Hey, I see that the level for a chain in the netPanTro2 is different between the genome browser and the table. I am looking at the following region in hg18, chr1:465-19,890. http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:465-19,890
The alignment displayed with "netPanTro2" - "full" has gaps at level 1 which are present in the table with a different level. Like this, Level: 1 Human position: chr1:10312-11327 http://genome.ucsc.edu/cgi-bin/hgc?hgsid=162777095&o=10311&t=11327&g=netPanTro2&i=2 But the same gap in the table hg18.netPanTro2 has level 2. #bin level tName tStart tEnd type human_size chimp_size 585 1 chr1 464 19890 top 19426 19150 585 2 chr1 631 641 gap 10 0 585 2 chr1 663 685 gap 22 0 585 2 chr1 691 709 gap 18 0 585 2 chr1 759 780 gap 21 0 585 2 chr1 1249 1311 gap 62 0 585 3 chr1 1249 1311 nonSyn 62 62 585 2 chr1 10311 11327 gap 1016 0 585 3 chr1 10311 11327 nonSyn 1016 1723 585 4 chr1 10681 10997 gap 316 1023 585 5 chr1 10770 10969 nonSyn 199 219 Similarly the non-Syn region *Type:* nonSyn *Level:* 3 *Human position:* chr1:10771-10969 *Chimp position:* chr12:57677594-57677812 But this record has level 5 in the table. Am I missing something here? My second question is, what do gaps of different length mean? I see in the table for the same region there is a gap with human_size=316 and chimp_size=1023 (level 4 in table and level 2 in browser). Are these basically gaps between best matching chains? Thanks, Vishal _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
