Annotated variant table

The annotated variant table holds the following information about each variant
Information about location, name etc
This is all basic information to locate the variant. Furthermore there is information about the reference sequence at the variant position.
Variant type
This can either be SNV (single-nucleotide variant), InDel (insertion or deletion) or MNV (multi-nucleotide variant).
Length
Allele variants
These are the alleles found by the variant caller in the sequencing data.
Counts
The number of reads supporting the alleles.
Coverage
The general read coverage at this position.
Frequencies
The number of reads supporting each allele divided by the number of overall reads. See Remove marginal variant calls on how to remove variants that are low-frequency.
Forward read count
The number of forward reads supporting each allele
Reverse read count
The number of reverse reads supporting each allele
Forward/reverse balance
In order to evaluate whether the distribution of forward and reverse reads is approximately random, this value is calculated as the minimum of the number of forward reads divided by the total number of reads and the number of reverse reads divided by the total number of reads supporting the variant (see Forward/Reverse balance calculation. An equal distribution of forward and reverse reads for a given allele would give a value of 0.5. See Remove marginal variant calls on how to remove variants that score poorly on the read balance.
Average quality
The average read quality score of the bases supporting a variant. See Remove marginal variant calls on how to remove variants that have a low average quality. If there are no values in this column, it is probably because the sequencing data was imported without quality scores (learn more about importing quality scores from different sequencing platforms in Import high-throughput sequencing data).
Overlapping annotation
. This shows if the variant is covered by an annotation. The annotation's type and name will displayed. For annotated reference sequences, this information can be used to tell if the variant is found in e.g. a coding or non-coding region of the genome. Note that annotations of type Variation and Source are not reported.
Coding region change
. For variants that fall within a coding region of a gene, the change is reported according to the standard conventions as outlined in http://www.hgvs.org/mutnomen/.
Amino acid change
. If the reference sequence of the is annotated with ORF or CDS annotations, the variant caller will also report whether the variant is synonymous or non-synonymous. If the variant changes the amino acid in the protein translation, the new amino acid will be reported. The nomenclature used for reporting is taken from http://www.hgvs.org/mutnomen/.

The table can be Exported (Image export) as a csv file (comma-separated values) and imported into e.g. Excel. Note that the CSV export includes all the information in the table, regardless of filtering and what has been chosen in the Side Panel. If you only want to use a subset of the information, simply select and Copy (Image copy) the information.

Note that if you make a split view of the table and the mapping, you will be able to browse through the variants by clicking in the table. This will cause the view to jump to the position of the variant.

This table view is not well-suited for downstream analysis, in which case we recommend working with tracks instead (see Variant tracks).