## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354374.sorted.bam --OUTPUT SRX7354374.markdup.sorted.bam --METRICS_FILE SRX7354374.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 23:46:57 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 56881 52702661 6763585 5949749 44669 22737597 0 0.431623 41833350 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 22904567 22904567 2.0 1.283704 4597786 4597786 3.0 1.364192 1103834 1103834 4.0 1.387027 399374 399374 5.0 1.393505 206868 206868 6.0 1.395343 131791 131791 7.0 1.395864 93312 93312 8.0 1.396012 69082 69082 9.0 1.396054 54050 54050 10.0 1.396066 43163 43163 11.0 1.396069 35364 35364 12.0 1.39607 29626 29626 13.0 1.396071 25165 25165 14.0 1.396071 21324 21324 15.0 1.396071 18639 18639 16.0 1.396071 16481 16481 17.0 1.396071 14488 14488 18.0 1.396071 12867 12867 19.0 1.396071 11516 11516 20.0 1.396071 10446 10446 21.0 1.396071 9453 9453 22.0 1.396071 8721 8721 23.0 1.396071 7780 7780 24.0 1.396071 7143 7143 25.0 1.396071 6588 6588 26.0 1.396071 6044 6044 27.0 1.396071 5520 5520 28.0 1.396071 5080 5080 29.0 1.396071 4851 4851 30.0 1.396071 4449 4449 31.0 1.396071 4273 4273 32.0 1.396071 3995 3995 33.0 1.396071 3650 3650 34.0 1.396071 3285 3285 35.0 1.396071 3255 3255 36.0 1.396071 3098 3098 37.0 1.396071 2818 2818 38.0 1.396071 2637 2637 39.0 1.396071 2609 2609 40.0 1.396071 2387 2387 41.0 1.396071 2317 2317 42.0 1.396071 2189 2189 43.0 1.396071 2091 2091 44.0 1.396071 1921 1921 45.0 1.396071 1913 1913 46.0 1.396071 1850 1850 47.0 1.396071 1728 1728 48.0 1.396071 1618 1618 49.0 1.396071 1558 1558 50.0 1.396071 1367 1367 51.0 1.396071 1437 1437 52.0 1.396071 1358 1358 53.0 1.396071 1246 1246 54.0 1.396071 1230 1230 55.0 1.396071 1146 1146 56.0 1.396071 1114 1114 57.0 1.396071 1090 1090 58.0 1.396071 1067 1067 59.0 1.396071 1054 1054 60.0 1.396071 943 943 61.0 1.396071 922 922 62.0 1.396071 893 893 63.0 1.396071 857 857 64.0 1.396071 813 813 65.0 1.396071 822 822 66.0 1.396071 813 813 67.0 1.396071 724 724 68.0 1.396071 711 711 69.0 1.396071 724 724 70.0 1.396071 652 652 71.0 1.396071 652 652 72.0 1.396071 619 619 73.0 1.396071 619 619 74.0 1.396071 591 591 75.0 1.396071 569 569 76.0 1.396071 572 572 77.0 1.396071 530 530 78.0 1.396071 553 553 79.0 1.396071 515 515 80.0 1.396071 491 491 81.0 1.396071 491 491 82.0 1.396071 484 484 83.0 1.396071 487 487 84.0 1.396071 473 473 85.0 1.396071 432 432 86.0 1.396071 400 400 87.0 1.396071 363 363 88.0 1.396071 388 388 89.0 1.396071 428 428 90.0 1.396071 379 379 91.0 1.396071 326 326 92.0 1.396071 340 340 93.0 1.396071 335 335 94.0 1.396071 323 323 95.0 1.396071 335 335 96.0 1.396071 343 343 97.0 1.396071 311 311 98.0 1.396071 315 315 99.0 1.396071 300 300 100.0 1.396071 292 292 101.0 0 284 284 102.0 0 272 272 103.0 0 255 255 104.0 0 249 249 105.0 0 253 253 106.0 0 255 255 107.0 0 235 235 108.0 0 225 225 109.0 0 239 239 110.0 0 229 229 111.0 0 196 196 112.0 0 212 212 113.0 0 221 221 114.0 0 198 198 115.0 0 171 171 116.0 0 207 207 117.0 0 212 212 118.0 0 180 180 119.0 0 176 176 120.0 0 178 178 121.0 0 172 172 122.0 0 156 156 123.0 0 147 147 124.0 0 172 172 125.0 0 157 157 126.0 0 149 149 127.0 0 145 145 128.0 0 182 182 129.0 0 132 132 130.0 0 145 145 131.0 0 158 158 132.0 0 149 149 133.0 0 137 137 134.0 0 128 128 135.0 0 131 131 136.0 0 136 136 137.0 0 124 124 138.0 0 131 131 139.0 0 124 124 140.0 0 128 128 141.0 0 105 105 142.0 0 100 100 143.0 0 115 115 144.0 0 116 116 145.0 0 102 102 146.0 0 128 128 147.0 0 97 97 148.0 0 113 113 149.0 0 111 111 150.0 0 104 104 151.0 0 86 86 152.0 0 107 107 153.0 0 89 89 154.0 0 91 91 155.0 0 85 85 156.0 0 90 90 157.0 0 96 96 158.0 0 82 82 159.0 0 79 79 160.0 0 93 93 161.0 0 91 91 162.0 0 78 78 163.0 0 80 80 164.0 0 82 82 165.0 0 88 88 166.0 0 68 68 167.0 0 68 68 168.0 0 70 70 169.0 0 90 90 170.0 0 67 67 171.0 0 86 86 172.0 0 69 69 173.0 0 73 73 174.0 0 81 81 175.0 0 74 74 176.0 0 72 72 177.0 0 57 57 178.0 0 61 61 179.0 0 68 68 180.0 0 75 75 181.0 0 63 63 182.0 0 74 74 183.0 0 52 52 184.0 0 62 62 185.0 0 58 58 186.0 0 54 54 187.0 0 57 57 188.0 0 54 54 189.0 0 48 48 190.0 0 44 44 191.0 0 52 52 192.0 0 60 60 193.0 0 40 40 194.0 0 48 48 195.0 0 45 45 196.0 0 51 51 197.0 0 51 51 198.0 0 42 42 199.0 0 46 46 200.0 0 53 53 201.0 0 37 37 202.0 0 50 50 203.0 0 52 52 204.0 0 41 41 205.0 0 49 49 206.0 0 38 38 207.0 0 47 47 208.0 0 30 30 209.0 0 29 29 210.0 0 28 28 211.0 0 46 46 212.0 0 40 40 213.0 0 39 39 214.0 0 39 39 215.0 0 32 32 216.0 0 39 39 217.0 0 25 25 218.0 0 40 40 219.0 0 26 26 220.0 0 31 31 221.0 0 31 31 222.0 0 29 29 223.0 0 36 36 224.0 0 39 39 225.0 0 36 36 226.0 0 24 24 227.0 0 29 29 228.0 0 25 25 229.0 0 29 29 230.0 0 33 33 231.0 0 29 29 232.0 0 42 42 233.0 0 29 29 234.0 0 30 30 235.0 0 37 37 236.0 0 28 28 237.0 0 23 23 238.0 0 19 19 239.0 0 33 33 240.0 0 28 28 241.0 0 33 33 242.0 0 21 21 243.0 0 32 32 244.0 0 29 29 245.0 0 30 30 246.0 0 30 30 247.0 0 22 22 248.0 0 22 22 249.0 0 20 20 250.0 0 21 21 251.0 0 26 26 252.0 0 11 11 253.0 0 19 19 254.0 0 17 17 255.0 0 28 28 256.0 0 29 29 257.0 0 23 23 258.0 0 31 31 259.0 0 15 15 260.0 0 22 22 261.0 0 16 16 262.0 0 20 20 263.0 0 24 24 264.0 0 27 27 265.0 0 25 25 266.0 0 28 28 267.0 0 25 25 268.0 0 19 19 269.0 0 19 19 270.0 0 25 25 271.0 0 11 11 272.0 0 23 23 273.0 0 18 18 274.0 0 19 19 275.0 0 20 20 276.0 0 12 12 277.0 0 11 11 278.0 0 22 22 279.0 0 14 14 280.0 0 20 20 281.0 0 19 19 282.0 0 14 14 283.0 0 19 19 284.0 0 17 17 285.0 0 13 13 286.0 0 10 10 287.0 0 14 14 288.0 0 11 11 289.0 0 13 13 290.0 0 18 18 291.0 0 24 24 292.0 0 21 21 293.0 0 16 16 294.0 0 14 14 295.0 0 10 10 296.0 0 16 16 297.0 0 15 15 298.0 0 8 8 299.0 0 7 7 300.0 0 15 15 301.0 0 19 19 302.0 0 12 12 303.0 0 11 11 304.0 0 8 8 305.0 0 13 13 306.0 0 18 18 307.0 0 14 14 308.0 0 14 14 309.0 0 13 13 310.0 0 17 17 311.0 0 14 14 312.0 0 11 11 313.0 0 13 13 314.0 0 9 9 315.0 0 15 15 316.0 0 13 13 317.0 0 18 18 318.0 0 12 12 319.0 0 10 10 320.0 0 16 16 321.0 0 14 14 322.0 0 11 11 323.0 0 17 17 324.0 0 9 9 325.0 0 6 6 326.0 0 10 10 327.0 0 13 13 328.0 0 6 6 329.0 0 11 11 330.0 0 5 5 331.0 0 9 9 332.0 0 11 11 333.0 0 6 6 334.0 0 10 10 335.0 0 7 7 336.0 0 8 8 337.0 0 15 15 338.0 0 11 11 339.0 0 10 10 340.0 0 12 12 341.0 0 10 10 342.0 0 11 11 343.0 0 11 11 344.0 0 16 16 345.0 0 12 12 346.0 0 9 9 347.0 0 10 10 348.0 0 8 8 349.0 0 9 9 350.0 0 4 4 351.0 0 7 7 352.0 0 9 9 353.0 0 14 14 354.0 0 9 9 355.0 0 10 10 356.0 0 7 7 357.0 0 9 9 358.0 0 10 10 359.0 0 9 9 360.0 0 9 9 361.0 0 7 7 362.0 0 12 12 363.0 0 11 11 364.0 0 8 8 365.0 0 9 9 366.0 0 3 3 367.0 0 4 4 368.0 0 4 4 369.0 0 11 11 370.0 0 14 14 371.0 0 8 8 372.0 0 6 6 373.0 0 4 4 375.0 0 7 7 376.0 0 7 7 377.0 0 9 9 378.0 0 8 8 379.0 0 5 5 380.0 0 6 6 381.0 0 10 10 382.0 0 5 5 383.0 0 8 8 384.0 0 7 7 385.0 0 5 5 386.0 0 5 5 387.0 0 4 4 388.0 0 5 5 389.0 0 10 10 390.0 0 9 9 391.0 0 6 6 392.0 0 4 4 393.0 0 5 5 394.0 0 11 11 395.0 0 5 5 396.0 0 9 9 397.0 0 9 9 398.0 0 7 7 399.0 0 5 5 400.0 0 10 10 401.0 0 6 6 402.0 0 10 10 403.0 0 6 6 404.0 0 5 5 405.0 0 6 6 406.0 0 5 5 407.0 0 3 3 408.0 0 3 3 409.0 0 2 2 410.0 0 8 8 411.0 0 8 8 412.0 0 6 6 413.0 0 5 5 414.0 0 7 7 415.0 0 5 5 416.0 0 5 5 417.0 0 4 4 418.0 0 6 6 419.0 0 4 4 420.0 0 2 2 422.0 0 4 4 423.0 0 4 4 424.0 0 2 2 425.0 0 5 5 426.0 0 5 5 427.0 0 7 7 428.0 0 10 10 429.0 0 3 3 430.0 0 7 7 431.0 0 4 4 432.0 0 6 6 433.0 0 4 4 434.0 0 4 4 435.0 0 1 1 436.0 0 4 4 437.0 0 5 5 438.0 0 4 4 439.0 0 4 4 440.0 0 4 4 441.0 0 2 2 442.0 0 3 3 443.0 0 1 1 444.0 0 1 1 445.0 0 2 2 446.0 0 5 5 447.0 0 5 5 448.0 0 3 3 449.0 0 4 4 450.0 0 4 4 451.0 0 5 5 452.0 0 4 4 453.0 0 6 6 454.0 0 3 3 455.0 0 3 3 456.0 0 5 5 457.0 0 2 2 458.0 0 2 2 459.0 0 4 4 460.0 0 6 6 461.0 0 2 2 462.0 0 2 2 463.0 0 2 2 464.0 0 5 5 465.0 0 5 5 466.0 0 6 6 467.0 0 1 1 468.0 0 1 1 469.0 0 1 1 470.0 0 8 8 471.0 0 1 1 472.0 0 2 2 473.0 0 2 2 474.0 0 7 7 475.0 0 3 3 476.0 0 2 2 477.0 0 2 2 478.0 0 6 6 479.0 0 3 3 480.0 0 2 2 481.0 0 4 4 482.0 0 4 4 483.0 0 4 4 484.0 0 3 3 485.0 0 3 3 486.0 0 4 4 487.0 0 2 2 488.0 0 3 3 489.0 0 4 4 490.0 0 1 1 493.0 0 5 5 494.0 0 2 2 495.0 0 7 7 497.0 0 3 3 499.0 0 2 2 500.0 0 4 4 501.0 0 2 2 502.0 0 2 2 503.0 0 1 1 504.0 0 8 8 505.0 0 2 2 506.0 0 3 3 507.0 0 1 1 508.0 0 5 5 509.0 0 1 1 510.0 0 4 4 511.0 0 4 4 512.0 0 5 5 513.0 0 3 3 514.0 0 4 4 515.0 0 4 4 516.0 0 2 2 517.0 0 2 2 518.0 0 2 2 519.0 0 2 2 520.0 0 4 4 521.0 0 2 2 522.0 0 2 2 523.0 0 2 2 525.0 0 1 1 526.0 0 3 3 527.0 0 4 4 528.0 0 2 2 529.0 0 1 1 530.0 0 3 3 531.0 0 7 7 532.0 0 3 3 533.0 0 2 2 534.0 0 1 1 535.0 0 2 2 536.0 0 3 3 537.0 0 1 1 538.0 0 5 5 539.0 0 3 3 540.0 0 4 4 541.0 0 3 3 542.0 0 2 2 543.0 0 1 1 544.0 0 2 2 545.0 0 3 3 546.0 0 1 1 547.0 0 1 1 548.0 0 2 2 549.0 0 7 7 550.0 0 1 1 551.0 0 1 1 552.0 0 1 1 553.0 0 3 3 554.0 0 2 2 555.0 0 3 3 556.0 0 3 3 557.0 0 1 1 558.0 0 4 4 559.0 0 2 2 560.0 0 1 1 561.0 0 4 4 562.0 0 2 2 564.0 0 1 1 565.0 0 6 6 566.0 0 2 2 567.0 0 1 1 568.0 0 1 1 569.0 0 2 2 570.0 0 3 3 571.0 0 2 2 573.0 0 1 1 574.0 0 2 2 575.0 0 2 2 576.0 0 5 5 577.0 0 3 3 579.0 0 2 2 580.0 0 2 2 581.0 0 2 2 584.0 0 2 2 586.0 0 4 4 587.0 0 2 2 589.0 0 3 3 590.0 0 3 3 592.0 0 4 4 593.0 0 1 1 594.0 0 2 2 596.0 0 1 1 598.0 0 4 4 600.0 0 4 4 601.0 0 5 5 602.0 0 1 1 603.0 0 1 1 606.0 0 2 2 607.0 0 1 1 608.0 0 1 1 610.0 0 2 2 611.0 0 2 2 612.0 0 4 4 613.0 0 2 2 614.0 0 2 2 615.0 0 4 4 616.0 0 3 3 617.0 0 1 1 618.0 0 1 1 620.0 0 1 1 621.0 0 1 1 623.0 0 1 1 624.0 0 2 2 626.0 0 3 3 627.0 0 1 1 628.0 0 1 1 629.0 0 1 1 630.0 0 1 1 631.0 0 1 1 635.0 0 1 1 638.0 0 2 2 639.0 0 2 2 640.0 0 3 3 642.0 0 2 2 643.0 0 2 2 644.0 0 1 1 645.0 0 1 1 646.0 0 1 1 647.0 0 2 2 648.0 0 1 1 649.0 0 2 2 650.0 0 1 1 651.0 0 4 4 653.0 0 3 3 654.0 0 2 2 655.0 0 2 2 656.0 0 1 1 658.0 0 1 1 660.0 0 1 1 661.0 0 4 4 663.0 0 2 2 666.0 0 1 1 670.0 0 1 1 671.0 0 1 1 672.0 0 3 3 673.0 0 1 1 674.0 0 1 1 675.0 0 2 2 676.0 0 1 1 678.0 0 2 2 680.0 0 1 1 681.0 0 1 1 684.0 0 2 2 685.0 0 1 1 687.0 0 1 1 688.0 0 1 1 689.0 0 1 1 691.0 0 2 2 695.0 0 2 2 696.0 0 1 1 697.0 0 1 1 699.0 0 2 2 701.0 0 1 1 703.0 0 1 1 704.0 0 1 1 708.0 0 2 2 709.0 0 1 1 711.0 0 1 1 712.0 0 5 5 721.0 0 2 2 723.0 0 2 2 724.0 0 1 1 726.0 0 1 1 727.0 0 2 2 728.0 0 1 1 731.0 0 2 2 737.0 0 2 2 742.0 0 2 2 743.0 0 1 1 744.0 0 1 1 746.0 0 1 1 747.0 0 2 2 752.0 0 1 1 753.0 0 1 1 754.0 0 1 1 756.0 0 1 1 758.0 0 1 1 759.0 0 1 1 761.0 0 2 2 764.0 0 1 1 770.0 0 1 1 771.0 0 1 1 772.0 0 1 1 774.0 0 1 1 775.0 0 1 1 776.0 0 1 1 778.0 0 1 1 782.0 0 2 2 783.0 0 1 1 790.0 0 1 1 799.0 0 1 1 800.0 0 1 1 802.0 0 1 1 805.0 0 1 1 809.0 0 1 1 811.0 0 1 1 815.0 0 1 1 816.0 0 1 1 817.0 0 1 1 822.0 0 1 1 826.0 0 1 1 827.0 0 1 1 828.0 0 2 2 832.0 0 2 2 834.0 0 1 1 837.0 0 1 1 838.0 0 1 1 840.0 0 1 1 851.0 0 1 1 857.0 0 1 1 858.0 0 1 1 861.0 0 1 1 863.0 0 1 1 864.0 0 1 1 865.0 0 1 1 869.0 0 1 1 872.0 0 2 2 873.0 0 1 1 877.0 0 1 1 878.0 0 1 1 879.0 0 1 1 882.0 0 1 1 883.0 0 1 1 885.0 0 1 1 899.0 0 1 1 901.0 0 2 2 904.0 0 1 1 906.0 0 1 1 914.0 0 1 1 917.0 0 1 1 921.0 0 1 1 923.0 0 1 1 924.0 0 2 2 928.0 0 1 1 932.0 0 1 1 937.0 0 1 1 945.0 0 1 1 946.0 0 1 1 951.0 0 1 1 956.0 0 1 1 958.0 0 2 2 959.0 0 1 1 963.0 0 1 1 966.0 0 1 1 967.0 0 1 1 969.0 0 1 1 976.0 0 1 1 982.0 0 1 1 984.0 0 1 1 985.0 0 1 1 1000.0 0 1 1 1005.0 0 1 1 1013.0 0 1 1 1026.0 0 1 1 1028.0 0 1 1 1044.0 0 1 1 1052.0 0 1 1 1060.0 0 1 1 1063.0 0 1 1 1065.0 0 1 1 1066.0 0 1 1 1072.0 0 1 1 1104.0 0 1 1 1112.0 0 1 1 1119.0 0 1 1 1150.0 0 1 1 1153.0 0 1 1 1162.0 0 1 1 1169.0 0 1 1 1173.0 0 1 1 1178.0 0 1 1 1181.0 0 1 1 1230.0 0 1 1 1234.0 0 1 1 1254.0 0 1 1 1262.0 0 1 1 1265.0 0 1 1 1337.0 0 1 1 1376.0 0 1 1 1387.0 0 1 1 1423.0 0 1 1 1487.0 0 1 1 1527.0 0 1 1 1529.0 0 1 1 1656.0 0 1 1 1739.0 0 1 1 1754.0 0 1 1 1784.0 0 1 1 2076.0 0 1 1 2079.0 0 1 1 2145.0 0 1 1