{
  "metadata": {
    "version": "1.0",
    "mode": "variant",
    "tools": [
      "contamination",
      "ngscheckmate",
      "bcftools",
      "snpeff"
    ]
  },
  "pairs": {
    "1029_BGFD-T1-TDNA-1_23FC2GLT4_s30_vs_1029_BGFD-N1-BDNA-1_2375WFLT3_s30": {
      "tumor_sample": "1029_BGFD-T1-TDNA-1_23FC2GLT4_s30",
      "normal_sample": "1029_BGFD-N1-BDNA-1_2375WFLT3_s30",
      "contamination": {
        "normal_contamination_pct": 0.074,
        "tumor_contamination_pct": 0.166
      },
      "sample_identity": {
        "tumor_normal_correlation": 0.983,
        "matched": true
      },
      "callers": {
        "mutect2": {
          "num_snps": 8834,
          "num_indels": 4571,
          "num_mnps": 782,
          "ts_tv_ratio": 2.86,
          "substitutions": {
            "A>C": 241,
            "A>G": 779,
            "A>T": 312,
            "C>A": 334,
            "C>G": 275,
            "C>T": 2551,
            "G>A": 2555,
            "G>C": 271,
            "G>T": 358,
            "T>A": 292,
            "T>C": 751,
            "T>G": 237
          },
          "snpeff": {
            "missense_silent_ratio": 1.611593,
            "impact_high": 0,
            "impact_moderate": 0,
            "impact_low": 0,
            "impact_modifier": 0
          }
        },
        "tnseq": {
          "num_snps": 31022,
          "num_indels": 5586,
          "num_mnps": 1231,
          "ts_tv_ratio": 3.05,
          "substitutions": {
            "A>C": 834,
            "A>G": 4433,
            "A>T": 705,
            "C>A": 1011,
            "C>G": 1227,
            "C>T": 7338,
            "G>A": 7357,
            "G>C": 1281,
            "G>T": 1027,
            "T>A": 726,
            "T>C": 4338,
            "T>G": 892
          },
          "snpeff": {
            "missense_silent_ratio": 1.013185,
            "impact_high": 0,
            "impact_moderate": 0,
            "impact_low": 0,
            "impact_modifier": 0
          }
        }
      }
    }
  }
}