Alignability As A Percent Or Coeficient Per Each Human Chromosome?

Question

[14134125465346445]

Is there a table somewhere that will tell me which of the human chromosomes are more easily alignable, or put differently, have a higher fraction of highly alignable regions than others, as a percentage?

Answer 1

[Pierre Lindenbaum]

there's something called the mappability: see http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability

The Duke Uniqueness tracks display how unique each sequence is on the positive strand starting at a particular base and of a particular length. Thus, the 20 bp track reflects the uniqueness of all 20 base sequences with the score being assigned to the first base of the sequence. Scores are normalized to between 0 and 1, with 1 representing a completely unique sequence and 0 representing a sequence that occurs more than 4 times in the genome (excluding chrN_random and alternative haplotypes). A score of 0.5 indicates the sequence occurs exactly twice, likewise 0.33 for three times and 0.25 for four times.