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Datasets:
bryan7264
/
LEDGER

Size:
1M<n<10M
Tags:
genomics
microbiology
horizontal-gene-transfer
crispr
causal-inference
License:
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LEDGER
File size: 2,215 Bytes
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{
  "cohort": {
    "n_genomes": 120,
    "n_defense_subtypes": 163,
    "n_lineage_clusters": 50,
    "median_cluster_size": 1.0,
    "mean_chromosomal_systems": 13.208333333333334,
    "sd_chromosomal_systems": 4.636622034292734,
    "crispr_columns_found": [
      "CAS_Class1-Subtype-I-C",
      "CAS_Class1-Subtype-I-E",
      "CAS_Class1-Subtype-I-F",
      "Rst_HelicaseDUF2290"
    ],
    "frac_genomes_with_crispr": 0.5166666666666667,
    "n_exposure_covariates": 21
  },
  "testA_all_defense_load": {
    "partial_r2": 0.5269544014510156,
    "null_mean_r2": 0.4320713085651996,
    "partial_r2_excess": 0.09488309288581598,
    "pvalue": 0.14770459081836326,
    "n": 120,
    "n_covariates_used": 21
  },
  "testA_crispr_only": {
    "partial_r2": 0.6165075616763955,
    "null_mean_r2": 0.3320706409474731,
    "partial_r2_excess": 0.28443692072892246,
    "pvalue": 0.007984031936127744,
    "n": 120,
    "n_covariates_used": 21
  },
  "testB_load_vs_extrachrom_len": {
    "spearman": -0.0618653189512368,
    "pvalue": 0.5020609247195801,
    "n": 120
  },
  "testB_load_vs_extrachrom_systems": {
    "spearman": -0.13813354433360708,
    "pvalue": 0.13243690866017466,
    "n": 120
  },
  "testB_crispr_vs_extrachrom_len": {
    "spearman": 0.19120821884001532,
    "pvalue": 0.03643852052574965,
    "n": 120
  },
  "per_system": {
    "n_tested": 19,
    "n_significant_p05": 4,
    "frac_significant": 0.21052631578947367,
    "median_partial_r2": 0.45165904520189054,
    "max_partial_r2": 0.7051780095912905,
    "worst_systems": [
      {
        "system": "RloC",
        "partial_r2": 0.7051780095912905,
        "pvalue": 0.0024937655860349127
      },
      {
        "system": "Zorya_TypeI",
        "partial_r2": 0.6426652297210771,
        "pvalue": 0.0798004987531172
      },
      {
        "system": "Gabija",
        "partial_r2": 0.6293146894559207,
        "pvalue": 0.0024937655860349127
      },
      {
        "system": "N6_RM_Type_I",
        "partial_r2": 0.5825399986303417,
        "pvalue": 0.004987531172069825
      },
      {
        "system": "GmrSD_RM_Type_IV",
        "partial_r2": 0.5769292825344523,
        "pvalue": 0.014962593516209476
      }
    ]
  }
}