Figure 26.19: Variant track. The figure shows a track list (top), consisting of a reference sequence track, a variant track and a read mapping. The variant track was produced by running the Fixed Ploidy Variant Detection tool on the reads track. The variant track has been opened in a separate table view by double-clicking on it in the track list. By selecting a row in the variant track table, the track list view is centered on the corresponding variant.
A variant track (figure 26.19) usually contains the following information for each variant:
- The name of the reference sequence on which the variant is located.
- The region on the reference sequence at which the variant is located. The region may be either a 'single position', a 'region' or a 'between position region'. Examples are given in figure 26.20.
Figure 26.20: Examples of variants with different types of 'Region' column contents. The left-most variant has a 'single position' region, the middle variant has a 'region' region and the right-most has a 'between positions' region.
- The type of variant. This can either be SNV (single-nucleotide variant), MNV (multi-nucleotide variant), insertion, deletion, or replacement. Learn more in Variant types.
- The reference sequence at the position of the variant.
- The allele sequence of the variant.
- Reference allele
- Describes whether the variant is identical to the reference. This will be the case one of the alleles for most, but not all, detected heterozygous variants (e.g. the variant detection tool might detect two variants, A and G, at a given position in which the reference is 'A'. In this case the variant corresponding to allele 'A' will have 'Yes' in the 'reference allele' column entry, and the variant corresponding to allele 'G' would have 'No'. Had the variant detection tool called the two variants 'C' and 'G' at the position, both would have had 'No' in the 'Reference allele' column).
- The length of the variant. The length is 1 for SNVs, and for MNVs it is the number of allele or reference bases (which will always be the same). For deletions, it is the length of the deleted sequence, and for insertions it is the length of the inserted sequence. For replacements, both the length of the replaced reference sequence and the length of the inserted sequence are considered, and the longest of those two is reported.
- The zygosity of the variant called, as determined by the variant detection tool. This will be either 'Homozygous', where there is only one variant called at that position or 'Heterozygous' where more than one variant was called at that position.
- The number of 'countable' reads supporting the allele. The 'countable' reads are those that are used by the variant detection tool when calling the variant. Which reads are 'countable' depends on the user settings when the variant calling is performed - if e.g. the user has chosen 'Ignore broken pairs', reads belonging to broken pairs are not 'countable'. Note that, although overlapping paired reads have two reads in their overlap region, they only represent one fragment, and are counted only as one. (Please see the column 'Read count' below for a column that reports the value for 'reads' rather than for 'fragments'). Note also that the count value reported in the table may differ from the one accessible from the track's tooltip, as the 'count' value in the table is generated taking into account quality score and frequency of sequencing errors.
- The fragment coverage at this position. Only 'countable' fragments are considered (see under 'Count' above for an explanation of 'countable' fragments). Note that, although overlapping paired reads have two reads in their overlap region, they only represent one fragment, and overlapping paired reads contribute only 1 to the coverage. (Please see the column 'Read coverage' below for a column that reports the value for 'reads' rather than for 'fragments'). Also see Detailed information about overlapping paired reads for how overlapping paired reads are treated.)
- The number of 'countable' reads supporting the allele divided by the
number of 'countable' reads covering the position of the variant ('see under 'Count' above for an explanation of 'countable' reads). Please see Remove marginal variant calls for a description of how to remove low frequency variants.
- The probability that this particular variant exists in the sample. (For further information please refer to the White paper on Probabilistic Variant Detection tool: http://resources.qiagenbioinformatics.com//white-papers/White_paper_on_probabilistic_variant_caller_1.1.pdf).
- and Reverse read count The number of 'countable' forward or reverse reads supporting the allele (see under 'Count' above for an explanation of 'countable' reads). Also see more information about Detailed information about overlapping paired reads.
- and Reverse read coverage Coverage for forward or reverse reads supporting the allele.
- Forward/reverse balance
- The minimum of the fraction of 'countable' forward reads and 'countable' reverse reads carrying the variant among all 'countable' reads carrying the variant (see under 'Count' above for an explanation of 'countable' reads). 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. 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 base quality score of the bases supporting
a variant. In the case of a deletion, the quality score is taken from the average quality of the two bases neighboring the deleted one, and the lowest is reported. Similarly for insertions, the quality in reads where the insertion is absent is taken from the minimum average of the two bases on either side of the position. It can be possible in rare cases, that the quality score reported in this column for a deletion or insertion is below the threshold set for 'Minimum central quality', because this parameter is not applied to any quality value calculated from positions outside of the central variant. To remove low quality variants from the output, use the Remove Marginal Variants tool (see Remove Marginal Variants).
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).
Please note that the variants in the variant track can be enriched with information using the annotation tools in Filtering and annotating variants.