mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Marginal read alignment evidence (highest frequency 20 of 34 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,054,894 | 0 | G | T | 43.8% | 74.9 / 43.9 | 89 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,054,888 | 0 | A | C | 38.6% | 127.1 / 22.9 | 91 | V186G (GTA→GGA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 58,065 | 0 | C | A | 38.2% | 143.8 / 22.4 | 102 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,054,886 | 0 | G | T | 36.3% | 124.0 / 33.5 | 91 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,334,966 | 0 | A | C | 34.8% | 167.3 / 44.8 | 132 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 1,097,118 | 0 | C | A | 34.4% | 22.9 / 14.2 | 32 | intergenic (+289/+447) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 2,477,265 | 0 | A | C | 32.9% | 136.0 / 31.4 | 85 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 847,955 | 0 | G | A | 32.8% | 165.4 / 60.8 | 134 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,916,117 | 0 | G | T | 32.1% | 144.8 / 10.2 | 82 | S420Y (TCC→TAC) | atpD | ATP synthase F1 complex subunit beta |
| * | NC_000913 | 1,001,094 | 0 | G | T | 32.0% | 199.4 / 10.0 | 122 | E627* (GAG→TAG) | elfC | putative fimbrial usher protein ElfC |
| * | NC_000913 | 3,911,533 | 0 | C | A | 31.3% | 248.5 / 13.6 | 131 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,097,158 | 0 | C | T | 31.2% | 29.3 / 16.0 | 32 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 1,922,815 | 0 | C | A | 30.3% | 135.4 / 15.4 | 99 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 4,296,191 | 0 | A | C | 29.7% | 32.4 / 17.8 | 38 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,434,642 | 0 | G | A | 29.7% | 301.5 / 154.1 | 175 | intergenic (‑236/+543) | ynaM/uspF | protein YnaM/universal stress protein F |
| * | NC_000913 | 1,286,831 | 0 | T | A | 28.8% | 76.9 / 44.7 | 59 | A41A (GCT→GCA) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 4,360,965 | 0 | C | A | 28.4% | 345.4 / 21.2 | 162 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,990,480 | 0 | C | A | 28.4% | 265.7 / 12.3 | 155 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 3,841,663 | 0 | G | A | 28.4% | 112.0 / 22.2 | 67 | A26V (GCG→GTG) | nepI | purine ribonucleoside exporter |
| * | NC_000913 | 442,025 | 0 | C | A | 27.9% | 118.8 / 10.4 | 68 | L159L (CTC→CTA) | thiI | tRNA uridine 4‑sulfurtransferase |
| Marginal new junction evidence (lowest skew 10 of 66 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 34 (0.340) | 31/598 | 2.1 | 16.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3653447 = | 167 (1.690) | pseudogene (212/478 nt) | yhiS | putative uncharacterized protein YhiS | |||||
| * | ? | NC_000913 | = 1469240 | NA (NA) | 33 (0.340) | 23/596 | 3.1 | 33.0% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1621961 | 67 (0.680) | coding (630/1188 nt) | ydeE | dipeptide exporter | |||||
| * | ? | NC_000913 | = 377429 | 47 (0.480) | 28 (0.320) | 19/524 | 3.2 | 39.1% | intergenic (+118/+106) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB |
| ? | NC_000913 | 377530 = | 46 (0.530) | intergenic (+219/+5) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 3186096 = | NA (NA) | 24 (0.240) | 21/598 | 3.5 | 16.1% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 4344206 = | 125 (1.270) | coding (838/1422 nt) | melB | melibiose:H(+)/Na(+)/Li(+) symporter | |||||
| * | ? | NC_000913 | 1621957 = | 68 (0.690) | 22 (0.220) | 21/598 | 3.5 | 24.4% | coding (626/1188 nt) | ydeE | dipeptide exporter |
| ? | NC_000913 | = 1651548 | NA (NA) | noncoding (706/706 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 42544 = | 72 (0.730) | 23 (0.230) | 21/598 | 3.5 | 24.2% | coding (142/771 nt) | fixA | putative electron transfer flavoprotein FixA |
| ? | NC_000913 | = 275149 | NA (NA) | noncoding (1/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 2070271 | NA (NA) | 22 (0.220) | 19/598 | 3.8 | 15.2% | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 2470126 | 123 (1.250) | coding (996/1332 nt) | yfdI | serotype‑specific glucosyl transferase YfdI | |||||
| * | ? | NC_000913 | 2068941 = | NA (NA) | 23 (0.230) | 19/598 | 3.8 | 15.0% | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | 2470122 = | 130 (1.320) | coding (992/1332 nt) | yfdI | serotype‑specific glucosyl transferase YfdI | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 20 (0.200) | 18/596 | 4.0 | 19.1% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2619893 | 85 (0.860) | coding (268/1290 nt) | uraA | uracil:H(+) symporter UraA | |||||
| * | ? | NC_000913 | = 1818157 | 94 (0.950) | 20 (0.210) | 17/588 | 4.2 | 17.7% | coding (344/1353 nt) | chbF | monoacetylchitobiose‑6‑phosphate hydrolase |
| ? | NC_000913 | 1818238 = | 94 (0.970) | coding (263/1353 nt) | chbF | monoacetylchitobiose‑6‑phosphate hydrolase | |||||