{ "metadata": { "version": "1.0", "mode": "postdedup", "tools": [ "samtools", "mosdepth", "picard" ] }, "samples": { "Filler-D0001886": { "samtools": { "raw_total_sequences": 135572498, "reads_mapped": 135572498, "reads_unmapped": 0, "reads_properly_paired": 130742004, "reads_duplicated": 0, "reads_mq0": 18997797, "bases_mapped_cigar": 18988698325, "mismatches": 194871483, "error_rate": 0.0102625, "average_length": 141, "average_quality": 38.8, "insert_size_average": 284.1, "insert_size_std_dev": 167.7, "properly_paired_percent": 96.4, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 4.85, "mean_coverage_target": 184.74 }, "picard": { "insert_size": { "median_insert_size": 202, "mean_insert_size": 272.517178 }, "panels": {} } }, "Filler-D0002767": { "samtools": { "raw_total_sequences": 146421452, "reads_mapped": 146421452, "reads_unmapped": 0, "reads_properly_paired": 143300467, "reads_duplicated": 0, "reads_mq0": 20669137, "bases_mapped_cigar": 20631651713, "mismatches": 202932629, "error_rate": 0.009835985, "average_length": 142, "average_quality": 39.1, "insert_size_average": 226.6, "insert_size_std_dev": 112.0, "properly_paired_percent": 97.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 4.79, "mean_coverage_target": 196.67 }, "picard": { "insert_size": { "median_insert_size": 180, "mean_insert_size": 202.172437 }, "panels": {} } }, "Filler-D0000276": { "samtools": { "raw_total_sequences": 147124299, "reads_mapped": 147124299, "reads_unmapped": 0, "reads_properly_paired": 142706630, "reads_duplicated": 0, "reads_mq0": 21475411, "bases_mapped_cigar": 20579407725, "mismatches": 205370367, "error_rate": 0.009979411, "average_length": 141, "average_quality": 38.9, "insert_size_average": 251.8, "insert_size_std_dev": 146.3, "properly_paired_percent": 97.0, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 4.97, "mean_coverage_target": 198.56 }, "picard": { "insert_size": { "median_insert_size": 186, "mean_insert_size": 220.834037 }, "panels": {} } }, "Filler-D0001618": { "samtools": { "raw_total_sequences": 147500754, "reads_mapped": 147500754, "reads_unmapped": 0, "reads_properly_paired": 142625305, "reads_duplicated": 0, "reads_mq0": 22336105, "bases_mapped_cigar": 20651045482, "mismatches": 211895985, "error_rate": 0.01026079, "average_length": 141, "average_quality": 38.8, "insert_size_average": 256.8, "insert_size_std_dev": 150.6, "properly_paired_percent": 96.7, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.04, "mean_coverage_target": 202.34 }, "picard": { "insert_size": { "median_insert_size": 187, "mean_insert_size": 226.515399 }, "panels": {} } }, "Filler-D0002301": { "samtools": { "raw_total_sequences": 154359568, "reads_mapped": 154359568, "reads_unmapped": 0, "reads_properly_paired": 149567656, "reads_duplicated": 0, "reads_mq0": 22727453, "bases_mapped_cigar": 21645578361, "mismatches": 219103027, "error_rate": 0.0101223, "average_length": 141, "average_quality": 38.9, "insert_size_average": 260.5, "insert_size_std_dev": 153.8, "properly_paired_percent": 96.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.29, "mean_coverage_target": 211.36 }, "picard": { "insert_size": { "median_insert_size": 188, "mean_insert_size": 228.78194 }, "panels": {} } }, "Filler-D0000977": { "samtools": { "raw_total_sequences": 155031616, "reads_mapped": 155031616, "reads_unmapped": 0, "reads_properly_paired": 150092882, "reads_duplicated": 0, "reads_mq0": 21370772, "bases_mapped_cigar": 21852239154, "mismatches": 215459702, "error_rate": 0.009859845, "average_length": 142, "average_quality": 38.9, "insert_size_average": 253.4, "insert_size_std_dev": 145.0, "properly_paired_percent": 96.8, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.29, "mean_coverage_target": 213.82 }, "picard": { "insert_size": { "median_insert_size": 186, "mean_insert_size": 217.228693 }, "panels": {} } }, "Filler-D0001839": { "samtools": { "raw_total_sequences": 144291741, "reads_mapped": 144291741, "reads_unmapped": 0, "reads_properly_paired": 136442030, "reads_duplicated": 0, "reads_mq0": 19734436, "bases_mapped_cigar": 20099176954, "mismatches": 215497027, "error_rate": 0.01072168, "average_length": 141, "average_quality": 38.4, "insert_size_average": 426.1, "insert_size_std_dev": 801.0, "properly_paired_percent": 94.6, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.43, "mean_coverage_target": 194.83 }, "picard": { "insert_size": { "median_insert_size": 299, "mean_insert_size": 347.166022 }, "panels": {} } }, "Filler-D0000692": { "samtools": { "raw_total_sequences": 155346790, "reads_mapped": 155346790, "reads_unmapped": 0, "reads_properly_paired": 149068217, "reads_duplicated": 0, "reads_mq0": 21640248, "bases_mapped_cigar": 21803291790, "mismatches": 220646033, "error_rate": 0.01011985, "average_length": 141, "average_quality": 38.7, "insert_size_average": 299.5, "insert_size_std_dev": 190.8, "properly_paired_percent": 96.0, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.56, "mean_coverage_target": 216.13 }, "picard": { "insert_size": { "median_insert_size": 201, "mean_insert_size": 283.864513 }, "panels": {} } }, "Filler-D0002488": { "samtools": { "raw_total_sequences": 168666682, "reads_mapped": 168666682, "reads_unmapped": 0, "reads_properly_paired": 163362774, "reads_duplicated": 0, "reads_mq0": 23160305, "bases_mapped_cigar": 23680949709, "mismatches": 238439062, "error_rate": 0.01006881, "average_length": 141, "average_quality": 38.9, "insert_size_average": 260.0, "insert_size_std_dev": 152.6, "properly_paired_percent": 96.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.79, "mean_coverage_target": 234.08 }, "picard": { "insert_size": { "median_insert_size": 188, "mean_insert_size": 229.543448 }, "panels": {} } }, "Filler-D0000939": { "samtools": { "raw_total_sequences": 160848053, "reads_mapped": 160848053, "reads_unmapped": 0, "reads_properly_paired": 154941062, "reads_duplicated": 0, "reads_mq0": 23816598, "bases_mapped_cigar": 22619462266, "mismatches": 229316807, "error_rate": 0.01013803, "average_length": 142, "average_quality": 38.7, "insert_size_average": 283.1, "insert_size_std_dev": 168.7, "properly_paired_percent": 96.3, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.73, "mean_coverage_target": 225.51 }, "picard": { "insert_size": { "median_insert_size": 198, "mean_insert_size": 261.479713 }, "panels": {} } }, "Filler-D0000941": { "samtools": { "raw_total_sequences": 181030129, "reads_mapped": 181030129, "reads_unmapped": 0, "reads_properly_paired": 175508737, "reads_duplicated": 0, "reads_mq0": 25785967, "bases_mapped_cigar": 25403668345, "mismatches": 253069773, "error_rate": 0.009961938, "average_length": 141, "average_quality": 39.0, "insert_size_average": 238.3, "insert_size_std_dev": 133.7, "properly_paired_percent": 97.0, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.98, "mean_coverage_target": 253.21 }, "picard": { "insert_size": { "median_insert_size": 180, "mean_insert_size": 205.734264 }, "panels": {} } }, "Filler-D0001395": { "samtools": { "raw_total_sequences": 176634295, "reads_mapped": 176634295, "reads_unmapped": 0, "reads_properly_paired": 172798904, "reads_duplicated": 0, "reads_mq0": 27426020, "bases_mapped_cigar": 24814739902, "mismatches": 243275070, "error_rate": 0.009803652, "average_length": 141, "average_quality": 39.0, "insert_size_average": 234.1, "insert_size_std_dev": 118.7, "properly_paired_percent": 97.8, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.87, "mean_coverage_target": 247.64 }, "picard": { "insert_size": { "median_insert_size": 183, "mean_insert_size": 208.79875 }, "panels": {} } }, "Filler-D0001916": { "samtools": { "raw_total_sequences": 174555268, "reads_mapped": 174555268, "reads_unmapped": 0, "reads_properly_paired": 168532016, "reads_duplicated": 0, "reads_mq0": 25553191, "bases_mapped_cigar": 24643197995, "mismatches": 241570684, "error_rate": 0.009802733, "average_length": 142, "average_quality": 38.9, "insert_size_average": 281.5, "insert_size_std_dev": 165.9, "properly_paired_percent": 96.5, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.23, "mean_coverage_target": 251.02 }, "picard": { "insert_size": { "median_insert_size": 197, "mean_insert_size": 254.30873 }, "panels": {} } }, "Filler-D0000950": { "samtools": { "raw_total_sequences": 180444340, "reads_mapped": 180444340, "reads_unmapped": 0, "reads_properly_paired": 175778196, "reads_duplicated": 0, "reads_mq0": 27215689, "bases_mapped_cigar": 25320757205, "mismatches": 250521179, "error_rate": 0.009893905, "average_length": 141, "average_quality": 39.0, "insert_size_average": 237.1, "insert_size_std_dev": 125.0, "properly_paired_percent": 97.4, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.02, "mean_coverage_target": 249.07 }, "picard": { "insert_size": { "median_insert_size": 182, "mean_insert_size": 210.653941 }, "panels": {} } }, "Filler-D0001802": { "samtools": { "raw_total_sequences": 172808905, "reads_mapped": 172808905, "reads_unmapped": 0, "reads_properly_paired": 167958498, "reads_duplicated": 0, "reads_mq0": 25526852, "bases_mapped_cigar": 24287184475, "mismatches": 243029183, "error_rate": 0.01000648, "average_length": 142, "average_quality": 38.9, "insert_size_average": 252.5, "insert_size_std_dev": 142.4, "properly_paired_percent": 97.2, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 5.89, "mean_coverage_target": 237.33 }, "picard": { "insert_size": { "median_insert_size": 187, "mean_insert_size": 219.410812 }, "panels": {} } }, "Filler-D0000617": { "samtools": { "raw_total_sequences": 182038111, "reads_mapped": 182038111, "reads_unmapped": 0, "reads_properly_paired": 176227016, "reads_duplicated": 0, "reads_mq0": 28708906, "bases_mapped_cigar": 25445044304, "mismatches": 254825792, "error_rate": 0.01001475, "average_length": 141, "average_quality": 38.9, "insert_size_average": 250.3, "insert_size_std_dev": 146.0, "properly_paired_percent": 96.8, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.13, "mean_coverage_target": 254.41 }, "picard": { "insert_size": { "median_insert_size": 185, "mean_insert_size": 219.589219 }, "panels": {} } }, "Filler-D0001949": { "samtools": { "raw_total_sequences": 177512355, "reads_mapped": 177512355, "reads_unmapped": 0, "reads_properly_paired": 171995121, "reads_duplicated": 0, "reads_mq0": 27358806, "bases_mapped_cigar": 24886403382, "mismatches": 252621759, "error_rate": 0.010151, "average_length": 141, "average_quality": 38.9, "insert_size_average": 258.0, "insert_size_std_dev": 147.3, "properly_paired_percent": 96.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.11, "mean_coverage_target": 246.88 }, "picard": { "insert_size": { "median_insert_size": 189, "mean_insert_size": 226.595321 }, "panels": {} } }, "Filler-D0002088": { "samtools": { "raw_total_sequences": 183521717, "reads_mapped": 183521717, "reads_unmapped": 0, "reads_properly_paired": 178424914, "reads_duplicated": 0, "reads_mq0": 28231643, "bases_mapped_cigar": 25840277808, "mismatches": 255319570, "error_rate": 0.009880682, "average_length": 142, "average_quality": 39.0, "insert_size_average": 250.4, "insert_size_std_dev": 137.7, "properly_paired_percent": 97.2, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.26, "mean_coverage_target": 259.34 }, "picard": { "insert_size": { "median_insert_size": 186, "mean_insert_size": 221.395168 }, "panels": {} } }, "Filler-D0002674": { "samtools": { "raw_total_sequences": 183552413, "reads_mapped": 183552413, "reads_unmapped": 0, "reads_properly_paired": 177301959, "reads_duplicated": 0, "reads_mq0": 27977200, "bases_mapped_cigar": 25833515249, "mismatches": 260576419, "error_rate": 0.01008676, "average_length": 142, "average_quality": 38.8, "insert_size_average": 279.8, "insert_size_std_dev": 162.0, "properly_paired_percent": 96.6, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.55, "mean_coverage_target": 259.99 }, "picard": { "insert_size": { "median_insert_size": 199, "mean_insert_size": 261.640657 }, "panels": {} } }, "Filler-D0001590": { "samtools": { "raw_total_sequences": 190415149, "reads_mapped": 190415149, "reads_unmapped": 0, "reads_properly_paired": 185501820, "reads_duplicated": 0, "reads_mq0": 30057781, "bases_mapped_cigar": 26759598051, "mismatches": 267477210, "error_rate": 0.009995562, "average_length": 142, "average_quality": 39.0, "insert_size_average": 239.9, "insert_size_std_dev": 131.1, "properly_paired_percent": 97.4, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.33, "mean_coverage_target": 264.9 }, "picard": { "insert_size": { "median_insert_size": 182, "mean_insert_size": 209.674879 }, "panels": {} } }, "Filler-D0000393": { "samtools": { "raw_total_sequences": 195903023, "reads_mapped": 195903023, "reads_unmapped": 0, "reads_properly_paired": 191348411, "reads_duplicated": 0, "reads_mq0": 29671326, "bases_mapped_cigar": 27614204990, "mismatches": 266452883, "error_rate": 0.009649123, "average_length": 142, "average_quality": 39.0, "insert_size_average": 243.2, "insert_size_std_dev": 125.6, "properly_paired_percent": 97.7, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.64, "mean_coverage_target": 279.96 }, "picard": { "insert_size": { "median_insert_size": 186, "mean_insert_size": 215.840088 }, "panels": {} } }, "Filler-D0001938": { "samtools": { "raw_total_sequences": 193833345, "reads_mapped": 193833345, "reads_unmapped": 0, "reads_properly_paired": 188481750, "reads_duplicated": 0, "reads_mq0": 27934587, "bases_mapped_cigar": 27335809327, "mismatches": 267295800, "error_rate": 0.00977823, "average_length": 142, "average_quality": 39.0, "insert_size_average": 250.0, "insert_size_std_dev": 136.7, "properly_paired_percent": 97.2, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.61, "mean_coverage_target": 277.75 }, "picard": { "insert_size": { "median_insert_size": 185, "mean_insert_size": 217.060798 }, "panels": {} } }, "Filler-D0002617": { "samtools": { "raw_total_sequences": 187251841, "reads_mapped": 187251841, "reads_unmapped": 0, "reads_properly_paired": 181334173, "reads_duplicated": 0, "reads_mq0": 27176972, "bases_mapped_cigar": 26430478806, "mismatches": 261230565, "error_rate": 0.009883686, "average_length": 142, "average_quality": 38.8, "insert_size_average": 286.3, "insert_size_std_dev": 160.1, "properly_paired_percent": 96.8, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.8, "mean_coverage_target": 272.77 }, "picard": { "insert_size": { "median_insert_size": 205, "mean_insert_size": 278.08466 }, "panels": {} } }, "Filler-D0000613": { "samtools": { "raw_total_sequences": 201577879, "reads_mapped": 201577879, "reads_unmapped": 0, "reads_properly_paired": 195742236, "reads_duplicated": 0, "reads_mq0": 27922282, "bases_mapped_cigar": 28461243075, "mismatches": 276866987, "error_rate": 0.00972786, "average_length": 142, "average_quality": 38.9, "insert_size_average": 260.4, "insert_size_std_dev": 143.0, "properly_paired_percent": 97.1, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.03, "mean_coverage_target": 292.0 }, "picard": { "insert_size": { "median_insert_size": 190, "mean_insert_size": 232.801639 }, "panels": {} } }, "Filler-D0001496": { "samtools": { "raw_total_sequences": 206211786, "reads_mapped": 206211786, "reads_unmapped": 0, "reads_properly_paired": 201075876, "reads_duplicated": 0, "reads_mq0": 31622590, "bases_mapped_cigar": 28870691385, "mismatches": 286434884, "error_rate": 0.009921303, "average_length": 141, "average_quality": 39.0, "insert_size_average": 222.9, "insert_size_std_dev": 116.9, "properly_paired_percent": 97.5, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.61, "mean_coverage_target": 288.5 }, "picard": { "insert_size": { "median_insert_size": 177, "mean_insert_size": 197.10152 }, "panels": {} } }, "Filler-D0002372": { "samtools": { "raw_total_sequences": 201160871, "reads_mapped": 201160871, "reads_unmapped": 0, "reads_properly_paired": 194829109, "reads_duplicated": 0, "reads_mq0": 33340667, "bases_mapped_cigar": 28366991978, "mismatches": 281334953, "error_rate": 0.009917687, "average_length": 142, "average_quality": 38.9, "insert_size_average": 264.1, "insert_size_std_dev": 150.8, "properly_paired_percent": 96.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.0, "mean_coverage_target": 291.32 }, "picard": { "insert_size": { "median_insert_size": 190, "mean_insert_size": 234.618836 }, "panels": {} } }, "Filler-D0001900": { "samtools": { "raw_total_sequences": 203223824, "reads_mapped": 203223824, "reads_unmapped": 0, "reads_properly_paired": 196900958, "reads_duplicated": 0, "reads_mq0": 28637624, "bases_mapped_cigar": 28727203035, "mismatches": 277486807, "error_rate": 0.009659374, "average_length": 142, "average_quality": 38.9, "insert_size_average": 277.2, "insert_size_std_dev": 156.3, "properly_paired_percent": 96.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.26, "mean_coverage_target": 299.8 }, "picard": { "insert_size": { "median_insert_size": 198, "mean_insert_size": 254.3574 }, "panels": {} } }, "Filler-D0000330": { "samtools": { "raw_total_sequences": 195947694, "reads_mapped": 195947694, "reads_unmapped": 0, "reads_properly_paired": 189839877, "reads_duplicated": 0, "reads_mq0": 34942902, "bases_mapped_cigar": 27498672179, "mismatches": 281814143, "error_rate": 0.01024828, "average_length": 141, "average_quality": 38.9, "insert_size_average": 243.9, "insert_size_std_dev": 137.3, "properly_paired_percent": 96.9, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 6.56, "mean_coverage_target": 274.46 }, "picard": { "insert_size": { "median_insert_size": 183, "mean_insert_size": 209.31564 }, "panels": {} } }, "Filler-D0000821": { "samtools": { "raw_total_sequences": 199030138, "reads_mapped": 199030138, "reads_unmapped": 0, "reads_properly_paired": 193162205, "reads_duplicated": 0, "reads_mq0": 29717493, "bases_mapped_cigar": 28168899682, "mismatches": 282867955, "error_rate": 0.01004185, "average_length": 143, "average_quality": 38.9, "insert_size_average": 264.6, "insert_size_std_dev": 144.3, "properly_paired_percent": 97.1, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.01, "mean_coverage_target": 287.76 }, "picard": { "insert_size": { "median_insert_size": 192, "mean_insert_size": 238.064694 }, "panels": {} } }, "Filler-D0002650": { "samtools": { "raw_total_sequences": 218316960, "reads_mapped": 218316960, "reads_unmapped": 0, "reads_properly_paired": 212608765, "reads_duplicated": 0, "reads_mq0": 29796894, "bases_mapped_cigar": 30922957895, "mismatches": 292761595, "error_rate": 0.009467451, "average_length": 143, "average_quality": 39.0, "insert_size_average": 254.5, "insert_size_std_dev": 135.0, "properly_paired_percent": 97.4, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.56, "mean_coverage_target": 319.82 }, "picard": { "insert_size": { "median_insert_size": 189, "mean_insert_size": 225.179686 }, "panels": {} } }, "Filler-D0000445": { "samtools": { "raw_total_sequences": 219828443, "reads_mapped": 219828443, "reads_unmapped": 0, "reads_properly_paired": 214703488, "reads_duplicated": 0, "reads_mq0": 34690617, "bases_mapped_cigar": 31088530457, "mismatches": 307832703, "error_rate": 0.00990181, "average_length": 142, "average_quality": 38.9, "insert_size_average": 248.8, "insert_size_std_dev": 129.1, "properly_paired_percent": 97.7, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.54, "mean_coverage_target": 319.41 }, "picard": { "insert_size": { "median_insert_size": 187, "mean_insert_size": 221.550453 }, "panels": {} } }, "Filler-D0001907": { "samtools": { "raw_total_sequences": 219707779, "reads_mapped": 219707779, "reads_unmapped": 0, "reads_properly_paired": 213567998, "reads_duplicated": 0, "reads_mq0": 35645197, "bases_mapped_cigar": 31092962464, "mismatches": 299360998, "error_rate": 0.009627934, "average_length": 142, "average_quality": 39.0, "insert_size_average": 250.8, "insert_size_std_dev": 135.3, "properly_paired_percent": 97.2, "duplication_rate": 0.0, "mapping_rate": 1.0 }, "mosdepth": { "mean_coverage": 7.54, "mean_coverage_target": 317.64 }, "picard": { "insert_size": { "median_insert_size": 186, "mean_insert_size": 216.708291 }, "panels": {} } } } }