closes #564

ga4gh · Dec 16, 2024 · 83e7d43 · 83e7d43
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diff --git a/docs/source/concepts/LocationAndReference/SequenceLocation.rst b/docs/source/concepts/LocationAndReference/SequenceLocation.rst
@@ -57,6 +57,9 @@ In some variant representation formats (e.g. HGVS, VCF) sequence variants are de
 (ref) and "alternate" (alt) alleles. When representing an Allele with VRS v2, it is also possible to describe the
 ref sequence (derived from the :ref:SequenceReference at the location) using the *sequence* property.
 
+The *sequence* property is **for descriptive purposes only**, and not a substitute for the *sequenceReference*
+property.
+
 .. admonition:: New in v2
 
    In VRS v1, sequence derived from the reference was not transmitted. This feature was added in VRS v2 due to
@@ -85,3 +88,12 @@ chromosome sequence to which it aligns. VRS intentionally does not allow for *st
 that use an offset system to represent sequence not found on the :ref:`SequenceReference`.
 
 .. TODO:: Describe and add a ref to an intronic variant profile
+
+CisPhasedBlocks and the Inferred SequenceReference
+##################################################
+
+When a :ref:`SequenceReference` is provided in a :ref:`CisPhasedBlock`, it is defined that all member
+:ref:`Allele` objects occur on that sequence. Consequently, `SequenceLocation` objects of those `Alleles`
+do not need to populate the `SequenceReference` property. There may be other contexts where this optional
+property may be omitted, but when this is done there SHOULD be a means of inferring the content of this
+property (as is explicitly described in `CisPhasedBlock`).
diff --git a/docs/source/concepts/LocationAndReference/SequenceReference.rst b/docs/source/concepts/LocationAndReference/SequenceReference.rst
@@ -16,17 +16,17 @@ such as the alphabet used (nucleic acid or amino acid), if the sequence represen
 and labels used to describe the sequence.
 
 Definition and Information Model
-################################
+@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 
 .. include::  ../../def/vrs/SequenceReference.rst
 
 Example
-#######
+@@@@@@@
 
 .. code-block:: json
 
     {
       "type": "SequenceReference",
       "refgetAccession": "SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
       "label": "NC_000007.14"
-    }    
+    }