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 24 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,054,886 | 0 | G | T | 42.9% | 75.1 / 32.7 | 70 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,097,158 | 0 | C | T | 41.7% | 11.6 / 27.8 | 24 | intergenic (+329/+407) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| * | NC_000913 | 3,054,894 | 0 | G | T | 33.3% | 90.5 / 18.6 | 70 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 847,955 | 0 | G | A | 32.6% | 146.6 / 40.9 | 98 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 3,741,871 | 0 | G | T | 31.6% | 160.9 / 15.5 | 98 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 2,990,480 | 0 | C | A | 31.5% | 291.3 / 26.6 | 163 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 1,334,966 | 0 | A | C | 30.3% | 162.8 / 23.4 | 109 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 29.8% | 199.8 / 18.6 | 121 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 58,065 | 0 | C | A | 28.6% | 116.6 / 10.2 | 77 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 2,457,177 | 0 | T | G | 28.4% | 117.8 / 18.2 | 69 | G661G (GGA→GGC) | fadJ | 3‑hydroxyacyl‑CoA dehydrogenase FadJ |
| * | NC_000913 | 782,194 | 0 | T | G | 28.1% | 159.9 / 19.3 | 97 | L37R (CTA→CGA) | nadA | quinolinate synthase |
| * | NC_000913 | 2,815,937 | 0 | G | T | 26.1% | 154.4 / 12.3 | 92 | S168* (TCG→TAG) | gshA | glutamate‑‑cysteine ligase |
| * | NC_000913 | 4,213,310 | 0 | G | T | 25.4% | 218.2 / 14.0 | 110 | G26V (GGA→GTA) | yjaA | stress response protein |
| * | NC_000913 | 3,903,015 | 0 | C | A | 25.0% | 193.4 / 35.9 | 84 | G229G (GGG→GGT) | bglB | 6‑phospho‑beta‑glucosidase B |
| * | NC_000913 | 1,502,772 | 0 | G | A | 24.4% | 140.0 / 20.2 | 78 | A106T (GCG→ACG) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 4,296,268 | 0 | T | C | 24.2% | 57.6 / 10.2 | 33 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 1,502,770 | 0 | T | C | 23.1% | 156.4 / 16.1 | 78 | I105T (ATA→ACA) | ydcL | DUF3313 domain‑containing lipoprotein YdcL |
| * | NC_000913 | 1,922,815 | 0 | C | A | 23.1% | 150.8 / 10.5 | 78 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 4,520,497 | 0 | G | T | 22.8% | 191.3 / 12.4 | 92 | intergenic (‑173/+174) | yjhU/yjhF | putative DNA‑binding transcriptional regulator YjhU/putative transporter YjhF |
| * | NC_000913 | 3,032,307 | 0 | C | T | 21.2% | 170.4 / 19.1 | 85 | T314M (ACG→ATG) | uacT | urate:H(+) symporter |
| Marginal new junction evidence (sorted from low to high skew) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 4606166 | 86 (1.040) | 10 (0.170) | 10/420 | 3.6 | 14.2% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 60 (1.030) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 1096961 = | 61 (0.740) | 7 (0.120) | 5/438 | 5.6 | 12.9% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 50 (0.830) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 2653419 | 61 (0.740) | 6 (0.080) | 6/548 | 6.2 | 9.7% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 56 (0.740) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||
| * | ? | NC_000913 | = 2518116 | 79 (0.960) | 3 (0.050) | 3/436 | 6.7 | 5.1% | noncoding (1/76 nt) | alaX | tRNA‑Ala |
| ? | NC_000913 | 2518232 = | 54 (0.900) | intergenic (‑1/‑235) | alaW/yfeC | tRNA‑Ala/DNA‑binding transcriptional dual regulator YfeC | |||||
| * | ? | NC_000913 | = 781446 | 29 (0.350) | 3 (0.050) | 3/442 | 6.7 | 10.1% | intergenic (+2/‑131) | lysZ/lysQ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781655 = | 32 (0.520) | intergenic (+3/‑430) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | 1469296 = | NA (NA) | 5 (0.060) | 5/598 | 7.1 | 4.2% | noncoding (1/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 4117985 | 113 (1.370) | coding (106/846 nt) | glpF | glycerol facilitator | |||||
| * | ? | NC_000913 | = 3648068 | 106 (1.280) | 4 (0.050) | 4/584 | 7.5 | 3.6% | noncoding (6/82 nt) | agrA | small RNA AgrA |
| ? | NC_000913 | 3648300 = | 110 (1.360) | noncoding (7/82 nt) | agrB | small regulatory RNA AgrB | |||||