X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=samtools.1;h=0108fdc72554e1f03d9a4dc32512f6fe3f572817;hb=5edf84137d9ca68041477d36f2be640c42f46651;hp=d2c78f1b32aeb00f4487f7944122ef9c7f5d596d;hpb=c18ba0d59383e9bc2cf7d36c227617b03faeab25;p=samtools.git

diff --git a/samtools.1 b/samtools.1
index d2c78f1..0108fdc 100644
--- a/samtools.1
+++ b/samtools.1
@@ -220,14 +220,16 @@ mapping quality. A symbol `$' marks the end of a read segment.
 
 If option
 .B -c
-is applied, the consensus base, consensus quality, SNP quality and RMS
-mapping quality of the reads covering the site will be inserted between
-the `reference base' and the `read bases' columns. An indel occupies an
-additional line. Each indel line consists of chromosome name,
-coordinate, a star, the genotype, consensus quality, SNP quality, RMS
-mapping quality, # covering reads, the first alllele, the second allele,
-# reads supporting the first allele, # reads supporting the second
-allele and # reads containing indels different from the top two alleles.
+is applied, the consensus base, Phred-scaled consensus quality, SNP
+quality (i.e. the Phred-scaled probability of the consensus being
+identical to the reference) and root mean square (RMS) mapping quality
+of the reads covering the site will be inserted between the `reference
+base' and the `read bases' columns. An indel occupies an additional
+line. Each indel line consists of chromosome name, coordinate, a star,
+the genotype, consensus quality, SNP quality, RMS mapping quality, #
+covering reads, the first alllele, the second allele, # reads supporting
+the first allele, # reads supporting the second allele and # reads
+containing indels different from the top two alleles.
 
 .B OPTIONS:
 .RS