96c296bf6fcb45403903e0768b48126c634a83de
max
  Tue Jun 3 14:09:56 2025 -0700
small changes to FAQformat, after call with Brian, no redmine

diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html
index ad9451a03d4..09adecd6a4e 100755
--- src/hg/htdocs/FAQ/FAQformat.html
+++ src/hg/htdocs/FAQ/FAQformat.html
@@ -1033,37 +1033,40 @@
     string name2;       	"Alternate name (e.g. gene_id from GTF)"
     string cdsStartStat; 	"Status of CDS start annotation (none, unknown, incomplete, or complete)"
     string cdsEndStat;   	"Status of CDS end annotation (none, unknown, incomplete, or complete)"
     lstring exonFrames; 	"Exon frame offsets {0,1,2}"
     )
 </code></pre>
 <p>The fields cdsStartStat and cdsEndStat can have the following values: 'none' = none,
 'unk' = unknown, 'incmpl' = incomplete, and 'cmpl' = complete. However, the values are not used for
 our display and cannot be used to identify which genes are coding or non-coding. For most purposes,
 to get more information about a transcript, other tables will need to be used.
 For instance, in the case of hg38, the tables named wgEncodeGencodeAttrsVxx, where xx is the
 Gencode Version number. See this <a href="../../FAQ/FAQgenes.html#coding"
 target="_blank">coding/non-coding genes FAQ</a> for more information.</p>
 
 <p>
-The field <code>exonFrames</code> is a comma-separated list of the numbers
+<b>The exonFrames field:</b> The field <code>exonFrames</code> is a comma-separated list of the numbers
 with the possible values 0, 1, 2 or -1, one per exon, in order of transcription.
-This order means that the first value for a transcript on the minus (-) strand is
+This is different than the exonStarts and exonEnds fields - if the transcript is on the negative strand,
+exonFrames are in the reverse order relative than exonStarts.
+Put differently, it means that the first value for a transcript on the minus (-) strand is
 the exon on the right of the screen on the Genome Browser. 
 A value of zero means that the first codon of the exon starts at the first nucleotide of the
 exon. A value of one means that the first codon starts after the first
 nucleotide and a value of two means that it starts after the second nucleotide. 
+See also our <a href="../../goldenPath/help/codonPhase.html">phase documentation</a>.
 UTRs are non-coding and their exonFrame value is -1.</p>
 
 <a name=RefFlat></a>
 <p><strong>Gene Predictions and RefSeq Genes with Gene Names</strong></p>
 <p>
 A version of genePred that associates the gene name with the gene prediction information. In 
 alternative-splicing situations, each transcript has a row in this table.</p>
 <pre><code>table refFlat
 "A gene prediction with additional geneName field."
     (
     string  geneName;           "Name of gene as it appears in Genome Browser."
     string  name;               "Name of gene"
     string  chrom;              "Chromosome name"
     char[1] strand;             "+ or - for strand"
     uint    txStart;            "Transcription start position"