Recommend always using the MM ? . encoding.

The '.' code is the default interpretation, but historically tools
omitting '?' and '.' have used both styles.  An explicit definition in
the MM string removes any ambiguity.

See samtools#654 comments for background.

SAMtags.tex

@@ -491,9 +491,12 @@ \subsection{Base modifications}
 Note `{\tt N}' may be used to match any base rather than specifically an `{\tt N}' call by the sequencing instrument.
 This may be used in situations where the base modification is not a derivation of a standard base type.
 This is followed by either plus or minus indicating the strand the modification was observed on (relative to the original sequenced strand of {\sf SEQ} with plus meaning same orientation),\footnote{Hence a tool that may reverse complement sequences does not need to understand how to manipulate the {\tt MM} and {\tt ML} tags.} and one or more base modification codes.
+
 Following the base modification codes is an optional `{\tt .}' or `{\tt ?}' describing how skipped seq bases of the stated base type should be interpreted by downstream tools.
 When this flag is `{\tt ?}' there is no information about the modification status of the skipped bases provided.
 When this flag is not present, or it is `{\tt .}', these bases should be assumed to have low probability of modification.\footnote{The decision whether a base is assumed to be unmodified or has a probability explicitly provided is up to the modification calling program. Some programs will elide calls with modification probabilites below a threshold to provide a more compact modification tag.}
+While optional with a default interpretation, it is strongly recommended that tools are explicit and always add either `{\tt ?}' or `{\tt .}' to avoid ambiguity.
+
 This is then followed by a comma separated list of how many seq bases of the stated base type to skip, stored as a delta to the last and starting with 0 as the first (or next) base, starting from the uncomplemented 5' end of the {\sf SEQ} field.
 This number series is comparable to the numbers in an {\tt MD} tag,
 albeit counting specific base types only and potentially reverse-complemented.