Setting | Description |
|---|---|
Summary display | |
Sample | The sample ID. |
Locus | The HLA locus on which the alleles are located. |
Allele 1 Allele 2 | HLA alleles for the reported genotype. Note: The values that you have specified for the Type Precision determine the naming scheme that is displayed for the alleles. See Type Precision. |
Score | The likelihood that the genotype for the two alleles is the correct genotype. Note: The closer that the score is to zero, the greater the likelihood that the genotype is the correct one. |
Coverage | The number of reads that mapped to the locus. |
Poor Covered Position | Number of poor covered positions for the allele based on the Allele Coverage report filter settings. See Allele Coverage Report Settings tab. |
Amino Acid Change | The number of mismatches in that are located in the coding regions that result in an amino acid change. |
Substitutions | The number of mismatches that are substitutions. |
Indels | The number of mismatches that are indels. |
Mismatches | The number of mismatches in the sample data as compared to the dictionary sequence. |
Mismatches in CDS | The number of mismatches that are located in the coding regions. |
Mismatches in Non-Coding Regions | The number of mismatches that are located in the non-coding regions. |
Synonymous Mismatches in CDS | The number of mismatches that are located in the coding regions that do not result in an amino acid change. |
Unmatched Read counts | The number of reads that align to the gene but don’t match to the consensus sequences for either of the selected alleles. Displayed in the Unmatched Reads pane for the HLA project view. See HLA analysis project view. |
Type precision - Indicates how to display the allele names in the HLA Summary report. The name is always the Gene Name followed by up to four separate codes, each of which are representative of one of the following different allele characteristics/properties - Serotype, Amino Acid Differences, Synonymous Differences, and Non-coding Differences. | |
• 2 group result | • Show Gene, Serotype, and Amino Acid Differences. |
• 3 group result | • Show Gene, Serotype, Amino Acid Differences, and Synonymous Differences. |
• 4 group result | • Show Gene, Serotype, Amino Acid Differences, Synonymous Differences and Non-coding Differences. |
Allele pairs | |
• 1 allele result | Display the sample data (top allele pair) that was the best matched to the dictionary data for the selected gene. |
• 2 alleles result | Display the sample data (top two allele pairs) that was the best matched to the dictionary data for the selected gene. |
• 3 alleles result | Display the sample data (top three allele pairs) that was the best matched to the dictionary data for the selected gene. |
• All alleles result | Display the sample data (top four allele pairs) that matched to the dictionary data for the selected gene. |