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 48 shown, sorted by frequency from high to low) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 2,477,265 | 0 | A | C | 39.0% | 184.3 / 42.9 | 124 | L122* (TTA→TGA) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 58,065 | 0 | C | A | 35.7% | 185.2 / 21.1 | 112 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 3,911,533 | 0 | C | A | 34.7% | 249.0 / 17.0 | 147 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,427,992 | 0 | G | T | 34.5% | 234.0 / 16.3 | 148 | P245P (CCC→CCA) | insH5 | IS5 family transposase and trans‑activator |
| * | NC_000913 | 1,922,815 | 0 | C | A | 32.8% | 183.6 / 23.2 | 116 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 4,136,467 | 0 | A | C | 31.2% | 143.2 / 19.5 | 82 | E120D (GAA→GAC) | yijE | cystine exporter |
| * | NC_000913 | 3,281,067 | 0 | C | A | 29.8% | 128.4 / 10.2 | 67 | intergenic (+377/‑909) | agaV/agaS | N‑acetyl‑D‑galactosamine specific PTS enzyme IIB component/putative galactosamine‑6‑phosphate deaminase/isomerase |
| * | NC_000913 | 3,054,894 | 0 | G | T | 29.4% | 143.0 / 17.9 | 85 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 1,351,463 | 0 | C | A | 29.2% | 219.3 / 13.1 | 137 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 3,054,886 | 0 | G | T | 29.1% | 146.7 / 23.9 | 86 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 3,741,871 | 0 | G | T | 28.8% | 229.2 / 17.0 | 125 | S221Y (TCC→TAC) | plaR | DNA‑binding transcriptional repressor PlaR |
| * | NC_000913 | 4,296,191 | 0 | A | C | 28.6% | 56.9 / 28.9 | 50 | intergenic (+397/+245) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 2,288,418 | 0 | G | T | 27.8% | 355.0 / 18.9 | 169 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| * | NC_000913 | 4,213,310 | 0 | G | T | 27.7% | 258.4 / 12.5 | 141 | G26V (GGA→GTA) | yjaA | stress response protein |
| * | NC_000913 | 2,477,264 | 0 | T | C | 27.6% | 285.8 / 10.4 | 124 | L122L (TTA→TTG) ‡ | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,286,870 | 0 | C | A | 27.6% | 191.0 / 50.8 | 107 | S54S (TCC→TCA) | ychS | putative uncharacterized protein YchS |
| * | NC_000913 | 2,159,413 | 0 | C | T | 27.6% | 102.0 / 17.2 | 58 | A343V (GCG→GTG) | mdtC | multidrug efflux pump RND permease subunit MdtC |
| * | NC_000913 | 2,990,480 | 0 | C | A | 27.5% | 324.3 / 18.4 | 171 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 4,360,965 | 0 | C | A | 27.5% | 334.5 / 23.5 | 154 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,704,512 | 0 | C | A | 27.4% | 203.4 / 17.0 | 106 | P266P (CCG→CCT) | lepB | signal peptidase I |
| Marginal new junction evidence (lowest skew 10 of 18 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 3648146 | 131 (1.090) | 14 (0.140) | 13/482 | 5.6 | 11.7% | intergenic (+2/‑148) | agrA/agrB | small RNA AgrA/small regulatory RNA AgrB |
| ? | NC_000913 | 3648378 = | 106 (1.090) | intergenic (+3/‑150) | agrB/arsR | small regulatory RNA AgrB/DNA‑binding transcriptional repressor ArsR | |||||
| * | ? | NC_000913 | = 781222 | 72 (0.600) | 12 (0.130) | 11/446 | 5.8 | 14.9% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 83 (0.930) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 780629 | 126 (1.050) | 11 (0.120) | 11/446 | 5.8 | 11.3% | noncoding (76/76 nt) | lysT | tRNA‑Lys |
| ? | NC_000913 | 780919 = | 78 (0.870) | intergenic (+1/‑149) | lysW/valZ | tRNA‑Lys/tRNA‑Val | |||||
| * | ? | NC_000913 | = 1287329 | 90 (0.750) | 10 (0.120) | 9/424 | 6.3 | 14.8% | intergenic (‑1/+209) | tyrV/tyrT | tRNA‑Tyr/tRNA‑Tyr |
| ? | NC_000913 | 1287624 = | 51 (0.600) | intergenic (‑2/+158) | tyrT/purU | tRNA‑Tyr/formyltetrahydrofolate deformylase | |||||
| * | ? | NC_000913 | = 696741 | 77 (0.640) | 8 (0.090) | 8/442 | 6.9 | 11.8% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 63 (0.710) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||
| * | ? | NC_000913 | = 1286906 | 82 (0.680) | 14 (0.120) | 11/558 | 7.2 | 16.4% | coding (198/276 nt) | ychS | putative uncharacterized protein YchS |
| ? | NC_000913 | 1287557 = | 66 (0.590) | noncoding (66/85 nt) | tyrT | tRNA‑Tyr | |||||
| * | ? | NC_000913 | = 4606166 | 116 (0.960) | 5 (0.060) | 5/420 | 8.1 | 6.1% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 72 (0.850) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | = 781322 | 60 (0.500) | 6 (0.060) | 6/520 | 8.9 | 7.1% | intergenic (+100/‑47) | lysY/lysZ | tRNA‑Lys/tRNA‑Lys |
| ? | NC_000913 | 781811 = | 104 (0.990) | intergenic (+159/‑274) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 4392437 | 102 (0.850) | 4 (0.050) | 4/442 | 9.0 | 4.5% | intergenic (+2/‑35) | glyV/glyX | tRNA‑Gly/tRNA‑Gly |
| ? | NC_000913 | 4392661 = | 94 (1.060) | intergenic (+3/‑231) | glyY/yjeV | tRNA‑Gly/uncharacterized protein YjeV | |||||
| * | ? | NC_000913 | = 2653419 | 101 (0.840) | 7 (0.060) | 6/548 | 9.2 | 6.9% | noncoding (37/100 nt) | timR | putative small regulatory RNA TimR |
| ? | NC_000913 | 2653746 = | 97 (0.880) | intergenic (‑291/‑109) | timR/ryfA | putative small regulatory RNA TimR/small regulatory RNA RyfA | |||||