mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 29 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_002947 | 699,722 | 0 | A | G | 54.3% | 11.6 / 82.9 | 70 | intergenic (+115/‑129) | PP_t06/PP_23SD | tRNA‑Ala/23S ribosomal RNA |
| * | NC_002947 | 1,327,121 | 0 | C | T | 53.8% | 12.6 / 99.7 | 78 | intergenic (+97/‑196) | PP_16SE/PP_23SE | 16S ribosomal RNA/23S ribosomal RNA |
| * | NC_002947 | 1,780,096 | 0 | T | G | 53.3% | 1.4 / 10.9 | 15 | intergenic (+55/+51) | PP_1587/dapC | NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase |
| * | NC_002947 | 195,634 | 0 | C | T | 51.1% | ‑2.5 / 55.9 | 45 | T380T (ACC→ACT) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 4,348,705 | 0 | A | G | 43.8% | 24.1 / 55.6 | 48 | intergenic (‑70/+404) | PP_3820/galU | group II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase |
| * | NC_002947 | 195,559 | 0 | C | A | 41.4% | 26.2 / 26.7 | 29 | T355T (ACC→ACA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,485,162 | 0 | T | C | 37.5% | 8.7 / 10.8 | 21 | intergenic (+68/‑79) | purH/purD | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase/phosphoribosylamine‑‑glycine ligase |
| * | NC_002947 | 5,988,905 | 0 | T | C | 37.0% | 19.7 / 22.9 | 27 | intergenic (+199/‑347) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,911 | 0 | A | . | 37.0% | 52.1 / 35.1 | 27 | intergenic (+205/‑341) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,809 | 0 | G | A | 32.4% | 41.2 / 24.1 | 35 | intergenic (+103/‑443) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,894 | 0 | C | T | 27.6% | 41.0 / 16.9 | 29 | intergenic (+188/‑358) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,895 | 0 | A | G | 27.6% | 39.0 / 17.0 | 29 | intergenic (+189/‑357) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 197,590 | 0 | T | C | 27.1% | 90.6 / 38.3 | 59 | D1032D (GAT→GAC) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,850 | 0 | C | T | 26.7% | 47.0 / 16.3 | 30 | intergenic (+144/‑402) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,837 | 0 | C | G | 25.8% | 54.3 / 16.8 | 31 | intergenic (+131/‑415) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,844 | 0 | C | G | 25.8% | 59.0 / 14.9 | 31 | intergenic (+138/‑408) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,848 | 0 | C | T | 25.8% | 50.5 / 15.4 | 31 | intergenic (+142/‑404) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 197,572 | 0 | G | A | 25.0% | 110.7 / 35.1 | 66 | K1026K (AAG→AAA) | PP_0168 | putative surface adhesion protein |
| * | NC_002947 | 5,988,889 | 0 | C | A | 24.0% | 50.3 / 10.2 | 25 | intergenic (+183/‑363) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| * | NC_002947 | 5,988,819 | 0 | T | C | 23.3% | 49.0 / 12.0 | 31 | intergenic (+113/‑433) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| Marginal new junction evidence (lowest skew 10 of 156 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_002947 | 4140139 = | 39 (1.170) | 5 (0.160) | 5/272 | 3.0 | 11.3% | intergenic (+31/‑234) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein |
| ? | NC_002947 | 4140178 = | 42 (1.340) | intergenic (+70/‑195) | PP_3644/PP_5609 | monooxygenase subunit/hypothetical protein | |||||
| * | ? | NC_002947 | 6175197 = | 37 (1.110) | 6 (0.190) | 5/274 | 3.1 | 14.8% | intergenic (‑21/+23) | atpC/atpD | ATP synthase subunit epsilon/ATP synthase subunit beta |
| ? | NC_002947 | 6175215 = | 34 (1.070) | intergenic (‑39/+5) | atpC/atpD | ATP synthase subunit epsilon/ATP synthase subunit beta | |||||
| * | ? | NC_002947 | 4536751 = | NA (NA) | 8 (0.250) | 5/278 | 3.1 | 28.3% | coding (86/1533 nt) | PP_4025 | transposase |
| ? | NC_002947 | = 4627474 | 21 (0.630) | coding (30/1533 nt) | PP_4091 | transposase | |||||
| * | ? | NC_002947 | = 4378781 | 30 (0.900) | 6 (0.190) | 5/278 | 3.1 | 17.4% | intergenic (‑69/‑20) | PP_3854/PP_5639 | lysozyme/hypothetical protein |
| ? | NC_002947 | = 4378793 | 28 (0.870) | intergenic (‑81/‑8) | PP_3854/PP_5639 | lysozyme/hypothetical protein | |||||
| * | ? | NC_002947 | = 746418 | NA (NA) | 8 (0.250) | 5/278 | 3.1 | NA | coding (81/1533 nt) | PP_0637 | transposase |
| ? | NC_002947 | = 746464 | NA (NA) | coding (35/1533 nt) | PP_0637 | transposase | |||||
| * | ? | NC_002947 | = 4609857 | 34 (1.020) | 4 (0.130) | 4/268 | 3.3 | 11.5% | coding (344/876 nt) | PP_4081 | type IV/VI secretion system protein |
| ? | NC_002947 | = 4609877 | 30 (0.970) | coding (364/876 nt) | PP_4081 | type IV/VI secretion system protein | |||||
| * | ? | NC_002947 | = 2837075 | 2 (0.060) | 6 (0.200) | 4/264 | 3.3 | 71.3% | intergenic (‑27/+156) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase |
| ? | NC_002947 | 2837172 = | 3 (0.100) | intergenic (‑124/+59) | sad‑I/PP_2489 | NAD+‑dependent succinate semialdehyde dehydrogenase/xenobiotic reductase | |||||
| * | ? | NC_002947 | = 5988757 | 21 (0.630) | 4 (0.130) | 4/272 | 3.4 | 19.1% | intergenic (+51/‑495) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA |
| ? | NC_002947 | 5988979 = | 14 (0.450) | intergenic (+273/‑273) | kefB‑III/PP_mr64 | glutathione‑regulated potassium/H+ antiporter/C4 ncRNA | |||||
| * | ? | NC_002947 | = 5949465 | 42 (1.260) | 4 (0.130) | 4/272 | 3.4 | 9.1% | coding (182/1503 nt) | ppx | exopolyphosphatase |
| ? | NC_002947 | = 5949479 | 40 (1.270) | coding (196/1503 nt) | ppx | exopolyphosphatase | |||||
| * | ? | NC_002947 | 5727157 = | 27 (0.810) | 4 (0.130) | 4/274 | 3.4 | 13.0% | coding (1481/1680 nt) | opgG | glucans biosynthesis protein G |
| ? | NC_002947 | 5727201 = | 28 (0.880) | coding (1437/1680 nt) | opgG | glucans biosynthesis protein G | |||||