{
    "general": {
        "date": "2019-11-16 00:04:03",
        "title": "ENCSR936XTK (subsampled 1/50, chr19 and chrM Only)",
        "description": "ZNF143 ChIP-seq on human GM12878",
        "pipeline_ver": "v1.3.3",
        "pipeline_type": "tf",
        "genome": "hg38_chr19_chrM",
        "paired_end": [
            true,
            true
        ],
        "aligner": "bowtie2",
        "peak_caller": "spp",
        "ctl_paired_end": [
            true,
            true
        ]
    },
    "align": {
        "samstat": {
            "rep1": {
                "total_reads": 1384648,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 150070,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 10.8,
                "paired_reads": 1384648,
                "paired_reads_qc_failed": 0,
                "read1": 692324,
                "read1_qc_failed": 0,
                "read2": 692324,
                "read2_qc_failed": 0,
                "properly_paired_reads": 110910,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 8.0,
                "with_itself": 118268,
                "with_itself_qc_failed": 0,
                "singletons": 31802,
                "singletons_qc_failed": 0,
                "pct_singletons": 2.3,
                "diff_chroms": 0,
                "diff_chroms_qc_failed": 0
            },
            "rep2": {
                "total_reads": 1734696,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 180208,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 10.4,
                "paired_reads": 1734696,
                "paired_reads_qc_failed": 0,
                "read1": 867348,
                "read1_qc_failed": 0,
                "read2": 867348,
                "read2_qc_failed": 0,
                "properly_paired_reads": 128428,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 7.3999999999999995,
                "with_itself": 138542,
                "with_itself_qc_failed": 0,
                "singletons": 41666,
                "singletons_qc_failed": 0,
                "pct_singletons": 2.4,
                "diff_chroms": 0,
                "diff_chroms_qc_failed": 0
            },
            "ctl1": {
                "total_reads": 1135028,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 106882,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 9.4,
                "paired_reads": 1135028,
                "paired_reads_qc_failed": 0,
                "read1": 567514,
                "read1_qc_failed": 0,
                "read2": 567514,
                "read2_qc_failed": 0,
                "properly_paired_reads": 75034,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 6.6000000000000005,
                "with_itself": 79904,
                "with_itself_qc_failed": 0,
                "singletons": 26978,
                "singletons_qc_failed": 0,
                "pct_singletons": 2.4,
                "diff_chroms": 2,
                "diff_chroms_qc_failed": 0
            },
            "ctl2": {
                "total_reads": 1085984,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 107693,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 9.9,
                "paired_reads": 1085984,
                "paired_reads_qc_failed": 0,
                "read1": 542992,
                "read1_qc_failed": 0,
                "read2": 542992,
                "read2_qc_failed": 0,
                "properly_paired_reads": 75712,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 7.000000000000001,
                "with_itself": 80994,
                "with_itself_qc_failed": 0,
                "singletons": 26699,
                "singletons_qc_failed": 0,
                "pct_singletons": 2.5,
                "diff_chroms": 6,
                "diff_chroms_qc_failed": 0
            }
        },
        "dup": {
            "rep1": {
                "unpaired_reads": 0,
                "paired_reads": 28515,
                "unmapped_reads": 0,
                "unpaired_duplicate_reads": 0,
                "paired_duplicate_reads": 95,
                "paired_optical_duplicate_reads": 0,
                "pct_duplicate_reads": 0.3332
            },
            "rep2": {
                "unpaired_reads": 0,
                "paired_reads": 27068,
                "unmapped_reads": 0,
                "unpaired_duplicate_reads": 0,
                "paired_duplicate_reads": 52,
                "paired_optical_duplicate_reads": 1,
                "pct_duplicate_reads": 0.1921
            },
            "ctl1": {
                "unpaired_reads": 0,
                "paired_reads": 14825,
                "unmapped_reads": 0,
                "unpaired_duplicate_reads": 0,
                "paired_duplicate_reads": 30,
                "paired_optical_duplicate_reads": 0,
                "pct_duplicate_reads": 0.20240000000000002
            },
            "ctl2": {
                "unpaired_reads": 0,
                "paired_reads": 15944,
                "unmapped_reads": 0,
                "unpaired_duplicate_reads": 0,
                "paired_duplicate_reads": 44,
                "paired_optical_duplicate_reads": 0,
                "pct_duplicate_reads": 0.27599999999999997
            }
        },
        "nodup_samstat": {
            "rep1": {
                "total_reads": 56840,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 56840,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 100.0,
                "paired_reads": 56840,
                "paired_reads_qc_failed": 0,
                "read1": 28420,
                "read1_qc_failed": 0,
                "read2": 28420,
                "read2_qc_failed": 0,
                "properly_paired_reads": 56840,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 100.0,
                "with_itself": 56840,
                "with_itself_qc_failed": 0,
                "singletons": 0,
                "singletons_qc_failed": 0,
                "pct_singletons": 0.0,
                "diff_chroms": 0,
                "diff_chroms_qc_failed": 0
            },
            "rep2": {
                "total_reads": 54032,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 54032,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 100.0,
                "paired_reads": 54032,
                "paired_reads_qc_failed": 0,
                "read1": 27016,
                "read1_qc_failed": 0,
                "read2": 27016,
                "read2_qc_failed": 0,
                "properly_paired_reads": 54032,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 100.0,
                "with_itself": 54032,
                "with_itself_qc_failed": 0,
                "singletons": 0,
                "singletons_qc_failed": 0,
                "pct_singletons": 0.0,
                "diff_chroms": 0,
                "diff_chroms_qc_failed": 0
            },
            "ctl1": {
                "total_reads": 29590,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 29590,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 100.0,
                "paired_reads": 29590,
                "paired_reads_qc_failed": 0,
                "read1": 14795,
                "read1_qc_failed": 0,
                "read2": 14795,
                "read2_qc_failed": 0,
                "properly_paired_reads": 29590,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 100.0,
                "with_itself": 29590,
                "with_itself_qc_failed": 0,
                "singletons": 0,
                "singletons_qc_failed": 0,
                "pct_singletons": 0.0,
                "diff_chroms": 0,
                "diff_chroms_qc_failed": 0
            },
            "ctl2": {
                "total_reads": 31800,
                "total_reads_qc_failed": 0,
                "duplicate_reads": 0,
                "duplicate_reads_qc_failed": 0,
                "mapped_reads": 31800,
                "mapped_reads_qc_failed": 0,
                "pct_mapped_reads": 100.0,
                "paired_reads": 31800,
                "paired_reads_qc_failed": 0,
                "read1": 15900,
                "read1_qc_failed": 0,
                "read2": 15900,
                "read2_qc_failed": 0,
                "properly_paired_reads": 31800,
                "properly_paired_reads_qc_failed": 0,
                "pct_properly_paired_reads": 100.0,
                "with_itself": 31800,
                "with_itself_qc_failed": 0,
                "singletons": 0,
                "singletons_qc_failed": 0,
                "pct_singletons": 0.0,
                "diff_chroms": 0,
                "diff_chroms_qc_failed": 0
            }
        }
    },
    "lib_complexity": {
        "lib_complexity": {
            "rep1": {
                "total_fragments": 24079,
                "distinct_fragments": 23992,
                "positions_with_one_read": 87,
                "NRF": 0.996387,
                "PBC1": 0.996374,
                "PBC2": 274.770115
            },
            "rep2": {
                "total_fragments": 24161,
                "distinct_fragments": 24117,
                "positions_with_one_read": 42,
                "NRF": 0.998179,
                "PBC1": 0.998217,
                "PBC2": 573.190476
            },
            "ctl1": {
                "total_fragments": 8144,
                "distinct_fragments": 8133,
                "positions_with_one_read": 11,
                "NRF": 0.998649,
                "PBC1": 0.998647,
                "PBC2": 738.363636
            },
            "ctl2": {
                "total_fragments": 8473,
                "distinct_fragments": 8459,
                "positions_with_one_read": 12,
                "NRF": 0.998348,
                "PBC1": 0.998463,
                "PBC2": 703.833333
            }
        }
    },
    "replication": {
        "reproducibility": {
            "overlap": {
                "Nt": 490,
                "N1": 336,
                "N2": 301,
                "Np": 511,
                "N_opt": 511,
                "N_consv": 490,
                "opt_set": "pooled-pr1_vs_pooled-pr2",
                "consv_set": "rep1_vs_rep2",
                "rescue_ratio": 1.042857142857143,
                "self_consistency_ratio": 1.1162790697674418,
                "reproducibility": "pass"
            },
            "idr": {
                "Nt": 251,
                "N1": 189,
                "N2": 143,
                "Np": 245,
                "N_opt": 251,
                "N_consv": 251,
                "opt_set": "rep1_vs_rep2",
                "consv_set": "rep1_vs_rep2",
                "rescue_ratio": 1.0244897959183674,
                "self_consistency_ratio": 1.3216783216783217,
                "reproducibility": "pass"
            }
        },
        "num_peaks": {
            "rep1": {
                "num_peaks": 1472
            },
            "rep2": {
                "num_peaks": 1601
            }
        }
    },
    "peak_stat": {
        "peak_region_size": {
            "rep1": {
                "min_size": 99.0,
                "25_pct": 396.0,
                "50_pct": 396.0,
                "75_pct": 396.0,
                "max_size": 457.0,
                "mean": 388.5713315217391
            },
            "rep2": {
                "min_size": 96.0,
                "25_pct": 384.0,
                "50_pct": 384.0,
                "75_pct": 384.0,
                "max_size": 417.0,
                "mean": 379.30918176139915
            },
            "idr_opt": {
                "min_size": 107.0,
                "25_pct": 327.5,
                "50_pct": 400.0,
                "75_pct": 400.0,
                "max_size": 758.0,
                "mean": 362.9402390438247
            },
            "overlap_opt": {
                "min_size": 107.0,
                "25_pct": 400.0,
                "50_pct": 400.0,
                "75_pct": 400.0,
                "max_size": 758.0,
                "mean": 381.79647749510764
            }
        }
    },
    "align_enrich": {
        "xcor_score": {
            "rep1": {
                "subsampled_reads": 27129,
                "estimated_fragment_len": 215,
                "corr_estimated_fragment_len": 0.166620142702605,
                "phantom_peak": 55,
                "corr_phantom_peak": 0.07393053,
                "argmin_corr": 1500,
                "min_corr": 0.01531093,
                "NSC": 10.88243,
                "RSC": 2.581205
            },
            "rep2": {
                "subsampled_reads": 28285,
                "estimated_fragment_len": 225,
                "corr_estimated_fragment_len": 0.0995979297625024,
                "phantom_peak": 50,
                "corr_phantom_peak": 0.06487183,
                "argmin_corr": 1500,
                "min_corr": 0.01813706,
                "NSC": 5.491404,
                "RSC": 1.743046
            }
        },
        "jsd": {
            "rep1": {
                "auc": 0.027826119171271313,
                "syn_auc": 0.47970258979213914,
                "x_intercept": 0.8491125145918764,
                "syn_x_intercept": 4.6382905671585126e-20,
                "elbow_pt": 0.866698594191186,
                "syn_elbow_pt": 0.5142923552146558,
                "jsd": 0.330666797582514,
                "syn_jsd": 0.5098388146136626,
                "pct_genome_enrich": 13.976872499426303,
                "diff_enrich": 43.40936236301788,
                "ch_div": 0.49954485530929726
            },
            "rep2": {
                "auc": 0.042776133405364576,
                "syn_auc": 0.47916570150109994,
                "x_intercept": 0.816809841659433,
                "syn_x_intercept": 5.146075782684759e-19,
                "elbow_pt": 0.8367944765382581,
                "syn_elbow_pt": 0.4827296689401493,
                "jsd": 0.31422570578123565,
                "syn_jsd": 0.42480029203850417,
                "pct_genome_enrich": 17.092599798457503,
                "diff_enrich": 41.531295409999075,
                "ch_div": 0.4853099905037958
            }
        }
    },
    "peak_enrich": {
        "frac_reads_in_peaks": {
            "spp": {
                "rep1": {
                    "frip": 0.4070900774102745
                },
                "rep2": {
                    "frip": 0.3310630737340835
                },
                "rep1-pr1": {
                    "frip": 0.3794862772695285
                },
                "rep2-pr1": {
                    "frip": 0.2903464613562333
                },
                "rep1-pr2": {
                    "frip": 0.36963406052076003
                },
                "rep2-pr2": {
                    "frip": 0.2843129997038792
                },
                "pooled": {
                    "frip": 0.4070369435024172
                },
                "pooled-pr1": {
                    "frip": 0.37527960170286456
                },
                "pooled-pr2": {
                    "frip": 0.36826250090194096
                }
            },
            "overlap": {
                "rep1_vs_rep2": {
                    "frip": 0.28396709719315966
                },
                "rep1-pr1_vs_rep1-pr2": {
                    "frip": 0.30830401125967627
                },
                "rep2-pr1_vs_rep2-pr2": {
                    "frip": 0.21764880071068995
                },
                "pooled-pr1_vs_pooled-pr2": {
                    "frip": 0.28670899776318637
                }
            },
            "idr": {
                "rep1_vs_rep2": {
                    "frip": 0.24920629194025543
                },
                "rep1-pr1_vs_rep1-pr2": {
                    "frip": 0.25900774102744545
                },
                "rep2-pr1_vs_rep2-pr2": {
                    "frip": 0.16769692034350014
                },
                "pooled-pr1_vs_pooled-pr2": {
                    "frip": 0.24770906991846453
                }
            }
        }
    }
}