## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354271.sorted.bam --OUTPUT SRX7354271.markdup.sorted.bam --METRICS_FILE SRX7354271.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 21:53:19 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 39597 41447561 4801689 2855393 32259 17254419 0 0.416485 34708063 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19927013 19927013 2.0 1.302953 2610196 2610196 3.0 1.394734 611175 611175 4.0 1.422539 265261 265261 5.0 1.430963 154237 154237 6.0 1.433515 103817 103817 7.0 1.434288 74817 74817 8.0 1.434522 56907 56907 9.0 1.434593 44694 44694 10.0 1.434615 36204 36204 11.0 1.434621 29766 29766 12.0 1.434623 25018 25018 13.0 1.434624 21263 21263 14.0 1.434624 18208 18208 15.0 1.434624 16172 16172 16.0 1.434624 13922 13922 17.0 1.434624 12373 12373 18.0 1.434624 11028 11028 19.0 1.434624 9899 9899 20.0 1.434624 8715 8715 21.0 1.434624 8157 8157 22.0 1.434624 7387 7387 23.0 1.434624 6637 6637 24.0 1.434624 6146 6146 25.0 1.434624 5660 5660 26.0 1.434624 5118 5118 27.0 1.434624 4835 4835 28.0 1.434624 4522 4522 29.0 1.434624 4030 4030 30.0 1.434624 3727 3727 31.0 1.434624 3643 3643 32.0 1.434624 3412 3412 33.0 1.434624 3154 3154 34.0 1.434624 2852 2852 35.0 1.434624 2777 2777 36.0 1.434624 2547 2547 37.0 1.434624 2457 2457 38.0 1.434624 2413 2413 39.0 1.434624 2148 2148 40.0 1.434624 2081 2081 41.0 1.434624 1955 1955 42.0 1.434624 1934 1934 43.0 1.434624 1778 1778 44.0 1.434624 1721 1721 45.0 1.434624 1591 1591 46.0 1.434624 1546 1546 47.0 1.434624 1430 1430 48.0 1.434624 1382 1382 49.0 1.434624 1327 1327 50.0 1.434624 1251 1251 51.0 1.434624 1178 1178 52.0 1.434624 1087 1087 53.0 1.434624 1086 1086 54.0 1.434624 1011 1011 55.0 1.434624 1027 1027 56.0 1.434624 994 994 57.0 1.434624 975 975 58.0 1.434624 935 935 59.0 1.434624 870 870 60.0 1.434624 840 840 61.0 1.434624 794 794 62.0 1.434624 747 747 63.0 1.434624 776 776 64.0 1.434624 693 693 65.0 1.434624 661 661 66.0 1.434624 678 678 67.0 1.434624 644 644 68.0 1.434624 619 619 69.0 1.434624 596 596 70.0 1.434624 617 617 71.0 1.434624 561 561 72.0 1.434624 561 561 73.0 1.434624 506 506 74.0 1.434624 498 498 75.0 1.434624 476 476 76.0 1.434624 521 521 77.0 1.434624 468 468 78.0 1.434624 443 443 79.0 1.434624 415 415 80.0 1.434624 467 467 81.0 1.434624 433 433 82.0 1.434624 375 375 83.0 1.434624 385 385 84.0 1.434624 359 359 85.0 1.434624 359 359 86.0 1.434624 372 372 87.0 1.434624 360 360 88.0 1.434624 335 335 89.0 1.434624 321 321 90.0 1.434624 336 336 91.0 1.434624 325 325 92.0 1.434624 287 287 93.0 1.434624 304 304 94.0 1.434624 287 287 95.0 1.434624 287 287 96.0 1.434624 270 270 97.0 1.434624 272 272 98.0 1.434624 281 281 99.0 1.434624 252 252 100.0 1.434624 228 228 101.0 0 234 234 102.0 0 232 232 103.0 0 227 227 104.0 0 215 215 105.0 0 196 196 106.0 0 220 220 107.0 0 207 207 108.0 0 219 219 109.0 0 205 205 110.0 0 192 192 111.0 0 209 209 112.0 0 209 209 113.0 0 208 208 114.0 0 172 172 115.0 0 163 163 116.0 0 149 149 117.0 0 170 170 118.0 0 155 155 119.0 0 149 149 120.0 0 156 156 121.0 0 146 146 122.0 0 140 140 123.0 0 144 144 124.0 0 152 152 125.0 0 138 138 126.0 0 154 154 127.0 0 148 148 128.0 0 114 114 129.0 0 127 127 130.0 0 116 116 131.0 0 124 124 132.0 0 123 123 133.0 0 123 123 134.0 0 118 118 135.0 0 114 114 136.0 0 109 109 137.0 0 129 129 138.0 0 112 112 139.0 0 101 101 140.0 0 105 105 141.0 0 110 110 142.0 0 103 103 143.0 0 116 116 144.0 0 113 113 145.0 0 92 92 146.0 0 83 83 147.0 0 104 104 148.0 0 110 110 149.0 0 78 78 150.0 0 82 82 151.0 0 87 87 152.0 0 83 83 153.0 0 95 95 154.0 0 76 76 155.0 0 74 74 156.0 0 89 89 157.0 0 64 64 158.0 0 75 75 159.0 0 71 71 160.0 0 96 96 161.0 0 79 79 162.0 0 83 83 163.0 0 66 66 164.0 0 83 83 165.0 0 78 78 166.0 0 62 62 167.0 0 63 63 168.0 0 73 73 169.0 0 66 66 170.0 0 73 73 171.0 0 68 68 172.0 0 56 56 173.0 0 61 61 174.0 0 61 61 175.0 0 56 56 176.0 0 54 54 177.0 0 60 60 178.0 0 69 69 179.0 0 55 55 180.0 0 65 65 181.0 0 46 46 182.0 0 64 64 183.0 0 53 53 184.0 0 59 59 185.0 0 60 60 186.0 0 41 41 187.0 0 50 50 188.0 0 46 46 189.0 0 46 46 190.0 0 43 43 191.0 0 49 49 192.0 0 45 45 193.0 0 44 44 194.0 0 34 34 195.0 0 44 44 196.0 0 46 46 197.0 0 52 52 198.0 0 43 43 199.0 0 38 38 200.0 0 54 54 201.0 0 44 44 202.0 0 34 34 203.0 0 35 35 204.0 0 41 41 205.0 0 38 38 206.0 0 32 32 207.0 0 43 43 208.0 0 47 47 209.0 0 42 42 210.0 0 52 52 211.0 0 27 27 212.0 0 32 32 213.0 0 33 33 214.0 0 30 30 215.0 0 23 23 216.0 0 35 35 217.0 0 36 36 218.0 0 36 36 219.0 0 33 33 220.0 0 27 27 221.0 0 32 32 222.0 0 31 31 223.0 0 35 35 224.0 0 28 28 225.0 0 34 34 226.0 0 42 42 227.0 0 31 31 228.0 0 22 22 229.0 0 25 25 230.0 0 26 26 231.0 0 31 31 232.0 0 25 25 233.0 0 25 25 234.0 0 21 21 235.0 0 31 31 236.0 0 34 34 237.0 0 25 25 238.0 0 24 24 239.0 0 23 23 240.0 0 30 30 241.0 0 27 27 242.0 0 32 32 243.0 0 21 21 244.0 0 19 19 245.0 0 28 28 246.0 0 26 26 247.0 0 22 22 248.0 0 18 18 249.0 0 13 13 250.0 0 24 24 251.0 0 18 18 252.0 0 21 21 253.0 0 22 22 254.0 0 15 15 255.0 0 28 28 256.0 0 29 29 257.0 0 20 20 258.0 0 31 31 259.0 0 20 20 260.0 0 13 13 261.0 0 15 15 262.0 0 18 18 263.0 0 20 20 264.0 0 16 16 265.0 0 18 18 266.0 0 23 23 267.0 0 22 22 268.0 0 19 19 269.0 0 15 15 270.0 0 19 19 271.0 0 14 14 272.0 0 19 19 273.0 0 21 21 274.0 0 19 19 275.0 0 17 17 276.0 0 29 29 277.0 0 20 20 278.0 0 12 12 279.0 0 21 21 280.0 0 17 17 281.0 0 15 15 282.0 0 12 12 283.0 0 16 16 284.0 0 20 20 285.0 0 9 9 286.0 0 12 12 287.0 0 14 14 288.0 0 14 14 289.0 0 16 16 290.0 0 15 15 291.0 0 20 20 292.0 0 11 11 293.0 0 18 18 294.0 0 18 18 295.0 0 16 16 296.0 0 16 16 297.0 0 13 13 298.0 0 8 8 299.0 0 11 11 300.0 0 8 8 301.0 0 13 13 302.0 0 17 17 303.0 0 14 14 304.0 0 16 16 305.0 0 15 15 306.0 0 13 13 307.0 0 15 15 308.0 0 7 7 309.0 0 13 13 310.0 0 17 17 311.0 0 8 8 312.0 0 19 19 313.0 0 15 15 314.0 0 9 9 315.0 0 9 9 316.0 0 9 9 317.0 0 3 3 318.0 0 10 10 319.0 0 12 12 320.0 0 10 10 321.0 0 9 9 322.0 0 8 8 323.0 0 10 10 324.0 0 8 8 325.0 0 15 15 326.0 0 9 9 327.0 0 11 11 328.0 0 13 13 329.0 0 10 10 330.0 0 13 13 331.0 0 9 9 332.0 0 10 10 333.0 0 8 8 334.0 0 8 8 335.0 0 12 12 336.0 0 11 11 337.0 0 9 9 338.0 0 8 8 339.0 0 8 8 340.0 0 10 10 341.0 0 4 4 342.0 0 8 8 343.0 0 7 7 344.0 0 11 11 345.0 0 14 14 346.0 0 9 9 347.0 0 6 6 348.0 0 5 5 349.0 0 11 11 350.0 0 9 9 351.0 0 9 9 352.0 0 7 7 353.0 0 6 6 354.0 0 6 6 355.0 0 11 11 356.0 0 6 6 357.0 0 8 8 358.0 0 8 8 359.0 0 6 6 360.0 0 7 7 361.0 0 10 10 362.0 0 6 6 363.0 0 10 10 364.0 0 9 9 365.0 0 8 8 366.0 0 9 9 367.0 0 6 6 368.0 0 6 6 369.0 0 3 3 370.0 0 6 6 371.0 0 8 8 372.0 0 7 7 373.0 0 7 7 374.0 0 7 7 375.0 0 6 6 376.0 0 7 7 377.0 0 7 7 378.0 0 11 11 379.0 0 1 1 380.0 0 9 9 381.0 0 8 8 382.0 0 4 4 383.0 0 3 3 384.0 0 10 10 385.0 0 7 7 386.0 0 9 9 387.0 0 5 5 388.0 0 8 8 390.0 0 7 7 391.0 0 1 1 392.0 0 6 6 393.0 0 5 5 394.0 0 6 6 395.0 0 6 6 396.0 0 5 5 397.0 0 4 4 398.0 0 4 4 399.0 0 4 4 400.0 0 5 5 401.0 0 3 3 402.0 0 6 6 403.0 0 4 4 404.0 0 1 1 405.0 0 9 9 406.0 0 4 4 407.0 0 6 6 408.0 0 2 2 409.0 0 6 6 410.0 0 2 2 411.0 0 3 3 412.0 0 4 4 413.0 0 5 5 414.0 0 4 4 415.0 0 4 4 416.0 0 2 2 417.0 0 9 9 418.0 0 8 8 419.0 0 4 4 420.0 0 5 5 421.0 0 5 5 422.0 0 5 5 423.0 0 7 7 424.0 0 3 3 425.0 0 4 4 426.0 0 6 6 427.0 0 4 4 428.0 0 3 3 429.0 0 9 9 430.0 0 5 5 431.0 0 3 3 432.0 0 3 3 433.0 0 4 4 434.0 0 7 7 435.0 0 7 7 436.0 0 4 4 437.0 0 5 5 438.0 0 1 1 439.0 0 6 6 440.0 0 6 6 441.0 0 9 9 442.0 0 3 3 443.0 0 5 5 444.0 0 5 5 445.0 0 8 8 446.0 0 8 8 447.0 0 6 6 448.0 0 3 3 449.0 0 5 5 450.0 0 8 8 451.0 0 8 8 452.0 0 6 6 453.0 0 4 4 454.0 0 2 2 455.0 0 2 2 456.0 0 2 2 457.0 0 1 1 458.0 0 5 5 459.0 0 9 9 460.0 0 5 5 461.0 0 4 4 462.0 0 5 5 463.0 0 2 2 464.0 0 5 5 465.0 0 3 3 466.0 0 5 5 467.0 0 4 4 468.0 0 5 5 469.0 0 4 4 470.0 0 5 5 471.0 0 6 6 472.0 0 3 3 473.0 0 1 1 474.0 0 1 1 475.0 0 4 4 476.0 0 2 2 477.0 0 3 3 478.0 0 6 6 479.0 0 2 2 480.0 0 6 6 481.0 0 1 1 483.0 0 4 4 484.0 0 4 4 485.0 0 3 3 486.0 0 5 5 487.0 0 4 4 488.0 0 3 3 489.0 0 2 2 490.0 0 2 2 491.0 0 2 2 493.0 0 4 4 494.0 0 2 2 495.0 0 4 4 497.0 0 1 1 499.0 0 2 2 500.0 0 1 1 501.0 0 1 1 502.0 0 1 1 503.0 0 5 5 504.0 0 6 6 505.0 0 1 1 506.0 0 3 3 507.0 0 2 2 508.0 0 1 1 509.0 0 3 3 510.0 0 3 3 511.0 0 2 2 512.0 0 2 2 513.0 0 3 3 514.0 0 1 1 516.0 0 4 4 517.0 0 1 1 518.0 0 3 3 519.0 0 6 6 521.0 0 3 3 522.0 0 2 2 523.0 0 4 4 524.0 0 1 1 525.0 0 3 3 526.0 0 2 2 527.0 0 3 3 528.0 0 1 1 529.0 0 4 4 530.0 0 3 3 532.0 0 3 3 533.0 0 2 2 534.0 0 4 4 535.0 0 5 5 536.0 0 1 1 537.0 0 4 4 538.0 0 3 3 539.0 0 1 1 540.0 0 1 1 541.0 0 1 1 542.0 0 2 2 543.0 0 4 4 544.0 0 1 1 545.0 0 1 1 546.0 0 2 2 547.0 0 2 2 548.0 0 1 1 549.0 0 1 1 550.0 0 1 1 551.0 0 1 1 552.0 0 4 4 553.0 0 4 4 554.0 0 2 2 555.0 0 3 3 556.0 0 3 3 557.0 0 4 4 558.0 0 1 1 559.0 0 5 5 560.0 0 2 2 561.0 0 2 2 562.0 0 2 2 563.0 0 1 1 564.0 0 2 2 566.0 0 1 1 567.0 0 2 2 568.0 0 4 4 569.0 0 3 3 571.0 0 2 2 574.0 0 2 2 575.0 0 1 1 576.0 0 1 1 577.0 0 2 2 578.0 0 1 1 579.0 0 2 2 580.0 0 1 1 581.0 0 1 1 582.0 0 2 2 583.0 0 1 1 585.0 0 2 2 586.0 0 2 2 587.0 0 1 1 588.0 0 1 1 589.0 0 1 1 590.0 0 3 3 591.0 0 1 1 592.0 0 2 2 594.0 0 1 1 595.0 0 1 1 596.0 0 1 1 597.0 0 1 1 598.0 0 6 6 599.0 0 2 2 600.0 0 1 1 602.0 0 1 1 605.0 0 1 1 606.0 0 2 2 607.0 0 1 1 608.0 0 1 1 611.0 0 1 1 612.0 0 2 2 614.0 0 3 3 616.0 0 2 2 617.0 0 1 1 621.0 0 3 3 622.0 0 1 1 623.0 0 1 1 624.0 0 1 1 625.0 0 2 2 626.0 0 1 1 628.0 0 3 3 629.0 0 2 2 630.0 0 1 1 632.0 0 1 1 634.0 0 3 3 635.0 0 1 1 636.0 0 1 1 637.0 0 3 3 638.0 0 1 1 639.0 0 1 1 640.0 0 2 2 641.0 0 1 1 642.0 0 1 1 643.0 0 1 1 644.0 0 3 3 646.0 0 3 3 648.0 0 1 1 649.0 0 2 2 650.0 0 1 1 651.0 0 1 1 652.0 0 1 1 653.0 0 3 3 654.0 0 1 1 657.0 0 1 1 659.0 0 1 1 660.0 0 2 2 661.0 0 1 1 662.0 0 4 4 664.0 0 2 2 667.0 0 1 1 668.0 0 2 2 669.0 0 4 4 670.0 0 1 1 671.0 0 2 2 672.0 0 1 1 673.0 0 2 2 674.0 0 1 1 678.0 0 3 3 680.0 0 2 2 681.0 0 2 2 682.0 0 2 2 683.0 0 1 1 686.0 0 1 1 687.0 0 1 1 688.0 0 1 1 692.0 0 1 1 693.0 0 2 2 694.0 0 2 2 697.0 0 2 2 698.0 0 1 1 699.0 0 2 2 703.0 0 2 2 706.0 0 3 3 707.0 0 1 1 708.0 0 1 1 710.0 0 2 2 712.0 0 1 1 713.0 0 3 3 715.0 0 2 2 720.0 0 1 1 723.0 0 1 1 725.0 0 1 1 726.0 0 2 2 727.0 0 1 1 728.0 0 1 1 730.0 0 2 2 734.0 0 1 1 735.0 0 1 1 736.0 0 2 2 737.0 0 2 2 739.0 0 1 1 741.0 0 1 1 743.0 0 1 1 744.0 0 1 1 745.0 0 1 1 746.0 0 1 1 749.0 0 1 1 752.0 0 1 1 756.0 0 1 1 759.0 0 1 1 760.0 0 2 2 763.0 0 1 1 769.0 0 1 1 773.0 0 1 1 774.0 0 1 1 775.0 0 1 1 776.0 0 1 1 780.0 0 2 2 783.0 0 1 1 788.0 0 1 1 789.0 0 1 1 790.0 0 1 1 791.0 0 1 1 795.0 0 1 1 796.0 0 1 1 799.0 0 1 1 801.0 0 1 1 802.0 0 1 1 804.0 0 2 2 806.0 0 1 1 808.0 0 1 1 810.0 0 1 1 819.0 0 1 1 821.0 0 1 1 822.0 0 1 1 826.0 0 1 1 832.0 0 1 1 844.0 0 1 1 849.0 0 1 1 850.0 0 1 1 852.0 0 1 1 855.0 0 1 1 861.0 0 1 1 866.0 0 1 1 870.0 0 1 1 876.0 0 1 1 877.0 0 1 1 878.0 0 1 1 881.0 0 1 1 892.0 0 1 1 895.0 0 1 1 900.0 0 1 1 903.0 0 1 1 904.0 0 1 1 909.0 0 1 1 910.0 0 1 1 911.0 0 1 1 912.0 0 1 1 914.0 0 2 2 923.0 0 2 2 927.0 0 1 1 929.0 0 1 1 938.0 0 1 1 940.0 0 1 1 941.0 0 1 1 945.0 0 1 1 953.0 0 1 1 957.0 0 1 1 966.0 0 1 1 967.0 0 3 3 971.0 0 1 1 972.0 0 1 1 974.0 0 1 1 975.0 0 1 1 981.0 0 1 1 986.0 0 5 5 988.0 0 1 1 999.0 0 1 1 1003.0 0 1 1 1007.0 0 1 1 1009.0 0 1 1 1020.0 0 1 1 1028.0 0 1 1 1029.0 0 1 1 1045.0 0 1 1 1049.0 0 1 1 1054.0 0 1 1 1069.0 0 1 1 1074.0 0 1 1 1076.0 0 1 1 1081.0 0 1 1 1103.0 0 1 1 1110.0 0 1 1 1120.0 0 1 1 1123.0 0 1 1 1133.0 0 1 1 1136.0 0 1 1 1140.0 0 1 1 1141.0 0 1 1 1157.0 0 1 1 1168.0 0 1 1 1174.0 0 1 1 1183.0 0 1 1 1200.0 0 2 2 1208.0 0 1 1 1215.0 0 1 1 1216.0 0 1 1 1217.0 0 1 1 1221.0 0 1 1 1236.0 0 1 1 1257.0 0 1 1 1260.0 0 1 1 1328.0 0 1 1 1355.0 0 1 1 1379.0 0 1 1 1410.0 0 1 1 1440.0 0 1 1 1455.0 0 1 1 1480.0 0 1 1 1497.0 0 1 1 1498.0 0 1 1 1519.0 0 1 1 1527.0 0 1 1 1537.0 0 1 1 1545.0 0 1 1 1592.0 0 1 1 1606.0 0 1 1 1650.0 0 1 1 1803.0 0 1 1 1951.0 0 1 1 2011.0 0 1 1 2055.0 0 1 1 2092.0 0 1 1 2115.0 0 1 1 2116.0 0 1 1 2122.0 0 1 1 2139.0 0 1 1 2347.0 0 1 1 4605.0 0 1 1