File Info

Filename
variant_qc.json
Full Path
s3://natera-rnd-pltf-dev-nextflow-data-01/users/mipeters/semiproductionize/sarek/69812fed/test_regression_recal_dev_b0193075/reports/variant_qc.json
Size
3.7 KB
Published
Feb 02, 2026 3:54 PM
{
  "metadata": {
    "version": "1.0",
    "mode": "variant",
    "tools": [
      "contamination",
      "ngscheckmate",
      "bcftools",
      "snpeff"
    ]
  },
  "pairs": {
    "1029_BG5-T1-TDNA-1_23FC2GLT4_s29_vs_1029_BG5-N1-BDNA-1_2375WFLT3_s29": {
      "tumor_sample": "1029_BG5-T1-TDNA-1_23FC2GLT4_s29",
      "normal_sample": "1029_BG5-N1-BDNA-1_2375WFLT3_s29",
      "contamination": {
        "normal_contamination_pct": 0.082,
        "tumor_contamination_pct": 0.646
      },
      "sample_identity": {
        "tumor_normal_correlation": 0.9521,
        "matched": true
      },
      "callers": {
        "mutect2": {
          "num_snps": 801,
          "num_indels": 217,
          "num_mnps": 47,
          "ts_tv_ratio": 1.94,
          "substitutions": {
            "A>C": 20,
            "A>G": 91,
            "A>T": 30,
            "C>A": 68,
            "C>G": 24,
            "C>T": 176,
            "G>A": 168,
            "G>C": 24,
            "G>T": 65,
            "T>A": 27,
            "T>C": 94,
            "T>G": 15
          },
          "snpeff": {
            "missense_silent_ratio": 2.130435,
            "impact_high": 0,
            "impact_moderate": 0,
            "impact_low": 0,
            "impact_modifier": 0
          }
        },
        "tnseq": {
          "num_snps": 20675,
          "num_indels": 784,
          "num_mnps": 406,
          "ts_tv_ratio": 2.94,
          "substitutions": {
            "A>C": 604,
            "A>G": 3524,
            "A>T": 371,
            "C>A": 749,
            "C>G": 930,
            "C>T": 4106,
            "G>A": 4274,
            "G>C": 913,
            "G>T": 711,
            "T>A": 377,
            "T>C": 3544,
            "T>G": 593
          },
          "snpeff": {
            "missense_silent_ratio": 0.90002,
            "impact_high": 0,
            "impact_moderate": 0,
            "impact_low": 0,
            "impact_modifier": 0
          }
        }
      }
    },
    "1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21_vs_1029_BBCQ-N1-BDNA-1_2375WFLT3_s21": {
      "tumor_sample": "1029_BBCQ-T1-TDNA-1_23FC2GLT4_s21",
      "normal_sample": "1029_BBCQ-N1-BDNA-1_2375WFLT3_s21",
      "contamination": {
        "normal_contamination_pct": 0.045,
        "tumor_contamination_pct": 0.518
      },
      "sample_identity": {
        "tumor_normal_correlation": 0.9521,
        "matched": true
      },
      "callers": {
        "mutect2": {
          "num_snps": 3704,
          "num_indels": 581,
          "num_mnps": 96,
          "ts_tv_ratio": 5.0,
          "substitutions": {
            "A>C": 43,
            "A>G": 133,
            "A>T": 72,
            "C>A": 146,
            "C>G": 53,
            "C>T": 1391,
            "G>A": 1426,
            "G>C": 57,
            "G>T": 151,
            "T>A": 66,
            "T>C": 138,
            "T>G": 30
          },
          "snpeff": {
            "missense_silent_ratio": 1.6128,
            "impact_high": 0,
            "impact_moderate": 0,
            "impact_low": 0,
            "impact_modifier": 0
          }
        },
        "tnseq": {
          "num_snps": 23603,
          "num_indels": 1227,
          "num_mnps": 443,
          "ts_tv_ratio": 3.22,
          "substitutions": {
            "A>C": 612,
            "A>G": 3562,
            "A>T": 457,
            "C>A": 778,
            "C>G": 913,
            "C>T": 5373,
            "G>A": 5510,
            "G>C": 1000,
            "G>T": 785,
            "T>A": 438,
            "T>C": 3572,
            "T>G": 620
          },
          "snpeff": {
            "missense_silent_ratio": 0.961299,
            "impact_high": 0,
            "impact_moderate": 0,
            "impact_low": 0,
            "impact_modifier": 0
          }
        }
      }
    }
  }
}