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% BED region > threshold
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Percentage of the total bases that is defined by the threshold included in the target regions BED file for the panel, with coverage that is greater than the Coverage Threshold value.
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% amplicons > threshold
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Percentage of the total number of amplicons in the panel that have coverage at all bases at a level greater than the Coverage Threshold value.
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Coverage Threshold
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A coverage adequacy setting.
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Total Number of Reads
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The total number of reads.
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Total Number of Bases (Mbp)
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The total number of bases, in million base pairs.
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Total Number of Bases (AQ20)(Mbp)
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The total number of bases at AQ20 (1% error rate) accuracy, in million base pairs.
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MAPD
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Median Absolute Pairwise Difference, a metric for noise in copy number data.
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Mean Coverage Depth (fold)
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The mean depth of coverage.
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Coverage within Target Region
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The percentage of positions in the target regions file for the panel that have coverage >1.
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Mean Read Length (AQ20)
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The mean read length at AQ20 (1% error rate) accuracy.
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Mean Read Length (AQ30)
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The mean read length at AQ30 (0.1% error rate) accuracy.
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Number of Homozygous SNVs
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The number of homozygous SNV calls.
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Number of Homozygous INDELs
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The number of homozygous INDEL calls.
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Number of Heterozygous SNVs
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The number of heterozygous SNV calls.
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Number of Homozygous MNVs
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The number of homozygous MNV calls.
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Number of Heterozygous MNVs
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The number of heterozygous MNV calls.
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Number of Heterozygous INDELs
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The number of heterozygous INDEL calls.
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Ti/Tv Ratio (SNPs)
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The ratio of transition to transversion substitutions.
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dbSNP concordance
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The overall dbSNP concordance, which is a ratio of the number of SNP and INDEL calls that appear in dbSNP with hit levels of "locus" or "allele", to the total number of SNP and INDEL calls.
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Heterozygotes/Homozygotes
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The ratio of heterozygotes to homozygotes.
This ratio is calculated from SNP and INDEL variants only. MNVs are not considered.
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INDELs/Total
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The ratio of INDEL calls to all variant calls.
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INDELs/kb
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The number of INDEL calls per 1,000 bases.
Note: For an analysis that uses a regions of interest BED file,
the number of bases in those regions is used.
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SNPs/kb
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The number of SNP calls per 1,000 bases.
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CNV/Total
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CNVs divided by total variant count minus no calls.
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LongDels/Total
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LongDels divided by total variant count minus no calls.
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Number of CNVs
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The number of CNV variants.
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Number of LongDels
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The number of LongDel variants.
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Total Mapped Fusion Panel Reads
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The sum of all reads for fusion variants and for the markers ASSAYS_5P_3P, and EXPRESSION_CONTROL on a fusion panel.
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Expression Controls Total Reads
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The number of all reads that are assigned to all of the expression control targets in the sample. If panels contain multiple pools, this metric is the aggregate sum from all expression control targets in all pools.
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POOL-n Expression Control Total Reads
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The sum of expression control reads for individual reads are also reported separately as POOL-1 ExpressionControlTotalReads and POOL-2 ExpressionControlTotalReads, and so on.
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