These tracks display the level of sequence uniqueness of the reference hg19 genome. They were generated using different window sizes and high signal will be found in areas where the sequence is unique.
The CRG Alignability tracks shows how uniquely k-mer sequences align to a region of the genome. To generate the data, sliding windows of k-mers (where k is 36, 40, 50, 75 or 100 nts) of the human genome sequence were mapped back to the genome using the GEM mapper aligner allowing 0, 1 or 2 mismatches. For each window, a mapability score was computed (S = 1/(number of bases of match found)). The CRG Alignability tracks show how uniquely k-mer sequences align to a region of the genome. To generate the data, the GEM-mappability program has been employed. The method is equivalent to mapping sliding windows of k-mers (where k has been set to 36, 40, 50, 75 or 100 nts to produce these tracks) back to the genome using the GEM mapper aligner (up to 2 mismatches were allowed in this case). For each window, a mapability score was computed (S = 1/(number of matches found in the genome): S=1 means exact match, S=0.5 is two matches, and so on). The CRG Alignability tracks were generated independently of the ENCODE project, in the framework of the GEM (GEnome Multitool) project.
The CRG Alignability track was created by Thomas Derrien and Paolo Ribeca (contact: paolo. ribeca@gmail. com) in Roderic Guigo's lab at the Centre for Genomic Regulation (CRG), Barcelona, Spain. TD was supported by funds from NHGRI for the ENCODE project, while PR was funded by a Consolider grant CDS2007-00050 from the Spanish Ministerio de Educación y Ciencia."
Data users may freely use all data in this track. ENCODE labs that contributed annotations have exempted their data here from the ENCODE data release policy restrictions.