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"TRANSCRIPT_percent": 4.439252, "UPSTREAM": 40.0, "UPSTREAM_percent": 9.345794, "UTR_3_PRIME": 7.0, "UTR_3_PRIME_percent": 1.635514, "UTR_5_PRIME": 12.0, "UTR_5_PRIME_percent": 2.803738, "Transitions": 262.0, "Transversions": 268.0, "Ts_Tv_ratio": 0.977612, "Het": 0.0, "Hom": 0.0, "Missing": 265.0 } }, "vep": { "HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann": { "Variant classes": { "insertion": 10, "deletion": 11, "SNV": 334 }, "Consequences (most severe)": { "stop_gained": 1, "frameshift_variant": 6, "stop_lost": 1, "inframe_insertion": 3, "inframe_deletion": 2, "missense_variant": 139, "splice_region_variant": 2, "synonymous_variant": 125, "5_prime_UTR_variant": 9, "3_prime_UTR_variant": 7, "non_coding_transcript_exon_variant": 7, "intron_variant": 51, "intergenic_variant": 2 }, "Consequences (all)": { "stop_gained": 1, "frameshift_variant": 6, "inframe_insertion": 2, "inframe_deletion": 2, "missense_variant": 128, "splice_region_variant": 4, "synonymous_variant": 127, "5_prime_UTR_variant": 3, "3_prime_UTR_variant": 8, "non_coding_transcript_exon_variant": 16, "intron_variant": 153, "non_coding_transcript_variant": 37, "upstream_gene_variant": 54, "downstream_gene_variant": 62, "regulatory_region_variant": 26, "intergenic_variant": 2 }, "Coding consequences": { "stop_gained": 1, "frameshift_variant": 6, "inframe_insertion": 2, "inframe_deletion": 2, "missense_variant": 128, "synonymous_variant": 127 }, "SIFT summary": { "deleterious_low_confidence": 11, "deleterious": 22, "tolerated_low_confidence": 24, "tolerated": 70 }, "PolyPhen summary": { "possibly_damaging": 7, "probably_damaging": 12, "unknown": 21, "benign": 84 }, "Variants by chromosome": { "chr21": 355 }, "Position in protein": { "00-10%": 27, "10-20%": 32, "20-30%": 22, "30-40%": 29, "40-50%": 29, "50-60%": 22, "60-70%": 26, "70-80%": 27, "80-90%": 27, "90-100%": 25 }, "General statistics": { "Lines of input read": 355, "Variants processed": 355, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 355, "Overlapped genes": 194, "Overlapped transcripts": 202, "Overlapped regulatory features": 16 } }, "HCC1395_BL_custom.ann_snpEff_VEP.ann": { "Variant classes": { "copy_number_variation": 1, "deletion": 2 }, "Consequences (most severe)": { "transcript_ablation": 1, "intron_variant": 2 }, "Consequences (all)": { "stop_lost": 1, "feature_truncation": 2, "coding_sequence_variant": 1, "5_prime_UTR_variant": 1, "3_prime_UTR_variant": 1, "non_coding_transcript_exon_variant": 1, "intron_variant": 4, "NMD_transcript_variant": 1, "downstream_gene_variant": 1, "regulatory_region_variant": 1 }, "Coding consequences": { "stop_lost": 1, "coding_sequence_variant": 1 }, "Variants by chromosome": { "chr1": 1, "chr9": 1, "chrX": 1 }, "General statistics": { "Lines of input read": 4, "Variants processed": 3, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 3, "Overlapped genes": 6, "Overlapped transcripts": 6, "Overlapped regulatory features": 1 } }, "HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann": { "General statistics": { "Lines of input read": 0, "Variants processed": 0, "Variants filtered out": 0, "Overlapped genes": 0, "Overlapped transcripts": 0, "Overlapped regulatory features": 0 } }, "HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann": { "General statistics": { "Lines of input read": 0, "Variants processed": 0, "Variants filtered out": 0, "Overlapped genes": 0, "Overlapped transcripts": 0, "Overlapped regulatory features": 0 } }, "HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann": { "Variant classes": { "insertion": 15, "deletion": 20 }, "Consequences (most severe)": { "inframe_insertion": 1, "inframe_deletion": 2, "splice_region_variant": 1, "splice_polypyrimidine_tract_variant": 5, "5_prime_UTR_variant": 1, "3_prime_UTR_variant": 3, "non_coding_transcript_exon_variant": 1, "intron_variant": 21 }, "Consequences (all)": { "inframe_insertion": 1, "inframe_deletion": 1, "splice_region_variant": 1, "splice_polypyrimidine_tract_variant": 6, "3_prime_UTR_variant": 3, "intron_variant": 33, "non_coding_transcript_variant": 4, "upstream_gene_variant": 8, "downstream_gene_variant": 10, "regulatory_region_variant": 4 }, "Coding consequences": { "inframe_insertion": 1, "inframe_deletion": 1 }, "Variants by chromosome": { "chr21": 35 }, "Position in protein": { "00-10%": 1, "10-20%": 0, "20-30%": 0, "30-40%": 0, "40-50%": 0, "50-60%": 0, "60-70%": 0, "70-80%": 0, "80-90%": 0, "90-100%": 1 }, "General statistics": { "Lines of input read": 35, "Variants processed": 35, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 35, "Overlapped genes": 51, "Overlapped transcripts": 51, "Overlapped regulatory features": 4 } }, "HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann": { "Variant classes": { "SNV": 369 }, "Consequences (most severe)": { "splice_acceptor_variant": 1, "splice_donor_variant": 3, "stop_gained": 3, "stop_lost": 1, "missense_variant": 76, "splice_donor_5th_base_variant": 3, "splice_region_variant": 5, "splice_donor_region_variant": 2, "splice_polypyrimidine_tract_variant": 8, "synonymous_variant": 37, "5_prime_UTR_variant": 9, "3_prime_UTR_variant": 11, "non_coding_transcript_exon_variant": 28, "intron_variant": 178, "upstream_gene_variant": 2, "intergenic_variant": 2 }, "Consequences (all)": { "splice_acceptor_variant": 1, "splice_donor_variant": 3, "stop_gained": 2, "stop_lost": 1, "missense_variant": 68, "splice_donor_5th_base_variant": 3, "splice_region_variant": 7, "splice_donor_region_variant": 2, "splice_polypyrimidine_tract_variant": 11, "synonymous_variant": 34, "5_prime_UTR_variant": 7, "3_prime_UTR_variant": 10, "non_coding_transcript_exon_variant": 6, "intron_variant": 303, "NMD_transcript_variant": 3, "non_coding_transcript_variant": 46, "upstream_gene_variant": 68, "downstream_gene_variant": 60, "regulatory_region_variant": 19, "intergenic_variant": 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"Overlapped genes": 3, "Overlapped transcripts": 3, "Overlapped regulatory features": 0 } }, "custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann": { "General statistics": { "Lines of input read": 0, "Variants processed": 0, "Variants filtered out": 0, "Overlapped genes": 0, "Overlapped transcripts": 0, "Overlapped regulatory features": 0 } }, "custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann": { "Variant classes": { "insertion": 25, "deletion": 41 }, "Consequences (most severe)": { "splice_acceptor_variant": 1, "frameshift_variant": 10, "inframe_deletion": 5, "splice_region_variant": 2, "splice_polypyrimidine_tract_variant": 7, "3_prime_UTR_variant": 3, "non_coding_transcript_exon_variant": 2, "intron_variant": 35, "intergenic_variant": 1 }, "Consequences (all)": { "frameshift_variant": 10, "inframe_deletion": 5, "splice_region_variant": 2, "splice_polypyrimidine_tract_variant": 9, "3_prime_UTR_variant": 3, 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