report: substrate vcf-warnings status global-coords alt-length gene-ID reference-transcript transcript-ID vcf-errors mapped-transcript ref-length alignment reference-transcript: source ID substrate gene score UTR end variants strand translation exons type begin exons: internal-exon single-exon final-exon initial-exon UTR: three_prime_UTR five_prime_UTR status: alternate-structures NMD protein-differs bad-donor premature-stop broken-acceptor new-upstream-start-codon noncoding-to-coding bad-acceptor broken-donor bad-start start-codon-change no-stop-codon weakened-donor frameshift weakened-acceptor mapped-transcript: source ID substrate gene score UTR end variants strand translation exons type begin premature-stop: protein-truncation AA-pos EJC-distance protein-length hypothetical-NMD noncoding-to-coding: alt-start-score ref-start-score reason transcript start-score-cutoff ORF-length transcript: source ID substrate gene score UTR end variants structure-change cryptic-site strand translation exons type begin fate protein-differs: percent-match variants: near-splice-variants CDS-variants UTR-variants splice-site-variants frameshift-variants NMD: EJC-distance start-codon-change: to from frameshift: nt-with-phase-mismatch percent-phase-mismatch new-upstream-start-codon: new-start reference old-start protein-differs transcript frameshift premature-stop ORF-length alternate-structures: transcript structure-change: new-upstream-start-codon start-codon-change fate: protein-differs EJC-distance percent-match frameshift premature-stop