From 79f23800d90ab64eef060b09d9edd61a14e612b2 Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Mon, 29 Jan 2024 16:50:25 +0000
Subject: [PATCH] Add SAM recommendation of MAPQ=0 for unmapped reads

We already have a recommendation that MAPQ of 255 should not be used.
Expand on this to recommend zero is used when unmapped.

This is purely a recommendation, made for maximum compatibility, and
not a specification requirement.

Fixes #727
---
 SAMv1.tex | 1 +
 1 file changed, 1 insertion(+)

diff --git a/SAMv1.tex b/SAMv1.tex
index c1d76d1a..5470b23e 100644
--- a/SAMv1.tex
+++ b/SAMv1.tex
@@ -737,6 +737,7 @@ \section{Recommended Practice for the SAM Format}
   \item Unmapped reads should be stored in the orientation in which they came
     off the sequencing machine and have their {\sf reverse} flag bit~(0x10)
     correspondingly unset.
+  \item Unmapped reads should have mapping quality zero.
   \end{enumerate}
 \item Multiple mapping
   \begin{enumerate}[label=\arabic*]