Setting | Description |
|---|---|
Display Options | |
Reference Position | The reference position where the mismatch occurs. |
Gene | The gene that is selected in the HLA Summary report. |
Coverage | The number of reads that mapped to the locus in the sample data. |
Reference Nucleotide | The nucleotide in the GenBank file at the reference position. |
Zygosity | The zygosity of the alleles (heterozygous or homozygous) in the sample data for the selected gene. |
Amino Acid Change | The number of mismatches in that are located in the coding regions that result in an amino acid change. |
Mutation Call: Genomic | Selected by default. List variant calls without positional information. |
Mutation Call: Relative to CDS | List variant calls relative to the CDS (coding sequence) position. |
Mutation Call: Relative to mRNA | List variant call positions relative to the mRNA sequence. |
Mutation Call: Forensic | List variant calls based on the mitochondrial forensic nomenclature as recommended by the Scientific Working Group on DNA Analysis (SWGDAM). |
Mutation Call: HGVS Genomic | Selected by default. List variant calls using the format that is recommended by the Human Genome Variation Society relative to the genomic position of the variant. |
Mutation Call: HGVS Coding | List variant calls using the format that is recommended by the Human Genome Variation Society relative to the coding base number position of the variant. |
Mutation Call: HGVC Protein | List variant calls using the format that is recommended by the Human Genome Variation Society relative to the amino acid position of the variant. |
A(#/F / #R), C(#/F / #R), G(#/F / #R), T(#/F / #R) | The actual number of reads that show the indicated base at the variant location in the forward direction and the actual number of reads that show the indicated base at the variant location in the reverse direction. |
Deletion (#F / #R) | The actual number of reads that show a deletion at the variant location in the forward direction and the actual number of reads that show a deletion at the variant location in the reverse direction. |
Insertion (#F / #R) | The actual number of reads that show an insertion at the variant location in the forward direction and the actual number of reads that show an insertion in the reverse direction at the variant location. |
A(%), C(%), G(%), T(%) | The percentage of reads that show the indicated base at the variant location. |
Deletion(%) | The percentage of reads that show a deletion at the variant location. |
Insertion(%) | The percentage of reads that show an insertion at the variant location. |
A Score, C Score, G Score, T Score | Essentially an allele balance score for each individual allele. It is scaled to be similar to the Overall Mutation score, but it does not contribute to the overall score. • If the allele F/R ratio is > 3 x the F/R ratio for all the reads at the indicated position, or is < 1/3 x the F/R ratio for all the reads at the indicated position, then the score for the allele is zero. • If the position has no calls that correspond to the indicated allele, then the score for the allele is again zero. • Otherwise, the score is calculated based on the F/R ratio for the allele and the F/R ratio for all the reads at the indicated position. The closer that these two values are, then higher the allele score. The maximum allele score for any allele is 27. |
Deletion Score | For deletion alleles. See the description for A Score, C Score, G Score, T Score. |
Insertion Score | For insertion alleles. See the description for A Score, C Score, G Score, T Score. |
Filter Options | |
Coverage Display Threshold | |
Min Coverage | The minimum coverage required for a position to be called as a low coverage position and included in the report. |
Zygosity • Heterozygous threshold | The zygosity of the variant at the reference position. • The requirements for a location to be considered heterozygous. More than one nucleotide must observed above the indicated threshold (the default value is 20%) for the location to be considered heterozygous. |
• Homozygous • Heterozygous | • Display the variants of the indicated zygosity in the report. |