diff --git a/SAMtags.tex b/SAMtags.tex index eba269c7..aa11ec3d 100644 --- a/SAMtags.tex +++ b/SAMtags.tex @@ -530,8 +530,9 @@ \subsection{Base modifications} If the modification is not one of the standard common types (listed below) it can be specified as a numeric ChEBI code. For example `{\tt C+76792,57;}' is the same as `{\tt C+h,57;}'. -An unmodified base of `{\tt N}' means count any base in {\sf SEQ}, not only those of `{\tt N}'. +A fundamental base of `{\tt N}' means count any base in {\sf SEQ}, not only those of `{\tt N}'. Thus `{\tt N+n,100;}' means the 101st base is Xanthosine (n), irrespective of the sequence composition. +A fundamental base of `{\tt N}' may also be used with a base-specific modification code to force the counting to be applied per base rather than per base-type. The standard code types and their associated ChEBI values are listed below, taken from Viner {\it et al.}% @@ -567,6 +568,7 @@ \subsection{Base modifications} \hline N & n & Xao & Xanthosine & 18107 \\ N & N & & Ambiguity code; any mod & \\ +N & any & & Mod applied to any base & \\ \end{tabular} \end{center}