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 |
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CHROM |
The chromosome on which the variant occurs. |
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POS |
Position, given as the base before the left-most deleted position. |
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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. |
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ALT |
The alternative allele (deletion) at the variant position. |
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ID |
An identifier for the variant, formatted as: <Gene>.<Transcript ID>.<Chromosome>:<1-based Start>-<1-based End>. |
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QUAL |
Will always be "." (missing). |
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FILTER |
Will always be "PASS". |
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INFO |
Consists of the following sub-fields:
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FORMAT |
Consists of the following sub-fields:
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