- Information about location, 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), insertion, deletion or replacement. Learn more in Variant types.
- These are the alleles found by the variant caller in the sequencing data. In the case where a heterozygous variant is found, there is an entry for each allele, except if one is the reference allele (this is the main difference between the annotated table output and the variant track which includes the reference alleles, see Variant tracks).
- The number of reads supporting the allele.
- The general read coverage at this position. (See also more information about Detailed information about overlapping paired reads.)
- 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 the allele. (See also more information about Detailed information about overlapping paired reads.)
- Reverse read count
- The number of reverse reads supporting the allele. (See also more information about Detailed information about overlapping paired reads.)
- Forward/reverse balance
- Some systematic sequencing errors can be triggered by a certain combination of bases. This means that sequencing one strand may lead to sequencing errors that are not seen when sequencing the other strand (see [Nguyen et al., 2011] for a recent study with Illumina data).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. An equal distribution of forward and reverse reads for a given allele would give a value of 0.5. (See also more information about Detailed information about overlapping paired reads.)
- Average quality
- The average read quality score of the bases supporting a variant. 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
Sourceare 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 mapping 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 () 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 () 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).