Annotations available in Ion Reporter™ Software
Ion Reporter™ Software provides several annotation sources are derived from public and private annotation databases for hg19 and GRCh38. Ion Reporter™ Software also provides annotation sets. An annotation set is a collection of annotation sources that you can use to annotate variants in your analyses. You can use annotation sets that are predefined in the software, or create custom annotation sets.
Each analysis workflow uses a different version of the annotation source. The versions are available in the analysis workflow, and in the TSV file. Every analysis workflow also has an associated annotation set that lists all of the annotation sources used, along with their versions.
To add custom annotation sources to an annotation set, see Import a custom annotation source.
The following annotation are included in Ion Reporter™ Software.
Annotations |
Description |
Source[1] |
|---|---|---|
5000 exomes |
Population frequency information from the 5000 exomes project |
|
Allele coverage |
Number of reads supporting the called allele |
|
Allele frequency |
Frequency of the allele observed from the raw data |
|
Amino acid change |
HGVS notation that represents an amino acid change |
|
Genetic category |
Unique genetic category that is used by Ion Reporter™ Software This annotation is for use only with trio analysis workflows. |
|
ClinVar |
Assessment of the impact of the variant observed from NCBI ClinVar database |
|
Coding |
HGVS notation that represents a nucleotide change |
|
Copy number |
The copy number ploidy state |
|
COSMIC |
Catalog of somatic mutations in tumor tissue |
|
Coverage |
Total coverage for a variant |
|
Custom |
See Import a custom annotation sourcefor more information |
|
Cytogenetic band |
The cytogenetic band where the CNV was detected This annotation is for use only with aneuploidy analysis workflows. |
|
DRA |
Disease Research Area |
|
dbSNP |
Single Nucleotide Polymorphism database. The dbSNP annotation source in the software contains a flag carried by a subset of its SNPs that have been curated by UCSC to be "UCSC Common SNPs". In order for a variant to be annotated as a UCSC Common SNP, the variant is first annotated as being present in dbSNP, and it might also be classified as a UCSC Common SNP. |
|
DGV |
Database of Genomic Variants: A curated database of human genomic structural variation |
|
DrugBank |
List of drugs known to target the gene(s) affected by the variant |
Note: When you create an hg19 annotation set, do not use the annotation source DrugBank version 20150107. Use instead annotation source DrugBank version 1 or DrugBank version 20161212 or 20180731, which the latest version available in Ion Reporter™ Software 5.12 for hg19. If you use the DrugBank version 20150107 in an hg19 annotation set, you will not be able to create a filter chain of DrugBank for any analysis that uses the annotation set. |
ExAC |
Exome Aggregation Consortium—Database catalog of variant frequencies |
|
Father genotype |
Genotype of father. This annotation is for use only with trio analysis workflows. |
|
FATHMM scores |
Prediction of the functional consequences of a variant. In Ion Reporter™ Software, FATHMM scores are available for COSMIC version 77 and later. These scores are populated when "COSMIC" is chosen as a part of the annotation preset that is used. |
|
Gene models |
Set of genes that overlap with the variant |
|
Gene panel |
Filter variants based on specific amplicon in an AmpliSeq panel. For example, Ion AmpliSeq CCP. |
|
Gene set |
Focus on variants found within a specific set of genes |
|
Genetic category |
The genetic category. For example, compound heterozygote of the variant identified. This annotation is for use only with trio analysis workflows. |
|
Genotype |
Genotype of the sample in each position |
|
Gene Ontology |
Standardized ontology for gene and gene products. For example, functional role or localization. |
|
GnomAD |
The gnomAD v2.1.1 data set (Exomes) |
|
Grantham score |
A measure of evolutionary distance. See Grantham score. |
|
Hotspot information |
Indicates whether a variant overlaps a hotspot file |
|
Location |
Position of the variant. For example, exonic. |
|
Locus |
Position of the variant. |
|
MAF |
Population frequency information from the 1000 genomes project. MAF numbers are provided by the dbSNP in Ion Reporter™ Software, which gets the MAF numbers from 1000 genomes. Therefore, the version of dbSNP annotation sources used within the Ion Reporter™ analysis may impact these MAF values. |
|
Mother genotype |
Genotype of mother This annotation is for use only with trio analysis workflows. |
|
MyVariants |
A personal knowledge base of genomic variants (formerly, VariantKB database) |
|
Named Variants |
A list of known variants in the CFTR gene panel |
|
OMIM |
Online Mendelian Inheritance in Man® |
|
Pfam |
Protein domain families in the coded protein |
|
PhyloP |
Measure of conservation of the protein across a wide range of organisms |
|
PolyPhen-2 |
Prediction of the functional effect of a variant on a protein |
|
Reference |
The reference allele (hg19) |
|
Reference / variant coverage |
Individual strand coverage information for the reference and variant calls |
|
SIFT |
Prediction of the functional effect of a variant on a protein |
|
Size |
Size of the variant |
|
Transcript set |
Preferred transcripts used to determine coding regions of genes. If you include a transcript file, only transcripts that are present in your selection of canonical transcripts are reported. Other transcripts are filtered out. |
|
Type |
Type of variant. For example, SNP, INDEL, CNV, and so on. |
|
UCSC common SNPs |
The dbSNP annotation source in the software contains a flag carried by a subset of its SNPs that have been curated by UCSC to be "UCSC Common SNPs". In order for a variant to be annotated as a UCSC Common SNP, the variant is first annotated as being present in dbSNP, and it might also be classified as a UCSC Common SNP. | |
Variant effect |
The effect of the variant on the coding sequence. For example, missense or stoploss. |