1eb778792659124aa071876e2c5541bc8e3d6b3d
max
  Tue Nov 4 01:54:21 2025 -0800
adding a link to more updated ancient dna tracks, refs #36592

diff --git src/hg/makeDb/trackDb/human/bamSLDenisova.html src/hg/makeDb/trackDb/human/bamSLDenisova.html
index a2f3ab9c52e..7497eefd6ba 100644
--- src/hg/makeDb/trackDb/human/bamSLDenisova.html
+++ src/hg/makeDb/trackDb/human/bamSLDenisova.html
@@ -4,32 +4,41 @@
     <IMG SRC="../images/denisovaCave.jpg" WIDTH=426 HEIGHT=640
 	ALT="Denisova cave">
   </TD></TR>
   <TR><TD ALIGN=RIGHT>
     <FONT SIZE=-1>Denisova cave entrance in the Altai Mountains
 	of Siberia, Russia where the bones were found from which
 	DNA was sequenced
     </FONT>
     <FONT SIZE=-2> (Copyright (C) 2010, Johannes Krause)
     </FONT>
   </TD></TR>
 </TABLE>
 
 <H2>Description</H2>
 <P>
-The Denisova track shows Denisova sequence reads mapped to the
-$organism genome. The Denisova sequence was generated from a phalanx bone
+This track shows Denisova sequence reads mapped to the
+human genome, but to the old hg18 assembly from 2006. We provide updated annotation
+tracks with the called variants on more recent assemblies: 
+<a href="hgTrackUi?g=dhcVcfDenisovaPinky&hgTracksConfigPage=configure">Denisova variants on hg19</a>, 
+and <a href="hgTrackUi?g=ancient&hgTracksConfigPage=configure">Neanderthal and Denisova variants on hg38</a>.
+There is no actual "Neanderthal" or "Denisova" genome assembly, the short fragments obtained from ancient
+samples can be aligned to the human genome and analyses are based on short variants.
+</P>
+
+<P>
+The Denisova sequence was generated from a phalanx bone
 excavated from Denisova Cave in the Altai Mountains in southern
 Siberia.
 </P>
 
 <H2>Methods</H2>
 <P>
 Denisova sequence libraries were prepared by treating DNA extracted
 from a single phalanx bone with two enzymes: uracil-DNA-glycosylase,
 which removes uracil residues from DNA to leave abasic sites, and
 endonuclease VIII, which cuts DNA at the 59 and 39 sides of abasic
 sites. Subsequent incubation with T4 polynucleotide kinase and T4 DNA
 polymerase was used to generate phosphorylated blunt ends that are
 amenable to adaptor ligation. Because the great majority of uracil
 residues occur close to the ends of ancient DNA molecules, this
 procedure leads to only a moderate reduction in average length of the