Display tab, Annotation sub-tab
 | If a column is an annotation column, then the column contains information only if an annotated reference sequence (a GenBank file or a preloaded reference with annotation) is used and only within regions of the reference where a coding sequence is annotated. |
Setting | Description |
|---|---|
Basic | |
Chrom | Selected by default. The name of the chromosome where the variant occurs. |
Pos | Selected by default. The nucleotide position in the chromosome where the variant occurs. |
Contig | Identifies the contig (segment of the reference) where the variant is located. |
Contig Pos | Position on the contig (segment of the reference) where the variation occurs. |
Ref Pos | The nucleotide position in the reference sequence based on a continuous count from the beginning to the end of the reference. |
Contig Ref | Selected by default. The reference nucleotide at the variant position. |
Cont Alt | The alternate (variant) nucleotide at the variant position. |
Contig Genotype | The genotype for the aligned reads at this position. Indicates whether the variant is homozygous or heterozygous. |
Zygosity | The zygosity (homozygous or heterozygous) of the variant. The zygosity is based on the Mutation percentage threshold value and the SNP allele count, which is specified in the Mutation Filter settings section for an Alignment project in the Project Wizard. (See Mutation Filter settings.) If both alleles are found above both these threshold values, then the variant is considered to be heterozygous. If only one allele is found above these threshold values, then the variant is considered to be homozygous. |
Description | If you have loaded a BED file on the Filter tab, ROI sub-tab or if you have loaded an Amplicon BED file in the Project Wizard, then the Description column displays the information that is contained in the Description (4th) column of the BED file. If no information is contained in the Description column for the loaded BED file, then this column is blank. |
Gene | |
Gene | Selected by default. The gene name if it is provided in the GenBank reference file or the preloaded reference. |
Trans. Type | The transcript type defined for the transcript that is shown in the Transcript Accession column. |
Trans. Accession | The transcript accession number from NCBI for the gene transcript that is used for annotating the variant. |
Strand | The strand (+/-) for the gene in which the variant is located. |
Entrez Gene ID | The unique integer ID generated for the gene by Entrez Gene. |
Exon | The exon number where the variant occurs. This number includes non-coding exons. |
CDS | Selected by default. The coding exon number where the variant occurs. |
Gene Ref | The reference nucleotide at the variant position relative to the gene direction. This value is the same as the Ref value for (+) strand genes and the complement of the Ref value for (-) strand genes. |
Gene Alt | The alternate (variant) nucleotide at the variant position relative to the gene direction. This value is the same as the Alt value for (+) strand genes and the complement of the Alt value for (-) strand genes. |
Gene Genotype | The genotype for the aligned reads at this position, relative to the gene direction. Indicates whether the variant is homozygous or heterozygous. |
Protein | |
Protein Accession | The protein accession for the gene from NCBI for the transcript that is used for annotating the variant. |
Amino Acid Change | Selected by default. The change in the amino acid that is caused by the variant. An “FS” is displayed for frameshift variants (indels in the coding sequence). “In-Frame” is displayed where an entire codon, or multiple entire codons, are inserted or deleted. |
Function | The functional consequence of the variant. Possible values are Non-coding, Synonymous, Missense, Nonsense, No-stop, In-frame, and Frameshift. |
Mutation Call – Select this option to identify the change (variant call) that occurs at the variant position. You can select multiple options. | |
• Genome | • Selected by default. List variant calls without positional information. |
• Relative to CDS | • List variant calls relative to the CDS (coding sequence) position. |
• Relative to mRNA | • List variant call positions relative to the mRNA sequence. |
• HGVS Genomic | • List variant calls using the format that is recommended by the Human Genome Variation Society relative to the genomic position of the variant. |
• 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. |
• HGVS 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. |
• Forensic (SWGDAM mtDNA) | • List variant calls based on the mitochondrial forensic nomenclature as recommended by the Scientific Working Group on DNA Analysis (SWGDAM). |
Reference Database ID | |
dbSNP | For variants that are found in the dbSNP database from NCBI, the rs accession number for the variant from the dbSNP database. |
Miscellaneous | |
Show all transcripts | If this option is not selected, then show the variant information only for the single preferred transcript for the gene; otherwise, show variant calls based on multiple transcripts only if: • There are overlapping genes. • Different transcripts of the same gene result in different amino acid changes. For example, if a variant is in the coding region in one transcript and in an intron in a different transcript. |
Comments | Variants that you have manually deleted or that the software has deleted show “Deleted” in this column. Mutations that you have added manually show “Added Manually” in this column. Mutations that you have manually confirmed show “Checked” in this column. |