Hi Jinyan, A high phastCons score means the site has a higher probability it is conserved. You can find more information on the track description page:
"PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns." Please contact us again at [email protected] if you have any further questions. --- Luvina Guruvadoo UCSC Genome Bioinformatics Group Jinyan Huang wrote: > Dear UCSC, > > I want to check whether my sequence is conserved in Mammal or not. > > I am using Human conservation track and Mammal Cons > (phastCons46wayPlacental) table on ucsc. I download the data and each > point have a score. In describe of ucsc, it said that "the phastCons > scores, by contrast, represent probabilities of negative selection and > range between 0 and 1." But I do not understand what it this mean. If > the phastCons scores is high (e.g. 1.0), does this mean that this site > is conserved? Or does this mean this site have a high substitution? > > Thank you very much for your time. > > The data is like fellow: > > variableStep chrom=chr10 span=1 > 102746256 0 > 102746257 0 > 102746258 0 > 102746259 0.015748 > 102746260 0.015748 > 102746261 0.0314961 > 102746262 0.0472441 > 102746263 0.015748 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
