-is applied, the consensus base, consensus quality, SNP quality and
-maximum 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, top two high-scoring ins/del sequences, the
-number of alignments containing the first indel allele, the number of
-alignments containing the second indel allele, and the number of
-alignments containing indels different from the top two alleles.
+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.