Column | Description |
|---|---|
General | |
Index | Unique system-generated identifier for the variant. |
Position | The nucleotide position in the chromosome where the variant occurs. |
Ref | The reference nucleotide at the variant position. |
Alt | The alternate (variant) nucleotide at the variant position. |
IUPAC | The IUPAC nucleotide code for the allele. If multiple alleles are called at a position, then the appropriate IUPAC ambiguity code is reported. Note: Mixtures of a deletion and other alleles use a lowercase letter. |
Variants | The standard variant call. |
Variant % | The variant frequency at the indicated position. |
Coverage | The total number of reads (total coverage) at the variant position. |
Coverage | |
A #(F,R), C #(F,R), G #(F,R), T#(F,R) | The number of reads that show the indicated nucleotide at the variant location in the forward direction and the number of reads that show the indicated nucleotide at the variant location in the reverse direction. |
Del #(F,R) | The number of reads that show a deletion at the variant location in the forward direction and the number of reads that show a deletion at the variant location in the reverse direction. |
Ins #(F,R) | The number of reads that show an insertion at the variant location in the forward direction and the number of reads that show an insertion in the reverse direction at the variant location. |
Coverage Percent | |
A(%), C(%), G(%), T(%) | The percentage of reads that show the indicated nucleotide at the variant location. |
Del(%) | The percentage of reads that show a deletion at the variant location. |
Ins(%) | The percentage of reads that show an insertion at the variant location. |
Score | |
A Score, C Score, G Score, T Score | The median Phred quality score for the indicated allele (SNP) in both the forward and reverse directions. |
Modifications | |
Category | Indicates the variant status for the project in the Variants table - Called, Removed, Added, |
Comment | Any comment that was entered for the added or deleted variant. |