1eb62c61ee677b7a3c90cc77465dcbeacec479ce
angie
  Tue Nov 5 13:30:58 2019 -0800
Oops, forgot to add some values to ucscNotesFilterValues.  refs #23283

diff --git src/hg/makeDb/trackDb/human/trackDb.ra src/hg/makeDb/trackDb/human/trackDb.ra
index b98d01c..24b4805 100644
--- src/hg/makeDb/trackDb/human/trackDb.ra
+++ src/hg/makeDb/trackDb/human/trackDb.ra
@@ -1619,48 +1619,52 @@
 
 track dbSnp153Composite
 compositeTrack on
 shortLabel dbSNP 153
 longLabel Short Genetic Variants from dbSNP release 153
 detailsTabUrls _dataOffset=/gbdb/hgFixed/dbSnp/dbSnp153Details.tab.gz
 group varRep
 visibility pack
 url https://www.ncbi.nlm.nih.gov/snp/$$
 urlLabel dbSNP: 
 type bigDbSnp
 freqSourceOrder 1000Genomes,GnomAD_exomes,TOPMED,ExAC,PAGE_STUDY,GnomAD,GoESP,Estonian,ALSPAC,TWINSUK,NorthernSweden,Vietnamese
 classFilterValues snv,mnv,ins,del,delins,identity
 classFilterType multipleListOr
 ucscNotesFilterValues \
+        altIsAmbiguous|Alternate allele contains IUPAC ambiguous base(s),\
         classMismatch|Variant class/type is inconsistent with allele sizes,\
         clinvar|Present in ClinVar,\
         clinvarBenign|ClinVar significance of benign and/or likely benign,\
         clinvarConflicting|ClinVar includes both benign and pathogenic reports,\
         clinvarPathogenic|ClinVar significance of pathogenic and/or likely pathogenic,\
         clusterError|Overlaps a variant with the same type/class and position,\
         commonAll|MAF >= 1% in all projects that report frequencies,\
         commonSome|MAF >= 1% in at least one project that reports frequencies,\
-        delMismatch|Deleted sequence mismatches genomic reference sequence,\
         diffMajor|Different projects report different major alleles,\
+        freqIsAmbiguous|Frequency reported for allele with IUPAC ambiguous base(s),\
+        freqNotRefAlt|Reference genome allele is not major allele in at least one project,\
         multiMap|Variant is placed in more than one genomic position,\
         overlapDiffClass|Variant overlaps other variant(s) of different type/class,\
         overlapSameClass|Variant overlaps other variant(s) of same type/class but different position,\
         rareAll|MAF < 1% in all projects that report frequencies (or no frequency data),\
         rareSome|MAF < 1% in at least one project that reports frequencies,\
+        refIsAmbiguous|Reference genome allele contains IUPAC ambiguous base(s),\
         refIsMinor|Reference genome allele is minor allele in at least one project that reports frequencies,\
         refIsRare|Reference genome allele frequency is <1% in at least one project,\
         refIsSingleton|Reference genome frequency is 0 in all projects that report frequencies,\
+        refMismatch|Reference allele mismatches reference genome sequence,\
         revStrand|Variant maps to opposite strand relative to dbSNP's preferred top-level placement
 #'
 ucscNotesFilterType multipleListOr
 maxFuncImpactFilterValues 0|(not annotated),0865|frameshift,1587|stop_gained,1574|splice_acceptor_variant,1575|splice_donor_variant,1821|inframe_insertion,1583|missense_variant,1590|terminator_codon_variant,1819|synonymous_variant,1580|coding_sequence_variant,1623|5_prime_UTR_variant,1624|3_prime_UTR_variant,1619|nc_transcript_variant,2153|genic_upstream_transcript_variant,1986|upstream_transcript_variant,2152|genic_downstream_transcript_variant,1987|downstream_transcript_variant,1627|intron_variant
 maxFuncImpactFilterType multipleListOr
 priority 0.8
 
     track dbSnp153Common
     parent dbSnp153Composite on
     shortLabel Common dbSNP (153)
     longLabel Common (1000 Genomes Phase 3 MAF >= 1%) Short Genetic Variants from dbSNP Release 153
     bigDataUrl /gbdb/$D/snp/dbSnp153Common.bb
     priority 1
 
     track dbSnp153ClinVar