{
"metadata": {
"version": "1.0",
"mode": "postdedup",
"tools": [
"samtools",
"mosdepth",
"picard"
]
},
"samples": {
"54158-12t": {
"samtools": {
"raw_total_sequences": 39546396,
"reads_mapped": 39546396,
"reads_unmapped": 0,
"reads_properly_paired": 38334530,
"reads_duplicated": 0,
"reads_mq0": 2274450,
"bases_mapped_cigar": 5610163373,
"mismatches": 43908063,
"error_rate": 0.007826522,
"average_length": 142,
"average_quality": 39.2,
"insert_size_average": 296.6,
"insert_size_std_dev": 156.6,
"properly_paired_percent": 96.9,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 1.47,
"mean_coverage_target": 59.4
},
"picard": {
"insert_size": {
"median_insert_size": 226,
"mean_insert_size": 299.288388
},
"panels": {}
}
},
"54158-12_2": {
"samtools": {
"raw_total_sequences": 107839714,
"reads_mapped": 107839714,
"reads_unmapped": 0,
"reads_properly_paired": 103110706,
"reads_duplicated": 0,
"reads_mq0": 7251210,
"bases_mapped_cigar": 15285025615,
"mismatches": 123814872,
"error_rate": 0.008100403,
"average_length": 142,
"average_quality": 39.0,
"insert_size_average": 315.8,
"insert_size_std_dev": 166.7,
"properly_paired_percent": 95.6,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 4.11,
"mean_coverage_target": 148.87
},
"picard": {
"insert_size": {
"median_insert_size": 292,
"mean_insert_size": 317.588429
},
"panels": {}
}
},
"54158-06_2": {
"samtools": {
"raw_total_sequences": 254931531,
"reads_mapped": 254931531,
"reads_unmapped": 0,
"reads_properly_paired": 246897991,
"reads_duplicated": 0,
"reads_mq0": 17739639,
"bases_mapped_cigar": 36043325373,
"mismatches": 295376241,
"error_rate": 0.008195033,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 273.5,
"insert_size_std_dev": 143.5,
"properly_paired_percent": 96.8,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 9.2,
"mean_coverage_target": 338.18
},
"picard": {
"insert_size": {
"median_insert_size": 203,
"mean_insert_size": 273.559211
},
"panels": {}
}
},
"B1": {
"samtools": {
"raw_total_sequences": 276167515,
"reads_mapped": 276167515,
"reads_unmapped": 0,
"reads_properly_paired": 267882135,
"reads_duplicated": 0,
"reads_mq0": 21069131,
"bases_mapped_cigar": 38880564734,
"mismatches": 327413613,
"error_rate": 0.008421009,
"average_length": 141,
"average_quality": 39.2,
"insert_size_average": 236.1,
"insert_size_std_dev": 123.8,
"properly_paired_percent": 97.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 9.16,
"mean_coverage_target": 358.85
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 210.231741
},
"panels": {}
}
},
"54158-06": {
"samtools": {
"raw_total_sequences": 298636151,
"reads_mapped": 298636151,
"reads_unmapped": 0,
"reads_properly_paired": 289091824,
"reads_duplicated": 0,
"reads_mq0": 20710673,
"bases_mapped_cigar": 42244212173,
"mismatches": 349515519,
"error_rate": 0.00827369,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 275.5,
"insert_size_std_dev": 145.2,
"properly_paired_percent": 96.8,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 10.81,
"mean_coverage_target": 398.06
},
"picard": {
"insert_size": {
"median_insert_size": 205,
"mean_insert_size": 276.141071
},
"panels": {}
}
},
"E1": {
"samtools": {
"raw_total_sequences": 319458229,
"reads_mapped": 319458229,
"reads_unmapped": 0,
"reads_properly_paired": 309184917,
"reads_duplicated": 0,
"reads_mq0": 22614853,
"bases_mapped_cigar": 45284448221,
"mismatches": 370548888,
"error_rate": 0.008182697,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 267.2,
"insert_size_std_dev": 142.2,
"properly_paired_percent": 96.8,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 11.31,
"mean_coverage_target": 420.39
},
"picard": {
"insert_size": {
"median_insert_size": 193,
"mean_insert_size": 249.18375
},
"panels": {}
}
},
"G1": {
"samtools": {
"raw_total_sequences": 457075586,
"reads_mapped": 457075586,
"reads_unmapped": 0,
"reads_properly_paired": 447887259,
"reads_duplicated": 0,
"reads_mq0": 29269453,
"bases_mapped_cigar": 64738972075,
"mismatches": 516036235,
"error_rate": 0.007971029,
"average_length": 142,
"average_quality": 39.3,
"insert_size_average": 237.5,
"insert_size_std_dev": 116.3,
"properly_paired_percent": 98.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 15.38,
"mean_coverage_target": 632.85
},
"picard": {
"insert_size": {
"median_insert_size": 183,
"mean_insert_size": 214.701876
},
"panels": {}
}
},
"F1": {
"samtools": {
"raw_total_sequences": 463896246,
"reads_mapped": 463896246,
"reads_unmapped": 0,
"reads_properly_paired": 452889171,
"reads_duplicated": 0,
"reads_mq0": 31807632,
"bases_mapped_cigar": 65582774651,
"mismatches": 521080219,
"error_rate": 0.007945382,
"average_length": 142,
"average_quality": 39.3,
"insert_size_average": 234.1,
"insert_size_std_dev": 115.9,
"properly_paired_percent": 97.6,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 15.44,
"mean_coverage_target": 626.13
},
"picard": {
"insert_size": {
"median_insert_size": 182,
"mean_insert_size": 210.365291
},
"panels": {}
}
},
"A2": {
"samtools": {
"raw_total_sequences": 733514788,
"reads_mapped": 733514788,
"reads_unmapped": 0,
"reads_properly_paired": 718410228,
"reads_duplicated": 0,
"reads_mq0": 43249183,
"bases_mapped_cigar": 103624225625,
"mismatches": 807115158,
"error_rate": 0.007788865,
"average_length": 142,
"average_quality": 39.3,
"insert_size_average": 233.7,
"insert_size_std_dev": 115.8,
"properly_paired_percent": 97.9,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 24.41,
"mean_coverage_target": 1053.84
},
"picard": {
"insert_size": {
"median_insert_size": 183,
"mean_insert_size": 209.977551
},
"panels": {}
}
},
"52949-ND0659": {
"samtools": {
"raw_total_sequences": 528573802,
"reads_mapped": 528573802,
"reads_unmapped": 0,
"reads_properly_paired": 517266853,
"reads_duplicated": 0,
"reads_mq0": 31753363,
"bases_mapped_cigar": 74986946284,
"mismatches": 570944212,
"error_rate": 0.007613915,
"average_length": 142,
"average_quality": 39.4,
"insert_size_average": 227.8,
"insert_size_std_dev": 108.8,
"properly_paired_percent": 97.9,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 17.37,
"mean_coverage_target": 746.19
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 203.450802
},
"panels": {}
}
},
"52949-ND0659_2": {
"samtools": {
"raw_total_sequences": 534543158,
"reads_mapped": 534543158,
"reads_unmapped": 0,
"reads_properly_paired": 522363093,
"reads_duplicated": 0,
"reads_mq0": 33320609,
"bases_mapped_cigar": 75806790713,
"mismatches": 586450344,
"error_rate": 0.007736119,
"average_length": 142,
"average_quality": 39.3,
"insert_size_average": 229.7,
"insert_size_std_dev": 111.4,
"properly_paired_percent": 97.7,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 17.63,
"mean_coverage_target": 747.62
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 205.394253
},
"panels": {}
}
},
"C1": {
"samtools": {
"raw_total_sequences": 508631211,
"reads_mapped": 508631211,
"reads_unmapped": 0,
"reads_properly_paired": 456689993,
"reads_duplicated": 0,
"reads_mq0": 35903363,
"bases_mapped_cigar": 71823032553,
"mismatches": 570497578,
"error_rate": 0.007943101,
"average_length": 142,
"average_quality": 39.4,
"insert_size_average": 206.8,
"insert_size_std_dev": 94.8,
"properly_paired_percent": 89.8,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 15.8,
"mean_coverage_target": 695.56
},
"picard": {
"insert_size": {
"median_insert_size": 172,
"mean_insert_size": 179.647401
},
"panels": {}
}
},
"52944-ND01001": {
"samtools": {
"raw_total_sequences": 610631632,
"reads_mapped": 610631632,
"reads_unmapped": 0,
"reads_properly_paired": 600742473,
"reads_duplicated": 0,
"reads_mq0": 36700474,
"bases_mapped_cigar": 86718256479,
"mismatches": 662427168,
"error_rate": 0.007638843,
"average_length": 142,
"average_quality": 39.3,
"insert_size_average": 232.4,
"insert_size_std_dev": 111.5,
"properly_paired_percent": 98.4,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 20.33,
"mean_coverage_target": 868.26
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 208.553061
},
"panels": {}
}
},
"H1": {
"samtools": {
"raw_total_sequences": 597849997,
"reads_mapped": 597849997,
"reads_unmapped": 0,
"reads_properly_paired": 528897321,
"reads_duplicated": 0,
"reads_mq0": 40325652,
"bases_mapped_cigar": 84317676175,
"mismatches": 658572102,
"error_rate": 0.007810605,
"average_length": 141,
"average_quality": 39.4,
"insert_size_average": 205.0,
"insert_size_std_dev": 92.7,
"properly_paired_percent": 88.5,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 18.48,
"mean_coverage_target": 833.07
},
"picard": {
"insert_size": {
"median_insert_size": 173,
"mean_insert_size": 178.626873
},
"panels": {}
}
},
"G2": {
"samtools": {
"raw_total_sequences": 710660392,
"reads_mapped": 710660392,
"reads_unmapped": 0,
"reads_properly_paired": 664906647,
"reads_duplicated": 0,
"reads_mq0": 44283614,
"bases_mapped_cigar": 100532901105,
"mismatches": 766020393,
"error_rate": 0.007619599,
"average_length": 142,
"average_quality": 39.4,
"insert_size_average": 210.1,
"insert_size_std_dev": 93.3,
"properly_paired_percent": 93.6,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 22.39,
"mean_coverage_target": 1013.87
},
"picard": {
"insert_size": {
"median_insert_size": 175,
"mean_insert_size": 185.761838
},
"panels": {}
}
}
}
}