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When the column GENE dispays the name of the gene associated with "_t00n", there are several alternative transcripts associated with the variant (n standing for the number of alternative transcripts). In this case, one same variant is displayed on n lines.
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The word "gap" in ALT, EFFECT, IMPACT or AA columns indicates a spanning deletion (see https://gatk.broadinstitute.org/hc/en-us/articles/360035531912-Spanning-or-overlapping-deletions-allele-)
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The QD column shows the QualByDepth score given by GATK software, i.e. the QUAL score normalized by allele depth (AD) for a variant. For further information, check this page :
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https://gatk.broadinstitute.org/hc/en-us/articles/360037592191-QualByDepth
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