fe4c75c272ca27de55c0b42396c47f2b00637a4a
jnavarr5
  Mon Sep 28 16:36:20 2026 -0700
Linking the encode4ProCap trackDb.ra, saying why PRO-cap and contribution scores are hg38 only on the container page, and limiting the ProCapNet prediction claim to the primary chromosomes, refs #35528

diff --git src/hg/makeDb/trackDb/human/proCapNet.html src/hg/makeDb/trackDb/human/proCapNet.html
index 4dc96db59b2..af2aac4b48f 100644
--- src/hg/makeDb/trackDb/human/proCapNet.html
+++ src/hg/makeDb/trackDb/human/proCapNet.html
@@ -3,31 +3,31 @@
 <p>
 ProCapNet is a neural network trained to predict PRO-cap signal from DNA
 sequence alone. PRO-cap is a run-on assay that captures the 5' end of each
 nascent RNA, so it reports the exact base and strand at which RNA polymerase II
 started transcribing, including at enhancers and at unstable transcripts that
 RNA-seq and CAGE miss. Six separate models were trained, one on each of six cell
 lines with ENCODE PRO-cap data.
 </p>
 
 <p>
 This track holds two kinds of output from those models:
 </p>
 
 <ul>
 <li><b>Predicted PRO-cap</b>: what the model expects the PRO-cap signal to be,
-at every base of the genome, on both strands. The sequence rules that govern
+at every base of the primary chromosomes, on both strands. The sequence rules that govern
 where initiation happens are largely shared between cell types, so any one model
 highlights sequence capable of driving initiation, including at regions where no
 PRO-cap experiment has been done.</li>
 <li><b>Sequence contribution scores</b>: how much each individual base pushed
 the model's prediction up or down. Bases inside a functional element such as a
 TATA box or an initiator carry high scores, and the pattern of high-scoring
 bases often spells out the recognition sequence of a promoter-associated
 transcription factor. These are computed only around MANE Select transcription
 start sites, so they cover about 1% of the genome and the track is empty
 everywhere else.</li>
 </ul>
 
 <p>
 The predictions are available on GRCh38/hg38 and T2T-CHM13/hs1. The contribution
 scores are available on GRCh38/hg38 only, because they are computed at MANE