89491842e0ec6b2250aa6f6dc2c83c294930e6d6
max
  Sun May 17 14:38:40 2026 -0700
Add ChinaMAP phase 1 variant frequencies subtrack on hg38

ChinaMAP (Cao et al. 2020, Cell Res, PMID 32355288) is a deep-WGS
cohort of 10,588 Chinese individuals across 27 provinces and 8 ethnic
groups, with 147.4 M autosomal variants (136.7 M SNPs + 10.7 M short
indels). The released VCF is already on GRCh38 with chr-prefixed
chromosomes and ships AC/AF/AN plus matched 1KGP_* INFO fields, so it
is served directly via vcfTabix.

The ChinaMAP Limitations on Use prohibit redistribution, so the gbdb
directory is _chinamap (hidden from hgdownload) and the trackDb stanza
has tableBrowser off. Registered in scripts/varFreqs/databases.tsv so
the next varFreqsAll combined rebuild picks it up; filter UI is
deliberately not added yet (WBBC/TPMI precedent).

, refs #36642

diff --git src/hg/makeDb/trackDb/human/varFreqs.ra src/hg/makeDb/trackDb/human/varFreqs.ra
index 2bb10d09a3a..e746bcd3e2c 100644
--- src/hg/makeDb/trackDb/human/varFreqs.ra
+++ src/hg/makeDb/trackDb/human/varFreqs.ra
@@ -351,30 +351,41 @@
         bigDataUrl /gbdb/$D/varFreqs/tommo61kjpn/tommo-61kjpn-20250616-GRCh38-snvindel-af-autosome.vcf.gz
         visibility dense
         dataVersion 2025-06-16
         priority 5
 
         track wbbc
         shortLabel China WBBC 4.5k WGS
         longLabel Variant Frequencies: Westlake BioBank for Chinese - 4,480 WGS, 4 regional Han groups
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/wbbc/wbbc.vcf.gz
         visibility dense
         dataVersion Phase I v20210103
         priority 5.5
 
+        track chinamap
+        shortLabel China ChinaMAP 10.5k WGS
+        longLabel Variant Frequencies: ChinaMAP phase 1 - 10,588 WGS at ~40x, Chinese natural population
+        type vcfTabix
+        parent varFreqs on
+        bigDataUrl /gbdb/$D/varFreqs/_chinamap/chinamap.vcf.gz
+        visibility dense
+        dataVersion Phase 1 (v2020-03.beta)
+        priority 5.55
+        tableBrowser off
+
         track tpmi
         shortLabel Taiwan TPMI Axiom array
         longLabel Variant Frequencies: Taiwan Precision Medicine Initiative - Axiom TPM1 chip, Han Chinese
         type vcfTabix
         parent varFreqs on
         bigDataUrl /gbdb/$D/varFreqs/_tpmi/tpmi.vcf.gz
         visibility dense
         dataVersion Axiom TPM1 2022-06
         priority 5.6
         tableBrowser off
 
         track alfaVcf
         shortLabel NCBI ALFA 408k mixed
         longLabel Variant Frequencies: NCBI ALFA (dbGaP data) - 408k mixed WGS/WES/array, 163M variants
         type vcfTabix