Quality Control (QC) metrics

Quality Control (QC) metrics can be viewed in QC reports and in final reports. The metrics are based on data that are included in an analysis. For example, metrics that describe fusions are available only for analyses that include fusions data. See Create a final report template from analysis results and Create a final report for more information how to add QC metric to final reports. See Quality Control (QC) reports more information about QC reports.

QC Metrics	Description
% BED region > threshold	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.
% amplicons > threshold	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.
Coverage Threshold	A coverage adequacy setting.
Total Number of Reads	The total number of reads.
Total Number of Bases (Mbp)	The total number of bases, in million base pairs.
Total Number of Bases (AQ20)(Mbp)	The total number of bases at AQ20 (1% error rate) accuracy, in million base pairs.
MAPD	Median Absolute Pairwise Difference, a metric for noise in copy number data.
Mean Coverage Depth (fold)	The mean depth of coverage.
Coverage within Target Region	The percentage of positions in the target regions file for the panel that have coverage >1.
Mean Read Length (AQ20)	The mean read length at AQ20 (1% error rate) accuracy.
Mean Read Length (AQ30)	The mean read length at AQ30 (0.1% error rate) accuracy.
Number of Homozygous SNVs	The number of homozygous SNV calls.
Number of Homozygous INDELs	The number of homozygous INDEL calls.
Number of Heterozygous SNVs	The number of heterozygous SNV calls.
Number of Homozygous MNVs	The number of homozygous MNV calls.
Number of Heterozygous MNVs	The number of heterozygous MNV calls.
Number of Heterozygous INDELs	The number of heterozygous INDEL calls.
Ti/Tv Ratio (SNPs)	The ratio of transition to transversion substitutions.
dbSNP concordance	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.
Heterozygotes/Homozygotes	The ratio of heterozygotes to homozygotes. This ratio is calculated from SNP and INDEL variants only. MNVs are not considered.
INDELs/Total	The ratio of INDEL calls to all variant calls.
INDELs/kb	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.
SNPs/kb	The number of SNP calls per 1,000 bases.
CNV/Total	CNVs divided by total variant count minus no calls.
LongDels/Total	LongDels divided by total variant count minus no calls.
Number of CNVs	The number of CNV variants.
Number of LongDels	The number of LongDel variants.
Total Mapped Fusion Panel Reads	The sum of all reads for fusion variants and for the markers ASSAYS_5P_3P, and EXPRESSION_CONTROL on a fusion panel.
Expression Controls Total Reads	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.
POOL-`n` Expression Control Total Reads	The sum of expression control reads for individual reads are also reported separately as POOL-1 ExpressionControlTotalReads and POOL-2 ExpressionControlTotalReads, and so on.

The following fields are included in each of the *_coverage_statistics.txt files.

Column	Description
#Id	The amplicon ID or gene name (if any).
Region	Usually the chromosome that contains the amplicon, gene, or hotspot region.
Start	The initial position of the amplicon, gene, or hotspot region.
End	The end position of the amplicon, gene, or hotspot region.
No	The number of reads with zero coverage.
Low	The number of reads with low coverage.
Medium	The number of reads with medium coverage.
High	The number of reads with high coverage.
TargetSize	The region size (in bases) of the amplicon, gene, or hotspot region.
Min	The minimum coverage of any base in the amplicon, gene, or hotspot region.
Max	The maximum coverage in the amplicon, gene, or hotspot region.
Avg	The average coverage in the amplicon, gene, or hotspot region.
1XBases	The number of bases with at least 1X coverage in the amplicon, gene, or hotspot region.
AvgBQ	The average base quality value.

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Quality Control (QC) metrics