28aa0d3b6f9ec11895b49f1eb8117d868393fa42
lrnassar
  Tue Oct 15 05:21:23 2024 -0700
Updating the description of the exon frame field, refs #32675

diff --git src/hg/htdocs/FAQ/FAQformat.html src/hg/htdocs/FAQ/FAQformat.html
index d452eb2..dc4d18d 100755
--- src/hg/htdocs/FAQ/FAQformat.html
+++ src/hg/htdocs/FAQ/FAQformat.html
@@ -1030,30 +1030,40 @@
     int score;            	"Score"
     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
+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
+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. 
+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"
     uint    txEnd;              "Transcription end position"
     uint    cdsStart;           "Coding region start"