‑125/+11) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein | |||||
| * | ? | NC_002947_CJ‑RC | = 5991586 | 40 (0.590) | 8 (0.120) | 8/276 | 7.4 | 17.1% | intergenic (+65/‑481) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947_CJ‑RC | 5991778 = | 40 (0.620) | intergenic (+257/‑289) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947_CJ‑RC | = 5558423 | 1 (0.010) | 10 (0.150) +GCC |
8/286 | 7.6 | 91.1% | intergenic (‑84/+87) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer |
| ? | NC_002947_CJ‑RC | 5558424 = | 1 (0.010) | intergenic (‑85/+86) | PP_4887/PP_4888 | hypothetical protein/methyl‑accepting chemotaxis transducer | |||||
| * | ? | NC_002947_CJ‑RC | = 2957080 | 26 (0.380) | 7 (0.110) | 7/282 | 8.0 | 20.9% | intergenic (+35/‑161) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein |
| ? | NC_002947_CJ‑RC | 2957165 = | 28 (0.430) | intergenic (+120/‑76) | PP_2588/PP_2589 | class III aminotransferase/aldehyde dehydrogenase family protein | |||||
| * | ? | NC_002947_CJ‑RC | 1967145 = | 23 (0.340) | 4 (0.080) | 4/226 | 8.2 | 18.7% | intergenic (+15/+104) | PP_1762/yciK | hypothetical protein/putative oxidoreductase |
| ? | NC_002947_CJ‑RC | 1967241 = | 17 (0.320) | intergenic (+111/+8) | PP_1762/yciK | hypothetical protein/putative oxidoreductase | |||||
| * | ? | NC_002947_CJ‑RC | = 1419549 | 11 (0.160) | 7 (0.100) +CT |
7/288 | 8.2 | 32.1% | intergenic (‑38/+98) | PP_1242/PP_1244 | hypothetical protein/hypothetical protein |
| ? | NC_002947_CJ‑RC | = 1780139 | 19 (0.280) | intergenic (+98/+8) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase | |||||
| * | ? | NC_002947_CJ‑RC | = 1487035 | 17 (0.250) | 4 (0.070) | 4/232 | 8.4 | 23.9% | intergenic (+51/+79) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS |
| ? | NC_002947_CJ‑RC | = 1487065 | 12 (0.220) | intergenic (+81/+49) | yhdZ/degS | amino acid ABC transporter ATP‑binding protein/serine endoprotease DegS | |||||