The variant track output
The variant track contains information on each of the variants called. When opened in the table view there is a number of columns for each of the variants (see figure 27.30).
Figure 27.30: A variant track shown in the table view.
The contents of these are:
- Chromosome
- The name of the reference sequence on which the variant is located.
- Region
- 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'.
- Type
- The type of variant. This can either be SNV (single-nucleotide variant), MNV (multi-nucleotide variant), insertion, deletion, or replacement.
- Reference
- The reference sequence at the position of the variant.
- Allele
- The allele sequence of the variant.
- Reference allele
- Describes whether the variant is identical to the reference. This will be the case for one of the alleles for most, but not all, detected heterozygous variants (e.g. the variant caller 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 caller called the two variants 'C' and 'G' at the position, both would have had 'No' in the 'Reference allele' column).
- Length
- 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.
- Zygosity
- The zygosity of the variant called, as determined by the variant caller. 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.
- Count
- The number of 'countable' fragments supporting the allele. The 'countable' fragments are those that are used by the variant caller when calling the variant. Which fragments 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').
- Coverage
- 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').
- Frequency
- 'Count' divided by 'Coverage'.
- Probability
- The contents of the Probability column (for Low frequency and Fixed Ploidy variant callers only) depend on the variant caller that produced and the type of variant:
- In the Fixed Ploidy Variant Detection Tool, the probability in the resulting variant track's 'Probability' column is NOT the probability referred to in the wizard. The probability referred to in the wizard, is the required minimum (posterior) probability that the site is NOT homozygous for the reference. The probability in the variant track 'Probability' column is the posterior probability of the particular site-type called. The fixed ploidy tool calculates the probability of the different possible configurations at each site. So using this tool, for single site variants the probability column just contains this quantity (for variants that span multiple positions see below).
- The rare variant tool makes statistical tests for the various possible explanations for each site. This means that the probability for the called variant must be estimated separately since it is not part of the actual variant calling. This is done by assigning prior probabilities to the various explanations for a site in a way that makes the probability for two explanations equal in exactly the situation where the statistical test shifts from preferring one explanation to the other. For a given single site variant, the probability is then calculated as the sum of probabilities for all the explanations containing that variant. So if a G variant is called, the reported probability is the sum of probabilities for these configurations: G, A/G, C/G, G/T, A/C/G, A/G/T, C/G/T, and A/C/G/T (and also all the configurations containing deletions together with G).
- Forward read count
- The number of 'countable' forward reads supporting the allele (see under 'Count' above for an explanation of 'countable' reads).
- Reverse read count
- The number of 'countable' reverse reads supporting the allele (see under 'Count' above for an explanation of 'countable' reads).
- 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).
- 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 neighbouring 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 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 Filter Marginal Variant Calls tool (see Filter Marginal Variant Calls).
- Read count
- The number of 'countable' reads supporting the allele. Only 'countable' reads are considered (see under 'Count' above for an explanation of 'countable' reads). Note that each read in an overlapping pair contribute 1. To view the reads in pairs in a reads track as single reads, check the 'Disconnect paired reads' option in the side-panel of the reads track. (Please see the column 'Count' above for a column that reports the value for 'fragments' rather than for 'reads').
- Read coverage
- The read coverage at this position. Only 'countable' reads are considered (see under 'Count' above for an explanation of 'countable' reads). Note that each read in an overlapping pair contribute 1. To view the reads in pairs in a reads track as single reads, check the 'Disconnect paired reads' option in the side-panel of the reads track. (Please see the column 'Coverage' above for a column that reports the value for 'fragments' rather than for 'reads').
- # Unique start positions
- The number of unique start positions for 'countable' fragments that support the variant. This value can be important to look at in cases with low coverage. If all reads supporting the variant have the same start position, you could suspect that it is a result of an amplification error.
- # Unique end positions
- The number of unique end positions for 'countable' fragments that support the variant. This value can be important to look at in cases with low coverage. If all reads supporting the variant have the same end position, you could suspect that it is a result of an amplification error.
- BaseQRankSum
- The BaseQRankSum column contains an evaluation of the quality scores in the reads that has a called variant compared with the quality scores of the reference allele. Variants for which no corresponding reference allele is called does not have a BaseQRankSum value. Likewise, no values are calculated for reference alleles. The score is a Z score, so a value of 2.0 means that the observed qualities for the variant two standard deviations below the qualities for the reference allele. The scoring is performed using a Mann-Whitney U for comparing the two sets of quality scores from the reference allele and the variant.
- Read position test probability
- The test probability for the test of whether the distribution of the read positions variant in the variant carrying reads is different from that of all the reads covering the variant position.
- Read direction test probability
- The test probability for the test of whether the distribution among forward and reverse reads of the variant carrying reads is different from that of all the reads covering the variant position.
- Hyper-allelic
- Basic and Fixed Ploidy Variant detectors only: Contains "yes", if the site contains more variants than the user-specified ploidy predicts, "no" if not.
- Genotype
- Fixed Ploidy only: Contains the most probable genotype for the site.
- Homopolymer
- The column contains "Yes" if the variant is likely to be a homopolymer error and "No" if not. This is assessed by inspecting all variants in homopolymeric regions longer than 2. A variant will get the mark "yes" if it is a homopolymeric length variation of the reference allele, or a length variation of another variant that is a homopolymeric variation of the reference allele. When several overlapping homopolymeric variants are identified, all except the most frequent are marked as being homopolymer. However, if one of the overlapping, homopolymeric variants is the reference variant, then all of them are marked as homopolymer.