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 the 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 for each analysis workflow are shown in the Presets tab, and in the TSV file for the analysis results. Every analysis workflow also has an associated annotation set that lists all annotation sources that are used, along with the 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 |
Ion Reporter™ Software |
|
Allele frequency |
Frequency of the allele observed from the raw data |
Ion Reporter™ Software |
|
Amino acid change |
HGVS notation that represents an amino acid change |
Ion Reporter™ Software |
|
Genetic category |
Unique genetic category that is used by Ion Reporter™ Software This annotation is for use only with trio analysis workflows. |
Ion Reporter™ Software |
|
ClinVar |
Assessment of the impact of the variant observed from NCBI ClinVar database |
|
|
Coding |
HGVS notation that represents a nucleotide change |
Ion Reporter™ Software |
|
Copy number |
The copy number ploidy state |
Ion Reporter™ Software |
|
COSMIC |
Catalog of somatic mutations in tumor tissue |
|
|
Coverage |
Total coverage for a variant |
Ion Reporter™ Software |
|
Custom |
See t_Import new or custom annotation sources_IRfor more information |
Ion Reporter™ Software |
|
Cytogenetic band |
The cytogenetic band where the CNV was detected This annotation is for use only with aneuploidy analysis workflows. |
Ion Reporter™ Software |
|
DRA |
Disease Research Area |
Ion Reporter™ Software |
|
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 or genes 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 are the latest versions available in Ion Reporter™ Software for hg19. If you use the DrugBank version 20150107 in an hg19 annotation set, cannot 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. |
Ion Reporter™ Software |
|
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. |
Ion Reporter™ Software |
|
Gene set |
Focus on variants found in a specific set of genes |
Ion Reporter™ Software |
|
Genetic category |
The genetic category. For example, compound heterozygote of the variant identified. This annotation is for use only with trio analysis workflows. |
Ion Reporter™ Software |
|
Genotype |
Genotype of the sample in each position |
Ion Reporter™ Software |
|
Gene Ontology |
Standardized ontology for gene and gene products. For example, functional role or localization. |
|
|
gnomAD |
The gnomAD v2.1.1 data set (Exomes). In Ion Reporter™ Software, GRCh38 gnomAD annotation source is added to the All_GRCh38 and All annotation sets. ExAC annotation source has been removed from the All annotation set. |
|
|
Grantham score |
A measure of evolutionary distance. See g_Grantham score_IR. |
Ion Reporter™ Software |
|
Hotspot information |
Indicates whether a variant overlaps a hotspot file |
Ion Reporter™ Software |
|
Location |
Position of the variant. For example, exonic. |
Ion Reporter™ Software |
|
Locus |
Position of the variant. |
Ion Reporter™ Software |
|
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 in the Ion Reporter™ analysis may impact these MAF values. |
|
|
Mother genotype |
Genotype of mother This annotation is for use only with trio analysis workflows. |
Ion Reporter™ Software |
|
MyVariants |
A personal knowledge base of genomic variants (formerly, VariantKB database) |
Ion Reporter™ Software |
|
Named Variants |
A list of known variants in the CFTR gene panel |
Ion Reporter™ Software |
|
OMIM |
Online Mendelian Inheritance in Man® |
|
|
p-value |
p-value of the variant call |
Ion Reporter™ Software |
|
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) |
Ion Reporter™ Software |
|
Reference / variant coverage |
Individual strand coverage information for the reference and variant calls |
Ion Reporter™ Software |
|
SIFT |
Prediction of the functional effect of a variant on a protein |
|
|
Size |
Size of the variant |
Ion Reporter™ Software |
|
Transcript set |
Preferred transcripts used to determine coding regions of genes. If you include a transcript file, only transcripts that are present in the selection of canonical transcripts are reported. Other transcripts are filtered out. |
|
|
Type |
Type of variant. For example, SNP, INDEL, CNV, and so on. |
Ion Reporter™ Software |
|
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. |
Ion Reporter™ Software |
|
Variant effect |
The effect of the variant on the coding sequence. For example, missense or stoploss. |
Ion Reporter™ Software |