Setting | Description |
|---|---|
Display Options | |
Reference Position | The reference position where the mismatch occurs. |
Reference Nucleotide | The nucleotide in the GenBank file at the reference position. |
Predicated Allele Nucleotide | The nucleotide in the dictionary file for the selected allele at the reference position. |
Observed Allele Nucleotide | The nucleotide in the consensus sequence for the sample data at the reference position. |
Allele Balance | The variant frequency in the sample data at the reference position. |
Read Balance | The read balance for the variant. Note: This value is identical to the value that is calculated for Balance Ratios and Frequencies in the Alignment settings. See Loading a Sequence Alignment Project in the NextGENe Viewer. |
Amino Acid Change | The number of mismatches in that are located in the coding regions that result in an amino acid change. |
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: Genomic | Selected by default. List variant calls without positional information. |
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 - All options are selected by default. | |
Display mismatches only | Display the mismatches for the consensus sequence for the sample data compared to the dictionary sequence for the allele pair that is selected in the HLA Summary report. Clear this option to show both matches and mismatches. |
Filter by statistics | |
• Allele Balance • Read Balance | • The Allele Balance is identical to the Allele Frequency. (See Allele Frequency.) Display only those alleles that have an allele balance > the indicated threshold. The default value is 0.5. • Display only those alleles that have a Read Balance > the indicated threshold. The default value is 0.5. |
Filter by annotation | |
Coding variants • Synonymous substitutions • Missense substitutions • Nonsense substitutions • No-stop substitution • Indels | By default, show the mismatches for the consensus sequence for the sample data compared to the dictionary sequence if the mismatch occurs for a position that is annotated as the indicated substitution type or as insertion or deletion. Clear the options for the substitution types that are not to be displayed in the report. |
Noncoding Variants | |
• Splicing Sites Intron [5] Exon [5] | • Select this option to show all variants in splicing site regions, and then specify the intron and exon values to define the splicing site region. |
• All other substitutions | • Selected by default. Show all substitutions that are located outside coding regions. |
• All other indels | • Selected by default. Show all indels that are located outside coding regions. |