Class RrbsSummaryMetrics


  • public final class RrbsSummaryMetrics
    extends MultilevelMetrics
    Holds summary statistics from RRBS processing QC
    • Field Detail

      • READS_ALIGNED

        public Integer READS_ALIGNED
        Number of mapped reads processed
      • NON_CPG_BASES

        public Integer NON_CPG_BASES
        Number of times a non-CpG cytosine was encountered
      • NON_CPG_CONVERTED_BASES

        public Integer NON_CPG_CONVERTED_BASES
        Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
      • PCT_NON_CPG_BASES_CONVERTED

        public Double PCT_NON_CPG_BASES_CONVERTED
        NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
      • CPG_BASES_SEEN

        public Integer CPG_BASES_SEEN
        Number of CpG sites encountered
      • CPG_BASES_CONVERTED

        public Integer CPG_BASES_CONVERTED
        Number of CpG sites that were converted (TG for +, CA for -)
      • PCT_CPG_BASES_CONVERTED

        public Double PCT_CPG_BASES_CONVERTED
        CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
      • MEAN_CPG_COVERAGE

        public Double MEAN_CPG_COVERAGE
        Mean coverage of CpG sites
      • MEDIAN_CPG_COVERAGE

        public Integer MEDIAN_CPG_COVERAGE
        Median coverage of CpG sites
      • READS_WITH_NO_CPG

        public Integer READS_WITH_NO_CPG
        Number of reads discarded for having no CpG sites
      • READS_IGNORED_SHORT

        public Integer READS_IGNORED_SHORT
        Number of reads discarded due to being too short
      • READS_IGNORED_MISMATCHES

        public Integer READS_IGNORED_MISMATCHES
        Number of reads discarded for exceeding the mismatch threshold
    • Constructor Detail

      • RrbsSummaryMetrics

        public RrbsSummaryMetrics()