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Analysis Output/Output Files/Exon Variant Files

Exon Variant File Format

exonvariants.csv

A comma-separated values (CSV) format file containing summary information for RnaExonVariant and RnaExonVariantWildType targets.

The file contains the following columns:

Column Heading

Description

Target ID

A unique alphanumeric identifier for the target.

Gene

The gene in which the target is located.

Transcript ID

The transcript identifier of the affected transcript.

Chromosome

The chromosome on which the variant is located.

Position

The position of the variant.

Exon

The number of the affected exon for the affected transcript.

Supporting Reads

The number of reads supporting the variant.

Wild Type

Boolean value that indicates if the variant matches the "wild-type" genotype.

Ratio to Wild Type

Calculated with the following equation:

Blank if there are no Wild Type targets for the gene.

Norm Count within Gene

Calculated with the following equation:

Value is 0 if Read count =0 regardless of the value of the denominator.

Contains DEL Variants

Boolean value that indicates the presence of deletions in the CIGAR string.

Present

Boolean value that indicates if Norm Count within Gene is greater than zero.

exonvariants.vcf.gz

This file contains detected DEL structural variants. These are reported from RnaExonVariant and RnaExonVariantWildType targets whose CIGAR string contains D operations and which have non-zero read counts.

The file is in VCF 4.1 format and compressed by the gzip compression software. In addition to a format-compliant header, the file contains the following columns:

Column Heading

Description

CHROM

The chromosome on which the variant occurs.

POS

Position, given as the base before the left-most deleted position.

REF

The reference base preceding the deletion. It is taken from the full amplicon sequence in the manifest and will be set to N if not available.

ALT

The alternative allele (deletion) at the variant position.

ID

An identifier for the variant, formatted as: <Gene>.<Transcript ID>.<Chromosome>:<1-based Start>-<1-based End>.

QUAL

Will always be "." (missing).

FILTER

Will always be "PASS".

INFO

Consists of the following sub-fields:

SVTYPE—"DEL"
READS—The number of reads supporting this variant
NORMREADSWITHINGENE—The within-gene normalized number of reads that support this splice variant
ANT—Annotation of the breakpoint formatted as: "Gene|Transcript|Strand", where strand is either + or -.

FORMAT

Consists of the following sub-fields:

DP—The number of reads supporting this variant
NR—The within-gene normalized number of reads that support this splice variant