Analysis Data

To view analysis data, select Analysis from the Subject Info page.

QC Metrics

The QC Metrics tab lists QC thresholds and values for the subjects in the case.

QC warnings indicate failed metrics and must be cleared before interpreting the case. For information, see Clear a QC Warning.

QC Metric

Definition

Percent autosome callability

The percent of non-N reference positions having a passing genotype call in targeted regions of autosomal chromosomes.

Average autosomal coverage over genome

Total number of bases that aligned to autosomes (or to the autosomal loci in the target region) divided by the total number of loci in the autosomes (or to the autosomal loci in the target region). If there was no autosome in the reference genome, this metric shows as NA.

AT dropout

The measurement of AT undercoverage relative to the mean.

GC dropout

The measurement of GC undercoverage relative to the mean.

Normalized coverage at GCs 81-100

The normalized coverage over the GC content range 81–100.

Estimated sample contamination

The percentage of reads in a sample that may be from another human source.

This metric is not included in the default QC thresholds. To include the metric, add the following line to the QC Thresholds when creating the test:

Estimated sample contamination, upper threshold: <percent>

where <percent> is the upper threshold percent.

Insert length median

Median length of the sequenced fragment. The fragment length is calculated based on the locations at which a read pair aligns to the reference.The read mapping information is parsed from the BAM files.

Mapped reads

The total number of mapped reads minus the number of unmapped reads.

Paired reads mapped to different chromosomes (MAPQ > 10)

The number of reads with MAPQ > 10 that have a mate mapped to a different chromosome.

Q30 bases

The percentage of bases with a 30 or above quality score.

Q30 bases R1

The percentage of Read 1 bases with a 30 or above quality score.

Q30 bases R2

The percentage of Read 2 bases with a 30 or above quality score.

Mismatched bases R1

The percentage of unique aligned Read 1 bases where the Read 1 base is different than the reference base.

Mismatched bases R2

The percentage of unique aligned Read 2 bases where the Read 2 base is different than the reference base.

Percent SNVs in large ROH (≥ 3 Mb)

The percentage of SNVs in a sample that occur in regions of homozygosity larger than three megabases.

Sex ploidy validation

The sex of the subject matches the predicted sex from the analysis.

This QC check is optional. To perform analysis without the check, set the QC Threshold test parameter value to false.

SNV Het/hom ratio

The ratio of the number of heterozygous SNPs and number of homozygous SNPs detected for the sample.

Ti/Tv ratio

The ratio of transitions and transversions in SNPs.

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Transitions are variants of the same nucleotide type (pyrimidine to pyrimidine, C and T; or purine to purine, A and G).

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Transversions are variants of a different nucleotide type (pyrimidine to purine, or purine to pyrimidine).

Trio concordance

The percentage of non-de novo SNPs computed by the concordance check for the proband.

This QC check is optional. To perform analysis without the check, set the QC Threshold test parameter value to false.

Files

The Files tab lists the output directory and all of the analysis files associated with the case.

Select a file to download it. To download files > 5 GB or multiple files at one time, use the CLI tool. For CLI download commands, see Command-Line Interface.

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BAM Files—Aligned sequences and quality scores in the BAM (*.bam) file format.

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VCF Files—Variant calls in the VCF (*.vcf.gz) file format.

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Genome VCF Files—Variants, references, and no calls for all sites in the genome VCF (gVCF) file format.

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QC Metrics Files—Statistics for each sample.

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Visualization Files—Files used to generate tracks in the IGV viewer. For more information about visualization tracks, see IGV Visualizations.

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Analysis Data