Class MolecularSequence.MolecularSequenceQualityComponent

    • Field Detail

      • start

        protected IntegerType start
        Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive.
      • end

        protected IntegerType end
        End position of the sequence. If the coordinate system is 0-based then end is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position.
      • score

        protected Quantity score
        The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685)).
      • truthTP

        protected DecimalType truthTP
        True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
      • queryTP

        protected DecimalType queryTP
        True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event.
      • truthFN

        protected DecimalType truthFN
        False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here.
      • queryFP

        protected DecimalType queryFP
        False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here.
      • gtFP

        protected DecimalType gtFP
        The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar).
      • fScore

        protected DecimalType fScore
        Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall).