Quality Control (QC) report contents

Quality Control (QC) reports include metrics that are based on which data are included in an analysis. For example, metrics about fusions are available only for analyses with fusions data.

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 thousand bases.

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 thousand 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.