title tajimas D
Go to http://hsb.upf.edu/ This is a browser for selection for the 1000Genomes project. This is the largest publicly available data set for humans with more than 2500 fully sequenced individuals.
- Uncheck everything except Tajima’s D
- Try the SLC45A2 gene in Europeans - this is one of the most selected genes in Europeans
Zoom out a factor 10X The score is a rank based score for how extreme the loci is. Just like a Q score for NGS data it can be transformed into a probability. This probability can be interpreted as the fraction of the genome that is more extreme than this loci.
| score | probability |
|---|---|
| 2.301 | 0.005 |
| 2 | 0.01 |
| 1.824 | 0.015 |
| 1.699 | 0.02 |
| 1.602 | 0.025 |
| 1.523 | 0.03 |
| 1.456 | 0.035 |
| 1.398 | 0.04 |
| 1.347 | 0.045 |
| 1.301 | 0.05 |
| 1.26 | 0.055 |
| 1.222 | 0.06 |
| 1.187 | 0.065 |
| 1.155 | 0.07 |
| 1.125 | 0.075 |
The maximum value is 1.72405. Is this an extreme loci? Try to go to the LCT loci. How extreme is this? Try to zoom out. Are the any sites in the genome that stick out What can you conclude on the performance of Tajima’s D