LEDGER / results /exclusion_audit_995.json
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{
"cohort": {
"n_genomes": 1200,
"n_defense_subtypes": 236,
"n_lineage_clusters": 184,
"median_cluster_size": 2.0,
"mean_chromosomal_systems": 12.339166666666667,
"sd_chromosomal_systems": 4.997579344598298,
"crispr_columns_found": [
"CAS_Class1-Subtype-I-C",
"CAS_Class1-Subtype-I-E",
"CAS_Class1-Subtype-I-F",
"CAS_Class1-Type-I",
"Rst_HelicaseDUF2290"
],
"frac_genomes_with_crispr": 0.5358333333333334,
"n_exposure_covariates": 21
},
"testA_all_defense_load": {
"partial_r2": 0.06686762998031304,
"null_mean_r2": 0.022745599413750803,
"partial_r2_excess": 0.044122030566562234,
"pvalue": 0.0004997501249375312,
"n": 1200,
"n_covariates_used": 21
},
"testA_crispr_only": {
"partial_r2": 0.059025287159522044,
"null_mean_r2": 0.02420408368577469,
"partial_r2_excess": 0.034821203473747356,
"pvalue": 0.0004997501249375312,
"n": 1200,
"n_covariates_used": 21
},
"testB_load_vs_extrachrom_len": {
"spearman": 0.15346876727421646,
"pvalue": 9.169772191035603e-08,
"n": 1200
},
"testB_load_vs_extrachrom_systems": {
"spearman": 0.08176611321456927,
"pvalue": 0.004593249117499305,
"n": 1200
},
"testB_crispr_vs_extrachrom_len": {
"spearman": -0.08849996099142415,
"pvalue": 0.002150958655249886,
"n": 1200
},
"per_system": {
"n_tested": 116,
"n_significant_p05_uncorrected": 73,
"n_expected_by_chance_p05": 5.800000000000001,
"n_significant_BH_q10": 79,
"frac_significant_BH_q10": 0.6810344827586207,
"median_partial_r2": 0.049194222796417164,
"max_partial_r2": 0.3668275957603121,
"worst_systems": [
{
"system": "BREX_II",
"partial_r2": 0.3668275957603121,
"pvalue": 0.0024937655860349127,
"pvalue_bh": 0.0072319201995012464
},
{
"system": "Rst_3HP",
"partial_r2": 0.32120304394733223,
"pvalue": 0.0024937655860349127,
"pvalue_bh": 0.0072319201995012464
},
{
"system": "DS-38",
"partial_r2": 0.3204451806382036,
"pvalue": 0.0024937655860349127,
"pvalue_bh": 0.0072319201995012464
},
{
"system": "pAgo_S2B",
"partial_r2": 0.2157603084681764,
"pvalue": 0.0024937655860349127,
"pvalue_bh": 0.0072319201995012464
},
{
"system": "BstA",
"partial_r2": 0.17701550672550082,
"pvalue": 0.0024937655860349127,
"pvalue_bh": 0.0072319201995012464
},
{
"system": "RnlAB",
"partial_r2": 0.15109916332945839,
"pvalue": 0.004987531172069825,
"pvalue_bh": 0.012309651403406376
}
]
}
}