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 30 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 | 40.9% | 86.4 / 28.1 | 66 | L122* (TTA→TGA) | dsdC | DNA‑binding transcriptional dual regulator DsdC |
| * | NC_000913 | 1,922,815 | 0 | C | A | 35.0% | 122.2 / 22.1 | 100 | G52V (GGA→GTA) | pphA | phosphoprotein phosphatase 1 |
| * | NC_000913 | 2,767,444 | 0 | C | A | 34.3% | 199.0 / 15.6 | 105 | intergenic (+89/‑266) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 2,326,713 | 0 | C | A | 33.7% | 158.8 / 18.0 | 95 | P202Q (CCG→CAG) | atoB | acetyl‑CoA acetyltransferase |
| * | NC_000913 | 4,296,268 | 0 | T | C | 33.3% | 62.7 / 35.5 | 45 | intergenic (+474/+168) | gltP/yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| * | NC_000913 | 3,054,886 | 0 | G | T | 32.9% | 128.3 / 21.4 | 79 | Q187K (CAA→AAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 2,767,445 | 0 | C | A | 31.4% | 192.1 / 17.7 | 105 | intergenic (+90/‑265) | rnlB/yfjP | antitoxin RnlB/putative GTP‑binding protein YfjP |
| * | NC_000913 | 3,911,533 | 0 | C | A | 30.8% | 201.5 / 16.0 | 120 | intergenic (‑8/+306) | pstS/glmS | phosphate ABC transporter periplasmic binding protein/L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| * | NC_000913 | 1,351,463 | 0 | C | A | 30.8% | 137.7 / 13.7 | 104 | E100* (GAG→TAG) | ycjD | DUF559 domain‑containing protein YcjD |
| * | NC_000913 | 3,054,894 | 0 | G | T | 30.8% | 123.3 / 20.6 | 78 | P184Q (CCA→CAA) | ygfB | PF03695 family protein YgfB |
| * | NC_000913 | 847,955 | 0 | G | A | 29.4% | 158.1 / 39.1 | 109 | A17V (GCG→GTG) | glnH | L‑glutamine ABC transporter periplasmic binding protein |
| * | NC_000913 | 1,334,966 | 0 | A | C | 28.8% | 230.6 / 36.8 | 156 | intergenic (+137/‑182) | cysB/ymiA | DNA‑binding transcriptional dual regulator CysB/uncharacterized protein YmiA |
| * | NC_000913 | 58,065 | 0 | C | A | 28.6% | 148.8 / 14.2 | 84 | P234P (CCC→CCA) | djlA | co‑chaperone protein DjlA |
| * | NC_000913 | 878,655 | 0 | C | A | 28.6% | 195.1 / 20.8 | 98 | intergenic (+24/‑87) | bssR/yliI | regulator of biofilm formation/aldose sugar dehydrogenase YliI |
| * | NC_000913 | 2,365,840 | 0 | T | G | 27.5% | 244.5 / 13.8 | 153 | intergenic (‑220/‑70) | ais/arnB | putative lipopolysaccharide core heptose(II)‑phosphate phosphatase/UDP‑4‑amino‑4‑deoxy‑L‑arabinose aminotransferase |
| * | NC_000913 | 147,802 | 0 | C | A | 26.7% | 245.7 / 10.8 | 120 | R279R (CGG→AGG) | rpnC | recombination‑promoting nuclease RpnC |
| * | NC_000913 | 2,990,480 | 0 | C | A | 26.5% | 276.0 / 17.9 | 162 | intergenic (‑120/‑788) | yqeK/ygeG | protein YqeK/TPR repeat‑containing putative chaperone YgeG |
| * | NC_000913 | 710,830 | 0 | G | T | 25.9% | 235.8 / 10.7 | 116 | intergenic (‑105/+105) | uof/fldA | RyhB‑regulated fur leader peptide/flavodoxin 1 |
| * | NC_000913 | 4,360,965 | 0 | C | A | 25.5% | 351.2 / 15.4 | 149 | E324* (GAG→TAG) | cadC | DNA‑binding transcriptional activator CadC |
| * | NC_000913 | 2,288,418 | 0 | G | T | 24.5% | 330.4 / 13.7 | 147 | pseudogene (497/2525 nt) | yejO | adhesin‑like autotransporter YejO |
| Marginal new junction evidence (lowest skew 10 of 21 shown) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 13 (0.140) | 12/598 | 5.3 | 9.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3206583 | 121 (1.290) | coding (121/912 nt) | ttdA | L(+)‑tartrate dehydratase subunit alpha | |||||
| * | ? | NC_000913 | = 1294286 | 91 (0.970) | 11 (0.120) | 11/598 | 5.6 | 10.8% | intergenic (+142/+1160) | tdk/adhE | thymidine/deoxyuridine kinase/fused acetaldehyde‑CoA dehydrogenase and iron‑dependent alcohol dehydrogenasealdehyde/alcohol dehydrogenase AdhE |
| ? | NC_000913 | 1294290 = | 90 (0.960) | intergenic (+146/+1156) | tdk/adhE | thymidine/deoxyuridine kinase/fused acetaldehyde‑CoA dehydrogenase and iron‑dependent alcohol dehydrogenasealdehyde/alcohol dehydrogenase AdhE | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 10 (0.110) | 10/598 | 5.9 | 7.6% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3206580 = | 121 (1.290) | coding (118/912 nt) | ttdA | L(+)‑tartrate dehydratase subunit alpha | |||||
| * | ? | NC_000913 | = 2357652 | 107 (1.140) | 7 (0.080) | 7/530 | 6.4 | 7.4% | coding (749/900 nt) | rpnE | inactive recombination‑promoting nuclease‑like protein RpnE |
| ? | NC_000913 | 2357836 = | 81 (0.970) | intergenic (+33/+206) | rpnE/yfaU | inactive recombination‑promoting nuclease‑like protein RpnE/2‑keto‑3‑deoxy‑L‑rhamnonate aldolase | |||||
| * | ? | NC_000913 | = 1470516 | NA (NA) | 8 (0.090) | 8/592 | 6.6 | 8.0% | noncoding (1221/1221 nt) | IS30 | repeat region |
| ? | NC_000913 | = 1909272 | 92 (0.990) | intergenic (+108/+36) | yobH/kdgR | uncharacterized protein YobH/DNA‑binding transcriptional repressor KdgR | |||||
| * | ? | NC_000913 | = 4606166 | 99 (1.060) | 4 (0.060) | 4/420 | 6.7 | 5.7% | intergenic (‑1/+34) | leuV/leuP | tRNA‑Leu/tRNA‑Leu |
| ? | NC_000913 | 4606403 = | 64 (0.970) | intergenic (‑2/+266) | leuQ/rsmC | tRNA‑Leu/16S rRNA m(2)G1207 methyltransferase | |||||
| * | ? | NC_000913 | 1096961 = | 84 (0.900) | 4 (0.060) | 4/438 | 6.9 | 6.0% | intergenic (+132/+604) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser |
| ? | NC_000913 | = 1097503 | 64 (0.930) | intergenic (+674/+62) | ycdU/serX | uncharacterized protein YcdU/tRNA‑Ser | |||||
| * | ? | NC_000913 | = 781222 | 41 (0.440) | 4 (0.060) | 4/446 | 7.0 | 8.8% | noncoding (76/76 nt) | lysY | tRNA‑Lys |
| ? | NC_000913 | 781653 = | 52 (0.740) | intergenic (+1/‑432) | lysQ/nadA | tRNA‑Lys/quinolinate synthase | |||||
| * | ? | NC_000913 | = 1251766 | 84 (0.900) | 6 (0.070) | 6/574 | 7.2 | 7.0% | coding (701/1920 nt) | dhaR | DNA‑binding transcriptional dual regulator DhaR |
| ? | NC_000913 | 1252103 = | 80 (0.890) | coding (1038/1920 nt) | dhaR | DNA‑binding transcriptional dual regulator DhaR | |||||
| * | ? | NC_000913 | = 696741 | 53 (0.560) | 3 (0.040) | 3/442 | 7.5 | 6.0% | intergenic (‑1/+15) | metU/glnW | tRNA‑Met/tRNA‑Gln |
| ? | NC_000913 | 697135 = | 55 (0.790) | intergenic (‑2/+378) | metT/asnB | tRNA‑Met/asparagine synthetase B | |||||