File Info
- Filename
- multiqc_data/multiqc_data.json
- Full Path
- s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6a/e5f9e499e2398646b31d9e6edf05fc/multiqc_data/multiqc_data.json
- Size
- 2.2 MB
- Attempt
Content
View in new tab{
"report_multiqc_command": "/opt/conda/bin/multiqc --force --config multiqc_config.yml .",
"report_data_sources": {
"Samtools Flagstat": {
"stats": {
"HCC1395_BL": "/tmp/nxf.uMOsqH3Syc/4/HCC1395_BL.stats",
"HCC1395_tumor": "/tmp/nxf.uMOsqH3Syc/3/HCC1395_tumor.stats",
"Sig_18_Blood": "/tmp/nxf.uMOsqH3Syc/5/Sig_18_Blood.stats",
"Sig_18_tissue": "/tmp/nxf.uMOsqH3Syc/10/Sig_18_tissue.stats"
}
},
"Mosdepth": {
"genome_results": {
"HCC1395_BL": "/tmp/nxf.uMOsqH3Syc/13/HCC1395_BL.mosdepth.region.dist.txt",
"HCC1395_tumor": "/tmp/nxf.uMOsqH3Syc/9/HCC1395_tumor.mosdepth.region.dist.txt",
"Sig_18_Blood": "/tmp/nxf.uMOsqH3Syc/11/Sig_18_Blood.mosdepth.region.dist.txt",
"Sig_18_tissue": "/tmp/nxf.uMOsqH3Syc/6/Sig_18_tissue.mosdepth.region.dist.txt"
}
},
"Bcftools": {
"stats": {
"HCC1395_BL": "/tmp/nxf.uMOsqH3Syc/40/HCC1395_BL.bcftools_stats.txt",
"HCC1395_BL.deconflicted_germline": "/tmp/nxf.uMOsqH3Syc/48/HCC1395_BL.deconflicted_germline.bcftools_stats.txt",
"HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv": "/tmp/nxf.uMOsqH3Syc/37/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv.bcftools_stats.txt",
"HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv": "/tmp/nxf.uMOsqH3Syc/38/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv.bcftools_stats.txt",
"HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels": "/tmp/nxf.uMOsqH3Syc/43/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels.bcftools_stats.txt",
"HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs": "/tmp/nxf.uMOsqH3Syc/44/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.bcftools_stats.txt",
"Sig_18_Blood": "/tmp/nxf.uMOsqH3Syc/39/Sig_18_Blood.bcftools_stats.txt",
"Sig_18_Blood.deconflicted_germline": "/tmp/nxf.uMOsqH3Syc/47/Sig_18_Blood.deconflicted_germline.bcftools_stats.txt",
"custom_Sig_18_tumor_normal.manta.diploid_sv": "/tmp/nxf.uMOsqH3Syc/41/custom_Sig_18_tumor_normal.manta.diploid_sv.bcftools_stats.txt",
"custom_Sig_18_tumor_normal.manta.somatic_sv": "/tmp/nxf.uMOsqH3Syc/42/custom_Sig_18_tumor_normal.manta.somatic_sv.bcftools_stats.txt",
"custom_Sig_18_tumor_normal.strelka.somatic_indels": "/tmp/nxf.uMOsqH3Syc/45/custom_Sig_18_tumor_normal.strelka.somatic_indels.bcftools_stats.txt",
"custom_Sig_18_tumor_normal.strelka.somatic_snvs": "/tmp/nxf.uMOsqH3Syc/46/custom_Sig_18_tumor_normal.strelka.somatic_snvs.bcftools_stats.txt"
}
},
"Vcftools": {
"all_sections": {
"TsTv by counts": "/tmp/nxf.uMOsqH3Syc/57/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.count",
"TsTv by quality": "/tmp/nxf.uMOsqH3Syc/69/custom_Sig_18_tumor_normal.strelka.somatic_snvs.TsTv.qual"
}
},
"SNPeff": {
"all_sections": {
"HCC1395_BL.deconflicted_germline_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/88/HCC1395_BL.deconflicted_germline_custom.ann_snpEff.csv",
"HCC1395_BL_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/19/HCC1395_BL_custom.ann_snpEff.csv",
"HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/17/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff.csv",
"HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/18/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff.csv",
"HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/25/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.csv",
"HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/27/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff.csv",
"Sig_18_Blood.deconflicted_germline_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/87/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff.csv",
"Sig_18_Blood_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/21/Sig_18_Blood_custom.ann_snpEff.csv",
"custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/20/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff.csv",
"custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/22/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff.csv",
"custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/34/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff.csv",
"custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff": "/tmp/nxf.uMOsqH3Syc/33/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff.csv"
}
},
"VEP": {
"all_sections": {
"HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/90/HCC1395_BL.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html",
"HCC1395_BL_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/28/HCC1395_BL_custom.ann_snpEff_VEP.ann.summary.html",
"HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/23/HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html",
"HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/24/HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html",
"HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/32/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html",
"HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/31/HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html",
"Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/89/Sig_18_Blood.deconflicted_germline_custom.ann_snpEff_VEP.ann.summary.html",
"Sig_18_Blood_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/30/Sig_18_Blood_custom.ann_snpEff_VEP.ann.summary.html",
"custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/29/custom_Sig_18_tumor_normal.manta.diploid_sv_custom.ann_snpEff_VEP.ann.summary.html",
"custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/26/custom_Sig_18_tumor_normal.manta.somatic_sv_custom.ann_snpEff_VEP.ann.summary.html",
"custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/36/custom_Sig_18_tumor_normal.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html",
"custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann": "/tmp/nxf.uMOsqH3Syc/35/custom_Sig_18_tumor_normal.strelka.somatic_snvs_custom.ann_snpEff_VEP.ann.summary.html"
}
}
},
"report_general_stats_data": {
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},
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},
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"HCC1395_tumor_vs_HCC1395_BL.manta.diploid_sv": {
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"HCC1395_tumor_vs_HCC1395_BL.manta.somatic_sv": {
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"splice_donor_variant": 1.0,
"splice_donor_variant_percent": 0.21322,
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"Number_of_known_variants (i.e. non-empty ID)_percent": 0.0,
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"Missense_Silent_ratio": 0.0,
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"5_prime_UTR_variant_percent": 0.724638,
"conservative_inframe_deletion": 1.0,
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"disruptive_inframe_deletion": 3.0,
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"downstream_gene_variant": 13.0,
"downstream_gene_variant_percent": 9.42029,
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"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,
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"SPLICE_SITE_REGION": 9.0,
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"UTR_5_PRIME_percent": 0.775194,
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"Transversions": 0.0,
"Ts_Tv_ratio": 0.0,
"Het": 0.0,
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},
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"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,
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"Change_rate": 197088.0,
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"MODERATE": 52.0,
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"MISSENSE": 52.0,
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"Missense_Silent_ratio": 2.166667,
"3_prime_UTR_variant": 9.0,
"3_prime_UTR_variant_percent": 2.290076,
"5_prime_UTR_premature_start_codon_gain_variant": 1.0,
"5_prime_UTR_premature_start_codon_gain_variant_percent": 0.254453,
"5_prime_UTR_variant": 4.0,
"5_prime_UTR_variant_percent": 1.017812,
"downstream_gene_variant": 33.0,
"downstream_gene_variant_percent": 8.396947,
"intergenic_region": 1.0,
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"intragenic_variant": 22.0,
"intragenic_variant_percent": 5.597964,
"intron_variant": 189.0,
"intron_variant_percent": 48.091603,
"missense_variant": 52.0,
"missense_variant_percent": 13.231552,
"non_coding_transcript_exon_variant": 5.0,
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"splice_region_variant": 12.0,
"splice_region_variant_percent": 3.053435,
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"stop_gained_percent": 0.508906,
"synonymous_variant": 24.0,
"synonymous_variant_percent": 6.10687,
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"SPLICE_SITE_REGION": 9.0,
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"UTR_5_PRIME": 5.0,
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"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": {
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"deletion": 23
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"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
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"20-30%": 0,
"30-40%": 1,
"40-50%": 0,
"50-60%": 0,
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"stop_gained": 2,
"stop_lost": 1,
"missense_variant": 62,
"splice_donor_5th_base_variant": 4,
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"non_coding_transcript_exon_variant": 23,
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"intergenic_variant": 1
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"intergenic_variant": 1
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"chr9": 1,
"chrX": 1
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