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Explicitly permit eg N+m in MM tag (PR#799) #799

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Explicitly permit eg N+m in MM tag (PR#799) #799

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4 changes: 3 additions & 1 deletion SAMtags.tex
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Expand Up @@ -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.}%
Expand Down Expand Up @@ -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}

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