This SpliceAI "Wildtype" container track shows the scores for the genome sequence itself, without variants, from predicted splice donor (5' intron boundaries) and splice acceptor (3' intron boundaries) sites. Predictions are strand-specific, with separate subtracks for the -plus and minus strands. These tracks are useful when looking at new transcript models to evaluate -how likely exon boundaries are and where possible splice acceptor sites are, in combination with -the variants track.
+plus and minus strands. These tracks are useful in combination with the variants track for +evaluating new transcript models. They can be used to assess potential exon boundaries or +possible splice acceptor sites. Why are some variants not scored by SpliceAI?SpliceAI only annotates variants within genes defined by the gene annotation file. Additionally, SpliceAI does not annotate variants if they are close to chromosome ends (5kb on either side), deletions of length greater than twice the input parameter -D, or inconsistent with the reference fasta file.
What are the differences between masked and unmasked tracks?The unmasked tracks include splicing changes corresponding to strengthening annotated splice sites and weakening unannotated splice sites, which are typically much less pathogenic than weakening annotated splice sites and strengthening unannotated splice sites. The delta scores of such splicing changes are set to 0 in the masked files. We recommend using the unmasked tracks for alternative