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control_metrics.json
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s3://natera-rnd-pltf-dev-s3-gitlab-results/daq/build2799527/baseline-run/63614093/reports/control_metrics.json
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Published
Jun 05, 2026 7:33 AM
[
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_abnormal_ploidy",
    "qc_value": "false"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_abnormal_ploidy_chromosomes",
    "qc_value": "NONE"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_del_dup_pass_ratio",
    "qc_value": "NA"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_del_pass_count",
    "qc_value": "1"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_dup_pass_count",
    "qc_value": "0"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_landmark_del_missed",
    "qc_value": "UGT2B17;UGT2B28"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_landmark_del_recovered_count",
    "qc_value": "0"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_landmark_del_truth_total",
    "qc_value": "2"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_qc_failed",
    "qc_value": "false"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b17_del_cn",
    "qc_value": "NA"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b17_del_filter",
    "qc_value": "NOT_CALLED"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b28_del_cn",
    "qc_value": "NA"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b28_del_filter",
    "qc_value": "NOT_CALLED"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_giab_missed_variants",
    "qc_value": "chr11:78079607:T:C;chr12:14928963:A:C;chr13:101721213:A:T;chr14:20060200:G:T;chr19:14799626:C:T;chr19:43848513:T:C;chr2:184937028:A:G;chr4:122894207:T:C;chr4:168448702:A:T;chr5:120686124:G:A;chr7:102934552:TGAA:T;chr9:94606867:C:T"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_giab_recovered_count",
    "qc_value": "0"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_giab_truth_total",
    "qc_value": "12"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_indel_count",
    "qc_value": "14"
  },
  {
    "control_type": "germline",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_snv_count",
    "qc_value": "312"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_abnormal_ploidy",
    "qc_value": "false"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_abnormal_ploidy_chromosomes",
    "qc_value": "NONE"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_del_dup_pass_ratio",
    "qc_value": "3.0000"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_del_pass_count",
    "qc_value": "3"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_dup_pass_count",
    "qc_value": "1"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_landmark_del_missed",
    "qc_value": "UGT2B17;UGT2B28"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_landmark_del_recovered_count",
    "qc_value": "0"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_landmark_del_truth_total",
    "qc_value": "2"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_qc_failed",
    "qc_value": "false"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b17_del_cn",
    "qc_value": "NA"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b17_del_filter",
    "qc_value": "NOT_CALLED"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b28_del_cn",
    "qc_value": "NA"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "cnv",
    "qc_metric_name": "germline_control_cnv_ugt2b28_del_filter",
    "qc_value": "NOT_CALLED"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_giab_missed_variants",
    "qc_value": "chr11:78079607:T:C;chr12:14928963:A:C;chr13:101721213:A:T;chr14:20060200:G:T;chr19:14799626:C:T;chr19:43848513:T:C;chr2:184937028:A:G;chr4:122894207:T:C;chr4:168448702:A:T;chr5:120686124:G:A;chr7:102934552:TGAA:T;chr9:94606867:C:T"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_giab_recovered_count",
    "qc_value": "0"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_giab_truth_total",
    "qc_value": "12"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_indel_count",
    "qc_value": "18"
  },
  {
    "control_type": "germline",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "germline_control_snv_indel_snv_count",
    "qc_value": "336"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_lci",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_max_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_mean_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_min_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_msi_status",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_uci",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "msi",
    "qc_metric_name": "negative_somatic_control_msi_total_sites",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "msi",
    "qc_metric_name": "negative_somatic_control_msi_unstable_pct",
    "qc_value": "0.00"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "msi",
    "qc_metric_name": "negative_somatic_control_msi_unstable_sites",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "negative_somatic_control_snv_indel_indel_count",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "snv_indel",
    "qc_metric_name": "negative_somatic_control_snv_indel_snv_count",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "tmb",
    "qc_metric_name": "negative_somatic_control_tmb_effective_coding_region_size",
    "qc_value": "34.15"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "tmb",
    "qc_metric_name": "negative_somatic_control_tmb_non_synonymous_count",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "HCC1395_BL",
    "variant_type": "tmb",
    "qc_metric_name": "negative_somatic_control_tmb_score",
    "qc_value": "0.0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_lci",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_max_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_mean_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_min_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_msi_status",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "mimsi",
    "qc_metric_name": "negative_somatic_control_mimsi_uci",
    "qc_value": "NA"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "msi",
    "qc_metric_name": "negative_somatic_control_msi_total_sites",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "msi",
    "qc_metric_name": "negative_somatic_control_msi_unstable_pct",
    "qc_value": "0.00"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "msi",
    "qc_metric_name": "negative_somatic_control_msi_unstable_sites",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "negative_somatic_control_snv_indel_indel_count",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "snv_indel",
    "qc_metric_name": "negative_somatic_control_snv_indel_snv_count",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "tmb",
    "qc_metric_name": "negative_somatic_control_tmb_effective_coding_region_size",
    "qc_value": "34.15"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "tmb",
    "qc_metric_name": "negative_somatic_control_tmb_non_synonymous_count",
    "qc_value": "0"
  },
  {
    "control_type": "negative_somatic",
    "sample_id": "Sig_18_Blood",
    "variant_type": "tmb",
    "qc_metric_name": "negative_somatic_control_tmb_score",
    "qc_value": "0.0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_lci",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_max_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_mean_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_min_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_msi_status",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_uci",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "msi",
    "qc_metric_name": "positive_somatic_control_msi_total_sites",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "msi",
    "qc_metric_name": "positive_somatic_control_msi_unstable_pct",
    "qc_value": "0.00"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "msi",
    "qc_metric_name": "positive_somatic_control_msi_unstable_sites",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_coa_missed_variants",
    "qc_value": "13655;163343;177678;13983;376002"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_coa_recovered_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_coa_truth_total",
    "qc_value": "5"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_indel_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_snv_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "tmb",
    "qc_metric_name": "positive_somatic_control_tmb_effective_coding_region_size",
    "qc_value": "34.15"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "tmb",
    "qc_metric_name": "positive_somatic_control_tmb_non_synonymous_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "HCC1395_tumor",
    "variant_type": "tmb",
    "qc_metric_name": "positive_somatic_control_tmb_score",
    "qc_value": "0.0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_lci",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_max_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_mean_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_min_msi_score",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_msi_status",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "mimsi",
    "qc_metric_name": "positive_somatic_control_mimsi_uci",
    "qc_value": "NA"
  },
  {
    "control_type": "positive_somatic",
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    "variant_type": "msi",
    "qc_metric_name": "positive_somatic_control_msi_total_sites",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
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    "variant_type": "msi",
    "qc_metric_name": "positive_somatic_control_msi_unstable_pct",
    "qc_value": "0.00"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "msi",
    "qc_metric_name": "positive_somatic_control_msi_unstable_sites",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_coa_missed_variants",
    "qc_value": "13655;163343;177678;13983;376002"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_coa_recovered_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_coa_truth_total",
    "qc_value": "5"
  },
  {
    "control_type": "positive_somatic",
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    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_indel_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
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    "variant_type": "snv_indel",
    "qc_metric_name": "positive_somatic_control_snv_indel_snv_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
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    "variant_type": "tmb",
    "qc_metric_name": "positive_somatic_control_tmb_effective_coding_region_size",
    "qc_value": "34.15"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "tmb",
    "qc_metric_name": "positive_somatic_control_tmb_non_synonymous_count",
    "qc_value": "0"
  },
  {
    "control_type": "positive_somatic",
    "sample_id": "Sig_18_tissue",
    "variant_type": "tmb",
    "qc_metric_name": "positive_somatic_control_tmb_score",
    "qc_value": "0.0"
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]