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"custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff": { "Number_of_variants_before_filter": 0.0, "Number_of_known_variants (i.e. non-empty ID)": 0.0, "Number_of_known_variants (i.e. non-empty ID)_percent": 0.0, "Number_of_effects": 0.0, "Genome_total_length": 63147197748.0, "Genome_effective_length": 0.0, "Change_rate": 0.0, "Missense_Silent_ratio": 0.0, "Transitions": 0.0, "Transversions": 0.0, "Ts_Tv_ratio": 0.0 }, "custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff": { "Number_of_variants_before_filter": 88.0, "Number_of_known_variants (i.e. non-empty ID)": 0.0, "Number_of_known_variants (i.e. non-empty ID)_percent": 0.0, "Number_of_effects": 129.0, "Genome_total_length": 63147197748.0, "Genome_effective_length": 46709983.0, "Change_rate": 530795.0, "HIGH": 8.0, "HIGH_percent": 6.20155, "LOW": 9.0, "LOW_percent": 6.976744, "MODERATE": 8.0, "MODERATE_percent": 6.20155, "MODIFIER": 104.0, "MODIFIER_percent": 80.620155, "Missense_Silent_ratio": 0.0, "3_prime_UTR_variant": 2.0, "3_prime_UTR_variant_percent": 1.449275, "5_prime_UTR_variant": 1.0, "5_prime_UTR_variant_percent": 0.724638, "conservative_inframe_deletion": 1.0, "conservative_inframe_deletion_percent": 0.724638, "disruptive_inframe_deletion": 3.0, "disruptive_inframe_deletion_percent": 2.173913, "disruptive_inframe_insertion": 4.0, "disruptive_inframe_insertion_percent": 2.898551, "downstream_gene_variant": 13.0, "downstream_gene_variant_percent": 9.42029, "frameshift_variant": 8.0, "frameshift_variant_percent": 5.797101, "intergenic_region": 1.0, "intergenic_region_percent": 0.724638, "intragenic_variant": 5.0, "intragenic_variant_percent": 3.623188, "intron_variant": 75.0, "intron_variant_percent": 54.347826, "non_coding_transcript_exon_variant": 3.0, "non_coding_transcript_exon_variant_percent": 2.173913, "splice_region_variant": 9.0, "splice_region_variant_percent": 6.521739, "upstream_gene_variant": 13.0, "upstream_gene_variant_percent": 9.42029, "DOWNSTREAM": 13.0, "DOWNSTREAM_percent": 10.077519, "EXON": 19.0, "EXON_percent": 14.728682, "INTERGENIC": 1.0, "INTERGENIC_percent": 0.775194, "INTRON": 66.0, "INTRON_percent": 51.162791, "SPLICE_SITE_REGION": 9.0, "SPLICE_SITE_REGION_percent": 6.976744, "TRANSCRIPT": 5.0, "TRANSCRIPT_percent": 3.875969, "UPSTREAM": 13.0, "UPSTREAM_percent": 10.077519, "UTR_3_PRIME": 2.0, "UTR_3_PRIME_percent": 1.550388, "UTR_5_PRIME": 1.0, "UTR_5_PRIME_percent": 0.775194, "Transitions": 0.0, "Transversions": 0.0, "Ts_Tv_ratio": 0.0, "Het": 0.0, "Hom": 0.0, "Missing": 88.0 }, "custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff": { "Number_of_variants_before_filter": 237.0, "Number_of_known_variants (i.e. non-empty ID)": 0.0, "Number_of_known_variants (i.e. non-empty ID)_percent": 0.0, "Number_of_effects": 381.0, "Genome_total_length": 63147197748.0, "Genome_effective_length": 46709983.0, "Change_rate": 197088.0, "HIGH": 2.0, "HIGH_percent": 0.524934, "LOW": 34.0, "LOW_percent": 8.923885, "MODERATE": 52.0, 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"splice_region_variant_percent": 3.053435, "stop_gained": 2.0, "stop_gained_percent": 0.508906, "synonymous_variant": 24.0, "synonymous_variant_percent": 6.10687, "upstream_gene_variant": 39.0, "upstream_gene_variant_percent": 9.923664, "DOWNSTREAM": 33.0, "DOWNSTREAM_percent": 8.661417, "EXON": 83.0, "EXON_percent": 21.784777, "INTERGENIC": 1.0, "INTERGENIC_percent": 0.262467, "INTRON": 180.0, "INTRON_percent": 47.244094, "SPLICE_SITE_REGION": 9.0, "SPLICE_SITE_REGION_percent": 2.362205, "TRANSCRIPT": 22.0, "TRANSCRIPT_percent": 5.774278, "UPSTREAM": 39.0, "UPSTREAM_percent": 10.23622, "UTR_3_PRIME": 9.0, "UTR_3_PRIME_percent": 2.362205, "UTR_5_PRIME": 5.0, "UTR_5_PRIME_percent": 1.312336, "Transitions": 262.0, "Transversions": 212.0, "Ts_Tv_ratio": 1.235849, "Het": 0.0, "Hom": 0.0, "Missing": 237.0 } }, "vep": { "HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann": { "Variant classes": { "insertion": 9, "deletion": 11, "SNV": 334 }, "Consequences (most severe)": { "stop_gained": 1, "frameshift_variant": 5, "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": 5, "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": 152, "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": 5, "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": 354 }, "Position in protein": { "00-10%": 27, "10-20%": 31, "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": 354, "Variants processed": 354, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 354, "Overlapped genes": 193, "Overlapped transcripts": 201, "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": { "Variant classes": { "indel": 1, "chromosome_breakpoint": 2 }, "Consequences (most severe)": { "feature_truncation": 2, "intron_variant": 1 }, "Consequences (all)": { "feature_truncation": 2, "intron_variant": 3, "upstream_gene_variant": 2 }, "Variants by chromosome": { "chr21": 3 }, "General statistics": { "Lines of input read": 3, "Variants processed": 3, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 3, "Overlapped genes": 4, "Overlapped transcripts": 4, "Overlapped regulatory features": 0 } }, "HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann": { "Variant classes": { "chromosome_breakpoint": 2 }, "Consequences (most severe)": { "feature_truncation": 2 }, "Consequences (all)": { "feature_truncation": 2, "3_prime_UTR_variant": 2, "downstream_gene_variant": 2 }, "Variants by chromosome": { "chr21": 2 }, "General statistics": { "Lines of input read": 2, "Variants processed": 2, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 2, "Overlapped genes": 2, "Overlapped transcripts": 2, "Overlapped regulatory features": 0 } }, "HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann": { "Variant classes": { "insertion": 19, "deletion": 23 }, "Consequences (most severe)": { "splice_acceptor_variant": 1, "inframe_insertion": 1, "inframe_deletion": 5, "splice_region_variant": 1, "splice_polypyrimidine_tract_variant": 5, "5_prime_UTR_variant": 2, "3_prime_UTR_variant": 2, "intron_variant": 25 }, "Consequences (all)": { "inframe_insertion": 1, "inframe_deletion": 4, "splice_region_variant": 1, "splice_polypyrimidine_tract_variant": 6, "3_prime_UTR_variant": 2, "intron_variant": 39, "non_coding_transcript_variant": 3, "upstream_gene_variant": 7, "downstream_gene_variant": 11, "regulatory_region_variant": 5 }, "Coding consequences": { "inframe_insertion": 1, "inframe_deletion": 4 }, "Variants by chromosome": { "chr21": 42 }, "Position in protein": { "00-10%": 2, "10-20%": 0, "20-30%": 0, "30-40%": 1, "40-50%": 0, "50-60%": 0, "60-70%": 0, "70-80%": 1, "80-90%": 0, "90-100%": 1 }, "General statistics": { "Lines of input read": 42, "Variants processed": 42, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 42, "Overlapped genes": 51, "Overlapped transcripts": 51, "Overlapped regulatory features": 5 } }, "HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann": { "Variant classes": { "SNV": 300 }, "Consequences (most severe)": { "splice_acceptor_variant": 1, "splice_donor_variant": 1, "stop_gained": 2, "stop_lost": 1, "missense_variant": 62, "splice_donor_5th_base_variant": 4, "splice_region_variant": 5, "splice_donor_region_variant": 2, "splice_polypyrimidine_tract_variant": 8, "synonymous_variant": 32, "5_prime_UTR_variant": 6, "3_prime_UTR_variant": 12, "non_coding_transcript_exon_variant": 23, "intron_variant": 140, "intergenic_variant": 1 }, "Consequences (all)": { "splice_acceptor_variant": 1, "splice_donor_variant": 1, "stop_gained": 1, "stop_lost": 1, "missense_variant": 56, "splice_donor_5th_base_variant": 4, "splice_region_variant": 6, "splice_donor_region_variant": 2, "splice_polypyrimidine_tract_variant": 11, "synonymous_variant": 32, "5_prime_UTR_variant": 5, "3_prime_UTR_variant": 11, "non_coding_transcript_exon_variant": 10, "intron_variant": 243, "NMD_transcript_variant": 1, "non_coding_transcript_variant": 35, "upstream_gene_variant": 59, "downstream_gene_variant": 44, "regulatory_region_variant": 18, "intergenic_variant": 1 }, "Coding consequences": { "stop_gained": 1, "stop_lost": 1, "missense_variant": 56, "synonymous_variant": 32 }, "SIFT summary": { "tolerated_low_confidence": 6, "deleterious_low_confidence": 9, "deleterious": 14, "tolerated": 27 }, "PolyPhen summary": { "probably_damaging": 4, "possibly_damaging": 5, "unknown": 17, "benign": 25 }, "Variants by chromosome": { "chr21": 300 }, "Position in protein": { "00-10%": 8, "10-20%": 8, "20-30%": 9, "30-40%": 13, "40-50%": 6, "50-60%": 13, "60-70%": 12, "70-80%": 4, "80-90%": 9, "90-100%": 8 }, "General statistics": { "Lines of input read": 300, "Variants processed": 300, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 300, "Overlapped genes": 162, "Overlapped transcripts": 169, "Overlapped regulatory features": 15 } }, "Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann": { "Variant classes": { "insertion": 12, "deletion": 14, "SNV": 369 }, "Consequences (most severe)": { "stop_gained": 2, "frameshift_variant": 7, "stop_lost": 1, "inframe_insertion": 3, "inframe_deletion": 3, "missense_variant": 150, "splice_region_variant": 4, "synonymous_variant": 128, "5_prime_UTR_variant": 8, "3_prime_UTR_variant": 15, "non_coding_transcript_exon_variant": 9, "intron_variant": 64, "intergenic_variant": 1 }, "Consequences (all)": { "stop_gained": 2, "frameshift_variant": 7, "inframe_insertion": 2, "inframe_deletion": 3, "missense_variant": 140, "splice_region_variant": 6, "synonymous_variant": 131, "5_prime_UTR_variant": 4, "3_prime_UTR_variant": 14, "non_coding_transcript_exon_variant": 18, "intron_variant": 153, "non_coding_transcript_variant": 31, "upstream_gene_variant": 73, "downstream_gene_variant": 47, "regulatory_region_variant": 28, "intergenic_variant": 1 }, "Coding consequences": { 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"Consequences (all)": { "splice_donor_variant": 1, "feature_truncation": 3, "splice_donor_5th_base_variant": 1, "5_prime_UTR_variant": 1, "3_prime_UTR_variant": 1, "intron_variant": 7, "non_coding_transcript_variant": 1, "upstream_gene_variant": 3, "downstream_gene_variant": 1 }, "Variants by chromosome": { "chr21": 6 }, "General statistics": { "Lines of input read": 6, "Variants processed": 6, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 6, "Overlapped genes": 10, "Overlapped transcripts": 10, "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": 36, "deletion": 52 }, "Consequences (most 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"90-100%": 2 }, "General statistics": { "Lines of input read": 88, "Variants processed": 88, "Variants filtered out": 0, "Novel variants": 0, "Existing variants": 88, "Overlapped genes": 81, "Overlapped transcripts": 81, "Overlapped regulatory features": 6 } }, "custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann": { "Variant classes": { "SNV": 237 }, "Consequences (most severe)": { "stop_gained": 2, "missense_variant": 53, "splice_donor_5th_base_variant": 2, "splice_region_variant": 3, "splice_donor_region_variant": 4, "splice_polypyrimidine_tract_variant": 8, "synonymous_variant": 23, "5_prime_UTR_variant": 5, "3_prime_UTR_variant": 11, "non_coding_transcript_exon_variant": 11, "intron_variant": 113, "upstream_gene_variant": 1, "intergenic_variant": 1 }, "Consequences (all)": { "stop_gained": 2, "missense_variant": 47, "splice_donor_5th_base_variant": 2, "splice_region_variant": 5, "splice_donor_region_variant": 4, "splice_polypyrimidine_tract_variant": 11, 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