{
"metadata": {
"version": "1.0",
"mode": "postdedup",
"tools": [
"samtools",
"mosdepth",
"picard"
]
},
"samples": {
"filler-D0002285": {
"samtools": {
"raw_total_sequences": 475391520,
"reads_mapped": 475391520,
"reads_unmapped": 0,
"reads_properly_paired": 464889230,
"reads_duplicated": 0,
"reads_mq0": 25530792,
"bases_mapped_cigar": 67190039870,
"mismatches": 545219834,
"error_rate": 0.008114593,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 237.0,
"insert_size_std_dev": 118.1,
"properly_paired_percent": 97.8,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 15.92,
"mean_coverage_target": 680.74
},
"picard": {
"insert_size": {
"median_insert_size": 185,
"mean_insert_size": 213.394722
},
"panels": {}
}
},
"filler-D0001376": {
"samtools": {
"raw_total_sequences": 507905962,
"reads_mapped": 507905962,
"reads_unmapped": 0,
"reads_properly_paired": 455694241,
"reads_duplicated": 0,
"reads_mq0": 30314496,
"bases_mapped_cigar": 71238683377,
"mismatches": 585072152,
"error_rate": 0.008212843,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 213.4,
"insert_size_std_dev": 100.2,
"properly_paired_percent": 89.7,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 16.03,
"mean_coverage_target": 719.22
},
"picard": {
"insert_size": {
"median_insert_size": 178,
"mean_insert_size": 196.683722
},
"panels": {}
}
},
"filler-D0001776": {
"samtools": {
"raw_total_sequences": 506295480,
"reads_mapped": 506295480,
"reads_unmapped": 0,
"reads_properly_paired": 474643038,
"reads_duplicated": 0,
"reads_mq0": 31378776,
"bases_mapped_cigar": 71373602299,
"mismatches": 578451098,
"error_rate": 0.008104552,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 234.0,
"insert_size_std_dev": 120.7,
"properly_paired_percent": 93.7,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 16.71,
"mean_coverage_target": 699.97
},
"picard": {
"insert_size": {
"median_insert_size": 183,
"mean_insert_size": 208.334563
},
"panels": {}
}
},
"filler-D0000668": {
"samtools": {
"raw_total_sequences": 528051830,
"reads_mapped": 528051830,
"reads_unmapped": 0,
"reads_properly_paired": 502650272,
"reads_duplicated": 0,
"reads_mq0": 29774524,
"bases_mapped_cigar": 74057897422,
"mismatches": 621017727,
"error_rate": 0.008385571,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 232.4,
"insert_size_std_dev": 122.8,
"properly_paired_percent": 95.2,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 17.29,
"mean_coverage_target": 739.87
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 207.416741
},
"panels": {}
}
},
"filler-D0000555": {
"samtools": {
"raw_total_sequences": 551378641,
"reads_mapped": 551378641,
"reads_unmapped": 0,
"reads_properly_paired": 527641579,
"reads_duplicated": 0,
"reads_mq0": 29123376,
"bases_mapped_cigar": 78005907955,
"mismatches": 629251160,
"error_rate": 0.008066711,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 231.0,
"insert_size_std_dev": 116.2,
"properly_paired_percent": 95.7,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 18.13,
"mean_coverage_target": 793.12
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 205.746027
},
"panels": {}
}
},
"filler-D0002607": {
"samtools": {
"raw_total_sequences": 654627651,
"reads_mapped": 654627651,
"reads_unmapped": 0,
"reads_properly_paired": 637015405,
"reads_duplicated": 0,
"reads_mq0": 36099087,
"bases_mapped_cigar": 92220392132,
"mismatches": 757676544,
"error_rate": 0.008215933,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 232.5,
"insert_size_std_dev": 113.1,
"properly_paired_percent": 97.3,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 21.74,
"mean_coverage_target": 938.89
},
"picard": {
"insert_size": {
"median_insert_size": 185,
"mean_insert_size": 211.521379
},
"panels": {}
}
},
"filler-D0002686": {
"samtools": {
"raw_total_sequences": 643663140,
"reads_mapped": 643663140,
"reads_unmapped": 0,
"reads_properly_paired": 553815994,
"reads_duplicated": 0,
"reads_mq0": 38305506,
"bases_mapped_cigar": 90679809079,
"mismatches": 747301756,
"error_rate": 0.008241104,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 216.2,
"insert_size_std_dev": 103.3,
"properly_paired_percent": 86.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 20.46,
"mean_coverage_target": 913.31
},
"picard": {
"insert_size": {
"median_insert_size": 178,
"mean_insert_size": 192.887747
},
"panels": {}
}
},
"filler-D0000644": {
"samtools": {
"raw_total_sequences": 658167422,
"reads_mapped": 658167422,
"reads_unmapped": 0,
"reads_properly_paired": 598138740,
"reads_duplicated": 0,
"reads_mq0": 38849324,
"bases_mapped_cigar": 93022524376,
"mismatches": 753882721,
"error_rate": 0.008104303,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 224.2,
"insert_size_std_dev": 107.3,
"properly_paired_percent": 90.9,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 21.42,
"mean_coverage_target": 932.99
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 200.44993
},
"panels": {}
}
},
"filler-D0000674": {
"samtools": {
"raw_total_sequences": 679437170,
"reads_mapped": 679437170,
"reads_unmapped": 0,
"reads_properly_paired": 670477606,
"reads_duplicated": 0,
"reads_mq0": 35971893,
"bases_mapped_cigar": 96164418745,
"mismatches": 771067102,
"error_rate": 0.008018216,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 236.8,
"insert_size_std_dev": 112.1,
"properly_paired_percent": 98.7,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 22.93,
"mean_coverage_target": 991.11
},
"picard": {
"insert_size": {
"median_insert_size": 186,
"mean_insert_size": 216.61131
},
"panels": {}
}
},
"filler-D0000114": {
"samtools": {
"raw_total_sequences": 656701520,
"reads_mapped": 656701520,
"reads_unmapped": 0,
"reads_properly_paired": 603921256,
"reads_duplicated": 0,
"reads_mq0": 38447983,
"bases_mapped_cigar": 92944774178,
"mismatches": 760449354,
"error_rate": 0.008181733,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 224.3,
"insert_size_std_dev": 108.0,
"properly_paired_percent": 92.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 21.37,
"mean_coverage_target": 923.62
},
"picard": {
"insert_size": {
"median_insert_size": 179,
"mean_insert_size": 201.680647
},
"panels": {}
}
},
"filler-D0001324": {
"samtools": {
"raw_total_sequences": 728124092,
"reads_mapped": 728124092,
"reads_unmapped": 0,
"reads_properly_paired": 671695720,
"reads_duplicated": 0,
"reads_mq0": 41635044,
"bases_mapped_cigar": 103038634678,
"mismatches": 825858808,
"error_rate": 0.00801504,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 224.3,
"insert_size_std_dev": 106.6,
"properly_paired_percent": 92.3,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 23.74,
"mean_coverage_target": 1042.55
},
"picard": {
"insert_size": {
"median_insert_size": 180,
"mean_insert_size": 200.607948
},
"panels": {}
}
},
"filler-D0001021": {
"samtools": {
"raw_total_sequences": 749485501,
"reads_mapped": 749485501,
"reads_unmapped": 0,
"reads_properly_paired": 708659428,
"reads_duplicated": 0,
"reads_mq0": 39875142,
"bases_mapped_cigar": 106183080716,
"mismatches": 860301897,
"error_rate": 0.008102062,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 223.5,
"insert_size_std_dev": 102.2,
"properly_paired_percent": 94.6,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 24.49,
"mean_coverage_target": 1085.47
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 204.036315
},
"panels": {}
}
},
"filler-D0000548": {
"samtools": {
"raw_total_sequences": 675509885,
"reads_mapped": 675509885,
"reads_unmapped": 0,
"reads_properly_paired": 662420896,
"reads_duplicated": 0,
"reads_mq0": 36959101,
"bases_mapped_cigar": 95725610753,
"mismatches": 776891234,
"error_rate": 0.008115814,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 243.4,
"insert_size_std_dev": 124.1,
"properly_paired_percent": 98.1,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 22.89,
"mean_coverage_target": 969.8
},
"picard": {
"insert_size": {
"median_insert_size": 186,
"mean_insert_size": 217.145024
},
"panels": {}
}
},
"T18-D0003137": {
"samtools": {
"raw_total_sequences": 686403742,
"reads_mapped": 686403742,
"reads_unmapped": 0,
"reads_properly_paired": 674039901,
"reads_duplicated": 0,
"reads_mq0": 35657322,
"bases_mapped_cigar": 96529176851,
"mismatches": 805615224,
"error_rate": 0.008345821,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 236.7,
"insert_size_std_dev": 120.9,
"properly_paired_percent": 98.2,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 22.85,
"mean_coverage_target": 999.68
},
"picard": {
"insert_size": {
"median_insert_size": 184,
"mean_insert_size": 213.715985
},
"panels": {}
}
},
"filler-D0002606": {
"samtools": {
"raw_total_sequences": 797785469,
"reads_mapped": 797785469,
"reads_unmapped": 0,
"reads_properly_paired": 743093790,
"reads_duplicated": 0,
"reads_mq0": 43259956,
"bases_mapped_cigar": 112976288619,
"mismatches": 921241250,
"error_rate": 0.008154289,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 222.6,
"insert_size_std_dev": 102.0,
"properly_paired_percent": 93.1,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 26.0,
"mean_coverage_target": 1151.25
},
"picard": {
"insert_size": {
"median_insert_size": 181,
"mean_insert_size": 203.174142
},
"panels": {}
}
},
"NTC-D0002235": {
"samtools": {
"raw_total_sequences": 699654851,
"reads_mapped": 699654851,
"reads_unmapped": 0,
"reads_properly_paired": 596623459,
"reads_duplicated": 0,
"reads_mq0": 42805485,
"bases_mapped_cigar": 98724437221,
"mismatches": 804828437,
"error_rate": 0.008152272,
"average_length": 141,
"average_quality": 39.1,
"insert_size_average": 213.1,
"insert_size_std_dev": 98.4,
"properly_paired_percent": 85.3,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 22.15,
"mean_coverage_target": 988.41
},
"picard": {
"insert_size": {
"median_insert_size": 177,
"mean_insert_size": 190.918845
},
"panels": {}
}
},
"filler-D0000329": {
"samtools": {
"raw_total_sequences": 733886327,
"reads_mapped": 733886327,
"reads_unmapped": 0,
"reads_properly_paired": 686119691,
"reads_duplicated": 0,
"reads_mq0": 39277057,
"bases_mapped_cigar": 103864942846,
"mismatches": 844305375,
"error_rate": 0.008128877,
"average_length": 142,
"average_quality": 39.2,
"insert_size_average": 217.3,
"insert_size_std_dev": 97.3,
"properly_paired_percent": 93.5,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 23.65,
"mean_coverage_target": 1057.73
},
"picard": {
"insert_size": {
"median_insert_size": 178,
"mean_insert_size": 198.88582
},
"panels": {}
}
},
"T18-D0003095": {
"samtools": {
"raw_total_sequences": 758643441,
"reads_mapped": 758643441,
"reads_unmapped": 0,
"reads_properly_paired": 684165054,
"reads_duplicated": 0,
"reads_mq0": 46705456,
"bases_mapped_cigar": 107501089739,
"mismatches": 871342244,
"error_rate": 0.008105427,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 222.9,
"insert_size_std_dev": 108.4,
"properly_paired_percent": 90.2,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 24.55,
"mean_coverage_target": 1074.46
},
"picard": {
"insert_size": {
"median_insert_size": 178,
"mean_insert_size": 198.142241
},
"panels": {}
}
},
"filler-D0002463": {
"samtools": {
"raw_total_sequences": 891567379,
"reads_mapped": 891567379,
"reads_unmapped": 0,
"reads_properly_paired": 753809704,
"reads_duplicated": 0,
"reads_mq0": 50585414,
"bases_mapped_cigar": 125953528344,
"mismatches": 1023251914,
"error_rate": 0.008124043,
"average_length": 141,
"average_quality": 39.2,
"insert_size_average": 213.8,
"insert_size_std_dev": 104.7,
"properly_paired_percent": 84.5,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 28.0,
"mean_coverage_target": 1276.23
},
"picard": {
"insert_size": {
"median_insert_size": 176,
"mean_insert_size": 186.088159
},
"panels": {}
}
},
"T21-D0002994": {
"samtools": {
"raw_total_sequences": 875282824,
"reads_mapped": 875282824,
"reads_unmapped": 0,
"reads_properly_paired": 763055359,
"reads_duplicated": 0,
"reads_mq0": 51168890,
"bases_mapped_cigar": 123211183325,
"mismatches": 1015122520,
"error_rate": 0.008238883,
"average_length": 141,
"average_quality": 39.2,
"insert_size_average": 208.6,
"insert_size_std_dev": 95.4,
"properly_paired_percent": 87.2,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 27.32,
"mean_coverage_target": 1268.78
},
"picard": {
"insert_size": {
"median_insert_size": 175,
"mean_insert_size": 189.137618
},
"panels": {}
}
},
"filler-D0000822": {
"samtools": {
"raw_total_sequences": 1030417327,
"reads_mapped": 1030417327,
"reads_unmapped": 0,
"reads_properly_paired": 926869462,
"reads_duplicated": 0,
"reads_mq0": 56174950,
"bases_mapped_cigar": 146008768120,
"mismatches": 1163993491,
"error_rate": 0.007972079,
"average_length": 142,
"average_quality": 39.2,
"insert_size_average": 217.4,
"insert_size_std_dev": 100.5,
"properly_paired_percent": 90.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 33.02,
"mean_coverage_target": 1518.67
},
"picard": {
"insert_size": {
"median_insert_size": 178,
"mean_insert_size": 192.401136
},
"panels": {}
}
},
"T21-D0002837": {
"samtools": {
"raw_total_sequences": 878235959,
"reads_mapped": 878235959,
"reads_unmapped": 0,
"reads_properly_paired": 860780658,
"reads_duplicated": 0,
"reads_mq0": 47214880,
"bases_mapped_cigar": 124358042847,
"mismatches": 1004478600,
"error_rate": 0.008077311,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 239.4,
"insert_size_std_dev": 119.1,
"properly_paired_percent": 98.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 29.59,
"mean_coverage_target": 1274.43
},
"picard": {
"insert_size": {
"median_insert_size": 186,
"mean_insert_size": 214.937981
},
"panels": {}
}
},
"filler-D0001310": {
"samtools": {
"raw_total_sequences": 1079535694,
"reads_mapped": 1079535694,
"reads_unmapped": 0,
"reads_properly_paired": 1014131784,
"reads_duplicated": 0,
"reads_mq0": 59739951,
"bases_mapped_cigar": 153123747453,
"mismatches": 1199989507,
"error_rate": 0.00783673,
"average_length": 142,
"average_quality": 39.2,
"insert_size_average": 220.1,
"insert_size_std_dev": 99.4,
"properly_paired_percent": 93.9,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 34.99,
"mean_coverage_target": 1604.4
},
"picard": {
"insert_size": {
"median_insert_size": 179,
"mean_insert_size": 197.83563
},
"panels": {}
}
},
"filler-D0000192": {
"samtools": {
"raw_total_sequences": 957879344,
"reads_mapped": 957879344,
"reads_unmapped": 0,
"reads_properly_paired": 796713395,
"reads_duplicated": 0,
"reads_mq0": 56929877,
"bases_mapped_cigar": 135353001968,
"mismatches": 1077775357,
"error_rate": 0.0079627,
"average_length": 142,
"average_quality": 39.2,
"insert_size_average": 209.3,
"insert_size_std_dev": 97.5,
"properly_paired_percent": 83.2,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 29.87,
"mean_coverage_target": 1384.53
},
"picard": {
"insert_size": {
"median_insert_size": 175,
"mean_insert_size": 181.343973
},
"panels": {}
}
},
"filler-D0002199": {
"samtools": {
"raw_total_sequences": 1083367904,
"reads_mapped": 1083367904,
"reads_unmapped": 0,
"reads_properly_paired": 926824166,
"reads_duplicated": 0,
"reads_mq0": 61046691,
"bases_mapped_cigar": 152811950434,
"mismatches": 1219468667,
"error_rate": 0.007980192,
"average_length": 141,
"average_quality": 39.2,
"insert_size_average": 210.6,
"insert_size_std_dev": 97.4,
"properly_paired_percent": 85.6,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 33.98,
"mean_coverage_target": 1579.61
},
"picard": {
"insert_size": {
"median_insert_size": 176,
"mean_insert_size": 187.937785
},
"panels": {}
}
},
"T21-D0003169": {
"samtools": {
"raw_total_sequences": 1085380388,
"reads_mapped": 1085380388,
"reads_unmapped": 0,
"reads_properly_paired": 1045381665,
"reads_duplicated": 0,
"reads_mq0": 68674650,
"bases_mapped_cigar": 153718096622,
"mismatches": 1288459145,
"error_rate": 0.008381961,
"average_length": 142,
"average_quality": 39.1,
"insert_size_average": 236.5,
"insert_size_std_dev": 118.3,
"properly_paired_percent": 96.3,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 36.28,
"mean_coverage_target": 1511.84
},
"picard": {
"insert_size": {
"median_insert_size": 183,
"mean_insert_size": 210.261681
},
"panels": {}
}
},
"T13-D0003273": {
"samtools": {
"raw_total_sequences": 1075896112,
"reads_mapped": 1075896112,
"reads_unmapped": 0,
"reads_properly_paired": 1011369698,
"reads_duplicated": 0,
"reads_mq0": 54601438,
"bases_mapped_cigar": 153088806005,
"mismatches": 1195777994,
"error_rate": 0.007811009,
"average_length": 142,
"average_quality": 39.2,
"insert_size_average": 222.8,
"insert_size_std_dev": 100.9,
"properly_paired_percent": 94.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 35.13,
"mean_coverage_target": 1612.69
},
"picard": {
"insert_size": {
"median_insert_size": 180,
"mean_insert_size": 199.318571
},
"panels": {}
}
},
"filler-D0002735": {
"samtools": {
"raw_total_sequences": 1407940351,
"reads_mapped": 1407940351,
"reads_unmapped": 0,
"reads_properly_paired": 1393662338,
"reads_duplicated": 0,
"reads_mq0": 69460976,
"bases_mapped_cigar": 200885323621,
"mismatches": 1569508604,
"error_rate": 0.007812958,
"average_length": 143,
"average_quality": 39.2,
"insert_size_average": 237.5,
"insert_size_std_dev": 106.5,
"properly_paired_percent": 99.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 47.96,
"mean_coverage_target": 2134.55
},
"picard": {
"insert_size": {
"median_insert_size": 187,
"mean_insert_size": 217.696497
},
"panels": {}
}
},
"T13-D0003573": {
"samtools": {
"raw_total_sequences": 1746582148,
"reads_mapped": 1746582148,
"reads_unmapped": 0,
"reads_properly_paired": 1466910804,
"reads_duplicated": 0,
"reads_mq0": 98497352,
"bases_mapped_cigar": 245813460031,
"mismatches": 1984704312,
"error_rate": 0.008074026,
"average_length": 141,
"average_quality": 39.2,
"insert_size_average": 194.0,
"insert_size_std_dev": 78.4,
"properly_paired_percent": 84.0,
"duplication_rate": 0.0,
"mapping_rate": 1.0
},
"mosdepth": {
"mean_coverage": 52.34,
"mean_coverage_target": 2601.89
},
"picard": {
"insert_size": {
"median_insert_size": 171,
"mean_insert_size": 170.883107
},
"panels": {}
}
}
}
}