## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354287.sorted.bam --OUTPUT SRX7354287.markdup.sorted.bam --METRICS_FILE SRX7354287.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Homo_sapiens_assembly38_noALT_noHLA_noDecoy_patched_ERCC92.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Oct 30 21:58:30 GMT 2023 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 21685 41160538 5723975 2350697 16207 15965682 0 0.387983 38199535 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21039032 21039032 2.0 1.340441 2549633 2549633 3.0 1.456341 589874 589874 4.0 1.495798 259210 259210 5.0 1.509231 152662 152662 6.0 1.513804 102147 102147 7.0 1.51536 73429 73429 8.0 1.51589 55738 55738 9.0 1.516071 43844 43844 10.0 1.516132 35244 35244 11.0 1.516153 29636 29636 12.0 1.51616 24396 24396 13.0 1.516163 20945 20945 14.0 1.516164 17797 17797 15.0 1.516164 15311 15311 16.0 1.516164 13520 13520 17.0 1.516164 11925 11925 18.0 1.516164 10798 10798 19.0 1.516164 9518 9518 20.0 1.516164 8684 8684 21.0 1.516164 7696 7696 22.0 1.516164 7068 7068 23.0 1.516164 6454 6454 24.0 1.516164 5850 5850 25.0 1.516164 5380 5380 26.0 1.516164 4894 4894 27.0 1.516164 4571 4571 28.0 1.516164 4181 4181 29.0 1.516164 3887 3887 30.0 1.516164 3604 3604 31.0 1.516164 3328 3328 32.0 1.516164 3108 3108 33.0 1.516164 2933 2933 34.0 1.516164 2734 2734 35.0 1.516164 2732 2732 36.0 1.516164 2403 2403 37.0 1.516164 2378 2378 38.0 1.516164 2198 2198 39.0 1.516164 2083 2083 40.0 1.516164 1984 1984 41.0 1.516164 1831 1831 42.0 1.516164 1756 1756 43.0 1.516164 1617 1617 44.0 1.516164 1605 1605 45.0 1.516164 1535 1535 46.0 1.516164 1393 1393 47.0 1.516164 1350 1350 48.0 1.516164 1299 1299 49.0 1.516164 1279 1279 50.0 1.516164 1212 1212 51.0 1.516164 1139 1139 52.0 1.516164 1035 1035 53.0 1.516164 1057 1057 54.0 1.516164 965 965 55.0 1.516164 945 945 56.0 1.516164 907 907 57.0 1.516164 865 865 58.0 1.516164 775 775 59.0 1.516164 796 796 60.0 1.516164 787 787 61.0 1.516164 757 757 62.0 1.516164 724 724 63.0 1.516164 665 665 64.0 1.516164 647 647 65.0 1.516164 611 611 66.0 1.516164 643 643 67.0 1.516164 607 607 68.0 1.516164 565 565 69.0 1.516164 561 561 70.0 1.516164 527 527 71.0 1.516164 459 459 72.0 1.516164 484 484 73.0 1.516164 486 486 74.0 1.516164 477 477 75.0 1.516164 420 420 76.0 1.516164 375 375 77.0 1.516164 397 397 78.0 1.516164 417 417 79.0 1.516164 363 363 80.0 1.516164 395 395 81.0 1.516164 368 368 82.0 1.516164 322 322 83.0 1.516164 379 379 84.0 1.516164 339 339 85.0 1.516164 329 329 86.0 1.516164 318 318 87.0 1.516164 313 313 88.0 1.516164 356 356 89.0 1.516164 323 323 90.0 1.516164 276 276 91.0 1.516164 263 263 92.0 1.516164 288 288 93.0 1.516164 261 261 94.0 1.516164 228 228 95.0 1.516164 249 249 96.0 1.516164 242 242 97.0 1.516164 242 242 98.0 1.516164 220 220 99.0 1.516164 252 252 100.0 1.516164 213 213 101.0 0 196 196 102.0 0 201 201 103.0 0 194 194 104.0 0 218 218 105.0 0 204 204 106.0 0 197 197 107.0 0 188 188 108.0 0 164 164 109.0 0 171 171 110.0 0 163 163 111.0 0 160 160 112.0 0 161 161 113.0 0 150 150 114.0 0 138 138 115.0 0 137 137 116.0 0 145 145 117.0 0 137 137 118.0 0 133 133 119.0 0 122 122 120.0 0 133 133 121.0 0 148 148 122.0 0 118 118 123.0 0 115 115 124.0 0 121 121 125.0 0 113 113 126.0 0 120 120 127.0 0 128 128 128.0 0 105 105 129.0 0 97 97 130.0 0 89 89 131.0 0 106 106 132.0 0 101 101 133.0 0 100 100 134.0 0 120 120 135.0 0 82 82 136.0 0 99 99 137.0 0 74 74 138.0 0 93 93 139.0 0 104 104 140.0 0 94 94 141.0 0 74 74 142.0 0 94 94 143.0 0 80 80 144.0 0 88 88 145.0 0 76 76 146.0 0 88 88 147.0 0 74 74 148.0 0 69 69 149.0 0 86 86 150.0 0 59 59 151.0 0 76 76 152.0 0 73 73 153.0 0 74 74 154.0 0 61 61 155.0 0 55 55 156.0 0 78 78 157.0 0 57 57 158.0 0 66 66 159.0 0 57 57 160.0 0 57 57 161.0 0 82 82 162.0 0 49 49 163.0 0 59 59 164.0 0 67 67 165.0 0 51 51 166.0 0 40 40 167.0 0 42 42 168.0 0 46 46 169.0 0 46 46 170.0 0 61 61 171.0 0 47 47 172.0 0 49 49 173.0 0 56 56 174.0 0 36 36 175.0 0 48 48 176.0 0 53 53 177.0 0 41 41 178.0 0 40 40 179.0 0 40 40 180.0 0 49 49 181.0 0 34 34 182.0 0 41 41 183.0 0 43 43 184.0 0 41 41 185.0 0 39 39 186.0 0 42 42 187.0 0 31 31 188.0 0 42 42 189.0 0 37 37 190.0 0 41 41 191.0 0 39 39 192.0 0 31 31 193.0 0 43 43 194.0 0 27 27 195.0 0 45 45 196.0 0 37 37 197.0 0 32 32 198.0 0 34 34 199.0 0 41 41 200.0 0 27 27 201.0 0 48 48 202.0 0 34 34 203.0 0 29 29 204.0 0 27 27 205.0 0 32 32 206.0 0 31 31 207.0 0 35 35 208.0 0 29 29 209.0 0 34 34 210.0 0 26 26 211.0 0 26 26 212.0 0 27 27 213.0 0 28 28 214.0 0 21 21 215.0 0 25 25 216.0 0 28 28 217.0 0 33 33 218.0 0 24 24 219.0 0 21 21 220.0 0 14 14 221.0 0 28 28 222.0 0 27 27 223.0 0 18 18 224.0 0 20 20 225.0 0 23 23 226.0 0 21 21 227.0 0 20 20 228.0 0 23 23 229.0 0 20 20 230.0 0 18 18 231.0 0 22 22 232.0 0 21 21 233.0 0 21 21 234.0 0 19 19 235.0 0 23 23 236.0 0 14 14 237.0 0 20 20 238.0 0 20 20 239.0 0 25 25 240.0 0 13 13 241.0 0 21 21 242.0 0 17 17 243.0 0 27 27 244.0 0 7 7 245.0 0 7 7 246.0 0 19 19 247.0 0 11 11 248.0 0 14 14 249.0 0 12 12 250.0 0 17 17 251.0 0 13 13 252.0 0 18 18 253.0 0 10 10 254.0 0 18 18 255.0 0 13 13 256.0 0 19 19 257.0 0 7 7 258.0 0 14 14 259.0 0 12 12 260.0 0 13 13 261.0 0 10 10 262.0 0 11 11 263.0 0 12 12 264.0 0 10 10 265.0 0 11 11 266.0 0 12 12 267.0 0 16 16 268.0 0 18 18 269.0 0 12 12 270.0 0 21 21 271.0 0 10 10 272.0 0 9 9 273.0 0 15 15 274.0 0 15 15 275.0 0 12 12 276.0 0 10 10 277.0 0 16 16 278.0 0 18 18 279.0 0 9 9 280.0 0 7 7 281.0 0 14 14 282.0 0 12 12 283.0 0 11 11 284.0 0 9 9 285.0 0 7 7 286.0 0 11 11 287.0 0 13 13 288.0 0 11 11 289.0 0 11 11 290.0 0 17 17 291.0 0 7 7 292.0 0 13 13 293.0 0 10 10 294.0 0 14 14 295.0 0 15 15 296.0 0 10 10 297.0 0 17 17 298.0 0 7 7 299.0 0 15 15 300.0 0 12 12 301.0 0 15 15 302.0 0 11 11 303.0 0 8 8 304.0 0 8 8 305.0 0 7 7 306.0 0 7 7 307.0 0 17 17 308.0 0 12 12 309.0 0 4 4 310.0 0 11 11 311.0 0 5 5 312.0 0 6 6 313.0 0 9 9 314.0 0 9 9 315.0 0 3 3 316.0 0 4 4 317.0 0 8 8 318.0 0 7 7 319.0 0 9 9 320.0 0 6 6 321.0 0 6 6 322.0 0 8 8 323.0 0 8 8 324.0 0 13 13 325.0 0 7 7 326.0 0 15 15 327.0 0 6 6 328.0 0 7 7 329.0 0 9 9 330.0 0 7 7 331.0 0 5 5 332.0 0 8 8 333.0 0 4 4 334.0 0 10 10 335.0 0 5 5 336.0 0 3 3 337.0 0 10 10 338.0 0 3 3 339.0 0 7 7 340.0 0 6 6 341.0 0 4 4 342.0 0 5 5 343.0 0 4 4 344.0 0 8 8 345.0 0 5 5 346.0 0 5 5 347.0 0 8 8 348.0 0 7 7 349.0 0 10 10 350.0 0 7 7 351.0 0 3 3 352.0 0 7 7 353.0 0 6 6 354.0 0 3 3 355.0 0 6 6 356.0 0 4 4 357.0 0 3 3 358.0 0 6 6 359.0 0 4 4 360.0 0 5 5 361.0 0 4 4 362.0 0 2 2 363.0 0 4 4 364.0 0 2 2 365.0 0 4 4 366.0 0 7 7 367.0 0 4 4 368.0 0 7 7 369.0 0 5 5 370.0 0 4 4 371.0 0 6 6 372.0 0 5 5 373.0 0 7 7 374.0 0 6 6 375.0 0 1 1 376.0 0 5 5 377.0 0 5 5 378.0 0 7 7 379.0 0 5 5 380.0 0 3 3 381.0 0 1 1 382.0 0 9 9 383.0 0 1 1 384.0 0 2 2 385.0 0 5 5 386.0 0 4 4 387.0 0 2 2 388.0 0 3 3 389.0 0 3 3 390.0 0 2 2 391.0 0 3 3 392.0 0 1 1 393.0 0 5 5 394.0 0 4 4 395.0 0 4 4 396.0 0 2 2 397.0 0 2 2 398.0 0 2 2 399.0 0 5 5 400.0 0 5 5 401.0 0 3 3 402.0 0 5 5 403.0 0 2 2 404.0 0 4 4 405.0 0 1 1 406.0 0 8 8 407.0 0 5 5 408.0 0 4 4 409.0 0 2 2 410.0 0 6 6 411.0 0 4 4 412.0 0 5 5 413.0 0 5 5 414.0 0 3 3 415.0 0 4 4 416.0 0 3 3 417.0 0 5 5 418.0 0 3 3 419.0 0 3 3 420.0 0 3 3 421.0 0 4 4 422.0 0 6 6 423.0 0 1 1 425.0 0 5 5 426.0 0 3 3 427.0 0 5 5 428.0 0 3 3 429.0 0 1 1 430.0 0 5 5 431.0 0 2 2 433.0 0 5 5 434.0 0 4 4 435.0 0 2 2 436.0 0 1 1 437.0 0 3 3 438.0 0 4 4 439.0 0 3 3 440.0 0 5 5 441.0 0 2 2 442.0 0 1 1 443.0 0 4 4 444.0 0 5 5 445.0 0 2 2 446.0 0 2 2 447.0 0 1 1 448.0 0 5 5 449.0 0 1 1 450.0 0 1 1 451.0 0 2 2 453.0 0 4 4 454.0 0 2 2 455.0 0 2 2 456.0 0 1 1 457.0 0 3 3 458.0 0 6 6 459.0 0 2 2 460.0 0 3 3 461.0 0 1 1 462.0 0 3 3 463.0 0 3 3 464.0 0 2 2 465.0 0 2 2 466.0 0 1 1 467.0 0 2 2 468.0 0 1 1 469.0 0 2 2 470.0 0 3 3 471.0 0 1 1 473.0 0 2 2 474.0 0 1 1 475.0 0 4 4 476.0 0 1 1 477.0 0 2 2 478.0 0 4 4 479.0 0 2 2 480.0 0 4 4 481.0 0 4 4 482.0 0 1 1 483.0 0 1 1 484.0 0 5 5 485.0 0 1 1 486.0 0 2 2 489.0 0 3 3 490.0 0 1 1 491.0 0 2 2 493.0 0 3 3 494.0 0 2 2 495.0 0 3 3 496.0 0 2 2 497.0 0 2 2 498.0 0 3 3 500.0 0 1 1 501.0 0 1 1 502.0 0 4 4 503.0 0 1 1 504.0 0 1 1 505.0 0 3 3 506.0 0 2 2 507.0 0 6 6 508.0 0 1 1 509.0 0 3 3 510.0 0 2 2 511.0 0 1 1 512.0 0 1 1 513.0 0 4 4 514.0 0 1 1 515.0 0 1 1 516.0 0 1 1 517.0 0 1 1 518.0 0 1 1 519.0 0 2 2 520.0 0 1 1 521.0 0 2 2 522.0 0 1 1 523.0 0 2 2 524.0 0 4 4 526.0 0 3 3 527.0 0 2 2 529.0 0 1 1 530.0 0 1 1 532.0 0 1 1 533.0 0 2 2 534.0 0 2 2 535.0 0 1 1 536.0 0 1 1 537.0 0 3 3 538.0 0 2 2 539.0 0 1 1 540.0 0 3 3 541.0 0 1 1 547.0 0 1 1 549.0 0 3 3 550.0 0 1 1 551.0 0 1 1 552.0 0 1 1 555.0 0 1 1 557.0 0 2 2 558.0 0 2 2 559.0 0 1 1 562.0 0 1 1 564.0 0 3 3 565.0 0 3 3 567.0 0 1 1 569.0 0 2 2 570.0 0 2 2 571.0 0 1 1 572.0 0 1 1 573.0 0 4 4 574.0 0 1 1 575.0 0 2 2 576.0 0 1 1 581.0 0 1 1 582.0 0 1 1 585.0 0 1 1 586.0 0 1 1 587.0 0 2 2 591.0 0 1 1 593.0 0 1 1 594.0 0 2 2 595.0 0 2 2 596.0 0 1 1 597.0 0 2 2 598.0 0 2 2 599.0 0 1 1 600.0 0 2 2 602.0 0 2 2 607.0 0 2 2 608.0 0 3 3 609.0 0 2 2 610.0 0 2 2 612.0 0 2 2 615.0 0 1 1 616.0 0 1 1 617.0 0 2 2 619.0 0 3 3 621.0 0 1 1 622.0 0 1 1 623.0 0 1 1 624.0 0 1 1 628.0 0 2 2 629.0 0 1 1 632.0 0 1 1 633.0 0 2 2 634.0 0 1 1 636.0 0 3 3 640.0 0 1 1 643.0 0 2 2 644.0 0 1 1 650.0 0 2 2 651.0 0 1 1 652.0 0 2 2 654.0 0 1 1 655.0 0 1 1 658.0 0 1 1 660.0 0 2 2 662.0 0 2 2 664.0 0 1 1 668.0 0 1 1 669.0 0 1 1 673.0 0 1 1 674.0 0 1 1 675.0 0 1 1 676.0 0 1 1 677.0 0 1 1 680.0 0 1 1 683.0 0 1 1 687.0 0 1 1 689.0 0 1 1 691.0 0 1 1 694.0 0 1 1 695.0 0 3 3 696.0 0 1 1 697.0 0 1 1 699.0 0 1 1 702.0 0 1 1 708.0 0 1 1 712.0 0 1 1 714.0 0 1 1 715.0 0 1 1 716.0 0 1 1 717.0 0 2 2 719.0 0 2 2 725.0 0 2 2 726.0 0 1 1 730.0 0 1 1 731.0 0 1 1 737.0 0 1 1 740.0 0 1 1 741.0 0 1 1 750.0 0 1 1 753.0 0 1 1 754.0 0 1 1 757.0 0 1 1 767.0 0 1 1 771.0 0 1 1 776.0 0 3 3 778.0 0 1 1 783.0 0 1 1 785.0 0 1 1 786.0 0 1 1 789.0 0 1 1 790.0 0 1 1 797.0 0 1 1 803.0 0 3 3 806.0 0 1 1 811.0 0 1 1 816.0 0 1 1 819.0 0 1 1 823.0 0 2 2 834.0 0 1 1 836.0 0 1 1 845.0 0 1 1 850.0 0 2 2 851.0 0 1 1 852.0 0 1 1 863.0 0 1 1 868.0 0 1 1 887.0 0 1 1 897.0 0 1 1 918.0 0 1 1 920.0 0 1 1 927.0 0 1 1 933.0 0 1 1 940.0 0 2 2 943.0 0 1 1 951.0 0 1 1 985.0 0 1 1 992.0 0 1 1 996.0 0 1 1 1015.0 0 1 1 1017.0 0 1 1 1020.0 0 1 1 1023.0 0 1 1 1034.0 0 1 1 1042.0 0 1 1 1046.0 0 1 1 1061.0 0 2 2 1087.0 0 1 1 1123.0 0 1 1 1183.0 0 1 1 1204.0 0 1 1 1214.0 0 1 1 1227.0 0 1 1 1262.0 0 1 1 1263.0 0 1 1 1270.0 0 1 1 1283.0 0 1 1 1286.0 0 1 1 1297.0 0 1 1 1300.0 0 1 1 1405.0 0 1 1 1517.0 0 1 1 1612.0 0 1 1 1779.0 0 1 1 1835.0 0 1 1 2001.0 0 1 1 2020.0 0 1 1 2194.0 0 1 1 2303.0 0 1 1 3622.0 0 1 1 5768.0 0 1 1