6cda00dc26e57ab505aa0c21746960e0aaa5cc73 hiram Fri Apr 1 16:54:51 2022 -0700 listing the genomes refs #29189 diff --git src/hg/makeDb/trackDb/human/homoSapiensChainNet.html src/hg/makeDb/trackDb/human/homoSapiensChainNet.html index e2eb84f..dbfec10 100644 --- src/hg/makeDb/trackDb/human/homoSapiensChainNet.html +++ src/hg/makeDb/trackDb/human/homoSapiensChainNet.html @@ -1,42 +1,51 @@ <H2>Description</H2> <P> This track shows regions of the human genome that are alignable to other Homo spiens genomes ("chain" subtracks) or in synteny ("net" subtracks). The alignable parts are shown with thick blocks that look like exons. Non-alignable parts between these are shown with thin lines like introns. More description on this display can be found below. </P> +<P> +Other assemblies included in this track: +<ul> +<li><a href="https://genome.ucsc.edu/h/GCA_009914755.4" target=_blank>GCA_009914755.4_CHM13_T2T_v2.0</a> human CHM13 T2T v2.0</li> +<li><a href="https://genome.ucsc.edu/h/GCA_021951015.1" target=_blank>GCA_021951015.1_HG002.mat.cur.20211005</a> human HG002 maternal</li> +<li><a href="https://genome.ucsc.edu/h/GCA_021950905.1" target=_blank>GCA_021950905.1_HG002.pat.cur.20211005</a> human HG002 paternal</li> +</ul> +</P> + <H3>Chain Track</H3> <P> The chain track shows alignments of the human genome to other Homo sapiens genomes using a gap scoring system that allows longer gaps than traditional affine gap scoring systems. It can also tolerate gaps in both source and target assemblies simultaneously. These "double-sided" gaps can be caused by local inversions and overlapping deletions in both species. <P> The chain track displays boxes joined together by either single or double lines. The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the -$o_organism assembly or an insertion in the $organism +query assembly or an insertion in the target assembly. assembly. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where multiple chains align over a particular region of -the $organism genome, the chains with single-lined gaps are often +the target genome, the chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.</P> <P> In the "pack" and "full" display modes, the individual feature names indicate the chromosome, strand, and location (in thousands) of the match for each matching alignment.</P> <H3>Net Track</H3> <P> The net track shows the best Homo sapiens chain for every part of this target human genome. It is useful for finding syntenic regions, possibly orthologs, and for studying genome rearrangement. </P>