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Median Functional Molecular Coverage per Amplicon
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A functional molecule is a collection of reads that covers the amplicon and satisfies all criteria associated with the parameters (for example,
min_tag_fam_size and
min_fam_per_strand_cov) in the parameter file. Molecular coverage is the number of functional molecules. The median is calculated across all amplicons.
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Uniformity of Molecular Coverage for all Amplicons
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Percentage of amplicons having molecular coverage between 0.5x and 2x of the median molecular coverage.
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Percentage of Amplicons larger than 0.8x Median Functional Molecular Coverage
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Percentage of amplicons having molecular coverage more than 0.8x of the median functional molecular coverage
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Median Total Molecular Coverage per Amplicon
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The number of molecules that satisfies size criteria in the parameters file. The median is calculated across all amplicons.
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Percentage of Reads with Perfect Molecular Tags
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Percentage of reads whose molecular tags are exactly the same with design.
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Median Functional Molecular Loss due to Strand Bias per Amplicon
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The metric is calculated by 1- (Functional Molecular Coverage) / (Molecular Coverage without Strand Constraint), which measures the loss of functional molecules due to strand constraint for molecular functionality. The median is calculated across all amplicons.
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Median Percentage of Functional Molecules out of Total Molecules per Amplicon
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The percentage of functional molecules out of the number of molecules that satisfies size criteria. The median is calculated across all amplicons.
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Median Reads per Functional Molecule
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For each amplicon, the number of reads supporting each functional molecule is averaged across all functional molecules for that amplicon to determine the number of reads per functional molecule at the amplicon level. The median is calculated across all amplicons.
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Median Reads Contributed to Functional Molecules per Amplicon
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For each amplicon, the percentage of reads supporting functional molecules is (Number of Reads Supporting Functional Molecules) / (Number of Reads). The median is calculated across all amplicons.
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Percentage of Amplicons below (around) n% LOD
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LOD is calculated based on the number of functional molecules for each amplicon and variant calling parameters in the parameter file. Around x n% means in the range from 0.5x n% to 2x n%.
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