Hello Lan, The Ns reflect uncertainty/gaps in other genomes. Here are a few relevant details from the Conservation track description page: -- from Description section: Missing sequence in the low-coverage assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below).
from Base Level section: When zoomed-in to the base-level display, the track shows the base composition of each alignment, with bases in annotated repetitive elements displayed in lower case. from Methods section: Pairwise alignments with the human genome were generated for each species using blastz from repeat-masked genomic sequence. Lineage-specific repeats were removed prior to alignment, then reinserted. -- There is also some information about display conventions in the Gap Annotation section that you should find useful. I hope this information is helpful. If you have further questions, please feel free to contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 01/18/09 16:58, Lan Lin wrote: > Hi, > > In the base-level view of the conservation track, there are often stretches > of 'Ns' in other genomes being aligned. Are these Ns the result of > repeatmasking or do they reflect uncertainty/gaps in other genomes? > > Lan Lin > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
