## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354193.sorted.bam --OUTPUT SRX7354193.markdup.sorted.bam --METRICS_FILE SRX7354193.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: Fri Oct 27 20:32:21 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 23396 48655482 6164281 1720638 17661 20842353 0 0.428444 39039316 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21158056 21158056 2.0 1.287561 4297683 4297683 3.0 1.370252 1036133 1036133 4.0 1.394031 388489 388489 5.0 1.400869 207979 207979 6.0 1.402835 132995 132995 7.0 1.403401 93638 93638 8.0 1.403563 69445 69445 9.0 1.40361 54418 54418 10.0 1.403624 42767 42767 11.0 1.403627 34905 34905 12.0 1.403629 28699 28699 13.0 1.403629 24655 24655 14.0 1.403629 20627 20627 15.0 1.403629 17855 17855 16.0 1.403629 15582 15582 17.0 1.403629 13406 13406 18.0 1.403629 12042 12042 19.0 1.403629 10818 10818 20.0 1.403629 9731 9731 21.0 1.403629 8698 8698 22.0 1.403629 7875 7875 23.0 1.403629 7150 7150 24.0 1.403629 6455 6455 25.0 1.403629 6058 6058 26.0 1.403629 5389 5389 27.0 1.403629 5037 5037 28.0 1.403629 4669 4669 29.0 1.403629 4280 4280 30.0 1.403629 3910 3910 31.0 1.403629 3620 3620 32.0 1.403629 3470 3470 33.0 1.403629 3201 3201 34.0 1.403629 2943 2943 35.0 1.403629 2834 2834 36.0 1.403629 2571 2571 37.0 1.403629 2504 2504 38.0 1.403629 2297 2297 39.0 1.403629 2230 2230 40.0 1.403629 2030 2030 41.0 1.403629 2005 2005 42.0 1.403629 1861 1861 43.0 1.403629 1764 1764 44.0 1.403629 1689 1689 45.0 1.403629 1599 1599 46.0 1.403629 1530 1530 47.0 1.403629 1446 1446 48.0 1.403629 1376 1376 49.0 1.403629 1346 1346 50.0 1.403629 1295 1295 51.0 1.403629 1191 1191 52.0 1.403629 1194 1194 53.0 1.403629 1085 1085 54.0 1.403629 985 985 55.0 1.403629 1062 1062 56.0 1.403629 920 920 57.0 1.403629 858 858 58.0 1.403629 851 851 59.0 1.403629 789 789 60.0 1.403629 795 795 61.0 1.403629 787 787 62.0 1.403629 702 702 63.0 1.403629 743 743 64.0 1.403629 665 665 65.0 1.403629 696 696 66.0 1.403629 657 657 67.0 1.403629 625 625 68.0 1.403629 616 616 69.0 1.403629 555 555 70.0 1.403629 534 534 71.0 1.403629 548 548 72.0 1.403629 516 516 73.0 1.403629 518 518 74.0 1.403629 432 432 75.0 1.403629 464 464 76.0 1.403629 437 437 77.0 1.403629 457 457 78.0 1.403629 434 434 79.0 1.403629 398 398 80.0 1.403629 379 379 81.0 1.403629 395 395 82.0 1.403629 408 408 83.0 1.403629 357 357 84.0 1.403629 372 372 85.0 1.403629 369 369 86.0 1.403629 336 336 87.0 1.403629 374 374 88.0 1.403629 312 312 89.0 1.403629 299 299 90.0 1.403629 318 318 91.0 1.403629 286 286 92.0 1.403629 299 299 93.0 1.403629 264 264 94.0 1.403629 257 257 95.0 1.403629 304 304 96.0 1.403629 249 249 97.0 1.403629 238 238 98.0 1.403629 240 240 99.0 1.403629 227 227 100.0 1.403629 232 232 101.0 0 213 213 102.0 0 219 219 103.0 0 194 194 104.0 0 232 232 105.0 0 216 216 106.0 0 190 190 107.0 0 181 181 108.0 0 184 184 109.0 0 202 202 110.0 0 187 187 111.0 0 177 177 112.0 0 175 175 113.0 0 191 191 114.0 0 151 151 115.0 0 152 152 116.0 0 155 155 117.0 0 141 141 118.0 0 136 136 119.0 0 158 158 120.0 0 141 141 121.0 0 154 154 122.0 0 128 128 123.0 0 146 146 124.0 0 146 146 125.0 0 117 117 126.0 0 121 121 127.0 0 135 135 128.0 0 125 125 129.0 0 115 115 130.0 0 103 103 131.0 0 112 112 132.0 0 107 107 133.0 0 116 116 134.0 0 101 101 135.0 0 95 95 136.0 0 106 106 137.0 0 117 117 138.0 0 97 97 139.0 0 94 94 140.0 0 82 82 141.0 0 85 85 142.0 0 87 87 143.0 0 81 81 144.0 0 88 88 145.0 0 78 78 146.0 0 92 92 147.0 0 72 72 148.0 0 83 83 149.0 0 73 73 150.0 0 69 69 151.0 0 84 84 152.0 0 76 76 153.0 0 76 76 154.0 0 76 76 155.0 0 75 75 156.0 0 62 62 157.0 0 81 81 158.0 0 69 69 159.0 0 57 57 160.0 0 67 67 161.0 0 74 74 162.0 0 66 66 163.0 0 55 55 164.0 0 51 51 165.0 0 69 69 166.0 0 61 61 167.0 0 65 65 168.0 0 60 60 169.0 0 62 62 170.0 0 57 57 171.0 0 63 63 172.0 0 58 58 173.0 0 63 63 174.0 0 59 59 175.0 0 43 43 176.0 0 53 53 177.0 0 56 56 178.0 0 43 43 179.0 0 41 41 180.0 0 57 57 181.0 0 53 53 182.0 0 58 58 183.0 0 38 38 184.0 0 47 47 185.0 0 43 43 186.0 0 35 35 187.0 0 50 50 188.0 0 39 39 189.0 0 29 29 190.0 0 39 39 191.0 0 42 42 192.0 0 38 38 193.0 0 44 44 194.0 0 45 45 195.0 0 31 31 196.0 0 43 43 197.0 0 47 47 198.0 0 31 31 199.0 0 27 27 200.0 0 41 41 201.0 0 25 25 202.0 0 30 30 203.0 0 36 36 204.0 0 36 36 205.0 0 37 37 206.0 0 28 28 207.0 0 31 31 208.0 0 44 44 209.0 0 47 47 210.0 0 30 30 211.0 0 28 28 212.0 0 27 27 213.0 0 28 28 214.0 0 38 38 215.0 0 32 32 216.0 0 25 25 217.0 0 27 27 218.0 0 31 31 219.0 0 21 21 220.0 0 27 27 221.0 0 28 28 222.0 0 20 20 223.0 0 24 24 224.0 0 25 25 225.0 0 30 30 226.0 0 26 26 227.0 0 18 18 228.0 0 31 31 229.0 0 28 28 230.0 0 17 17 231.0 0 23 23 232.0 0 24 24 233.0 0 27 27 234.0 0 26 26 235.0 0 22 22 236.0 0 37 37 237.0 0 23 23 238.0 0 19 19 239.0 0 20 20 240.0 0 14 14 241.0 0 25 25 242.0 0 28 28 243.0 0 20 20 244.0 0 18 18 245.0 0 13 13 246.0 0 19 19 247.0 0 20 20 248.0 0 23 23 249.0 0 18 18 250.0 0 20 20 251.0 0 19 19 252.0 0 22 22 253.0 0 11 11 254.0 0 15 15 255.0 0 20 20 256.0 0 15 15 257.0 0 17 17 258.0 0 16 16 259.0 0 17 17 260.0 0 15 15 261.0 0 23 23 262.0 0 23 23 263.0 0 16 16 264.0 0 21 21 265.0 0 14 14 266.0 0 18 18 267.0 0 23 23 268.0 0 10 10 269.0 0 14 14 270.0 0 21 21 271.0 0 9 9 272.0 0 15 15 273.0 0 17 17 274.0 0 19 19 275.0 0 17 17 276.0 0 20 20 277.0 0 10 10 278.0 0 14 14 279.0 0 15 15 280.0 0 15 15 281.0 0 11 11 282.0 0 11 11 283.0 0 16 16 284.0 0 5 5 285.0 0 9 9 286.0 0 6 6 287.0 0 12 12 288.0 0 6 6 289.0 0 15 15 290.0 0 19 19 291.0 0 14 14 292.0 0 15 15 293.0 0 12 12 294.0 0 20 20 295.0 0 13 13 296.0 0 14 14 297.0 0 12 12 298.0 0 17 17 299.0 0 13 13 300.0 0 11 11 301.0 0 18 18 302.0 0 13 13 303.0 0 13 13 304.0 0 8 8 305.0 0 7 7 306.0 0 7 7 307.0 0 14 14 308.0 0 9 9 309.0 0 9 9 310.0 0 11 11 311.0 0 10 10 312.0 0 11 11 313.0 0 14 14 314.0 0 9 9 315.0 0 10 10 316.0 0 5 5 317.0 0 7 7 318.0 0 12 12 319.0 0 9 9 320.0 0 10 10 321.0 0 9 9 322.0 0 8 8 323.0 0 7 7 324.0 0 4 4 325.0 0 7 7 326.0 0 5 5 327.0 0 12 12 328.0 0 7 7 329.0 0 9 9 330.0 0 13 13 331.0 0 9 9 332.0 0 13 13 333.0 0 4 4 334.0 0 6 6 335.0 0 6 6 336.0 0 13 13 337.0 0 6 6 338.0 0 9 9 339.0 0 8 8 340.0 0 4 4 341.0 0 8 8 342.0 0 4 4 343.0 0 3 3 344.0 0 12 12 345.0 0 7 7 346.0 0 6 6 347.0 0 5 5 348.0 0 6 6 349.0 0 8 8 350.0 0 7 7 351.0 0 10 10 352.0 0 10 10 353.0 0 12 12 354.0 0 5 5 355.0 0 9 9 356.0 0 8 8 357.0 0 8 8 358.0 0 4 4 359.0 0 6 6 360.0 0 8 8 361.0 0 6 6 362.0 0 7 7 363.0 0 3 3 364.0 0 5 5 365.0 0 2 2 366.0 0 3 3 367.0 0 5 5 368.0 0 6 6 369.0 0 10 10 370.0 0 2 2 371.0 0 4 4 372.0 0 6 6 373.0 0 7 7 374.0 0 5 5 375.0 0 10 10 376.0 0 3 3 377.0 0 11 11 378.0 0 2 2 379.0 0 2 2 380.0 0 6 6 381.0 0 8 8 382.0 0 5 5 383.0 0 6 6 384.0 0 11 11 385.0 0 2 2 386.0 0 5 5 387.0 0 2 2 388.0 0 1 1 389.0 0 8 8 390.0 0 5 5 391.0 0 5 5 392.0 0 5 5 393.0 0 8 8 394.0 0 5 5 395.0 0 4 4 396.0 0 3 3 397.0 0 6 6 398.0 0 5 5 399.0 0 3 3 400.0 0 8 8 401.0 0 8 8 402.0 0 7 7 403.0 0 3 3 404.0 0 2 2 405.0 0 3 3 406.0 0 6 6 407.0 0 5 5 408.0 0 13 13 409.0 0 6 6 410.0 0 4 4 411.0 0 7 7 412.0 0 6 6 413.0 0 4 4 414.0 0 4 4 415.0 0 3 3 416.0 0 5 5 417.0 0 5 5 418.0 0 8 8 419.0 0 5 5 420.0 0 10 10 421.0 0 7 7 422.0 0 7 7 423.0 0 2 2 424.0 0 2 2 425.0 0 2 2 426.0 0 4 4 427.0 0 5 5 428.0 0 5 5 429.0 0 3 3 430.0 0 2 2 431.0 0 4 4 432.0 0 2 2 433.0 0 6 6 434.0 0 5 5 435.0 0 4 4 436.0 0 4 4 437.0 0 6 6 438.0 0 4 4 439.0 0 3 3 440.0 0 3 3 441.0 0 3 3 442.0 0 1 1 444.0 0 2 2 445.0 0 6 6 446.0 0 7 7 447.0 0 8 8 448.0 0 6 6 449.0 0 6 6 450.0 0 3 3 451.0 0 1 1 452.0 0 2 2 453.0 0 2 2 454.0 0 2 2 455.0 0 3 3 456.0 0 3 3 457.0 0 2 2 458.0 0 2 2 459.0 0 4 4 460.0 0 1 1 461.0 0 4 4 462.0 0 2 2 463.0 0 7 7 464.0 0 5 5 465.0 0 2 2 466.0 0 2 2 467.0 0 4 4 468.0 0 5 5 469.0 0 1 1 470.0 0 1 1 471.0 0 5 5 472.0 0 6 6 473.0 0 3 3 474.0 0 4 4 475.0 0 2 2 476.0 0 3 3 477.0 0 2 2 478.0 0 1 1 479.0 0 5 5 480.0 0 3 3 481.0 0 2 2 482.0 0 2 2 483.0 0 4 4 484.0 0 2 2 485.0 0 2 2 486.0 0 2 2 487.0 0 2 2 488.0 0 2 2 489.0 0 2 2 490.0 0 2 2 491.0 0 6 6 492.0 0 1 1 493.0 0 1 1 494.0 0 2 2 495.0 0 3 3 497.0 0 2 2 498.0 0 2 2 499.0 0 2 2 500.0 0 1 1 501.0 0 3 3 502.0 0 1 1 503.0 0 2 2 504.0 0 1 1 505.0 0 2 2 506.0 0 2 2 507.0 0 3 3 508.0 0 3 3 509.0 0 1 1 510.0 0 1 1 511.0 0 1 1 512.0 0 2 2 513.0 0 3 3 515.0 0 3 3 516.0 0 3 3 518.0 0 4 4 519.0 0 4 4 520.0 0 4 4 521.0 0 5 5 522.0 0 4 4 523.0 0 3 3 524.0 0 1 1 526.0 0 1 1 527.0 0 2 2 528.0 0 3 3 529.0 0 1 1 530.0 0 1 1 531.0 0 1 1 532.0 0 1 1 533.0 0 1 1 534.0 0 3 3 535.0 0 1 1 536.0 0 2 2 537.0 0 3 3 538.0 0 1 1 540.0 0 2 2 542.0 0 2 2 543.0 0 2 2 544.0 0 3 3 545.0 0 1 1 546.0 0 2 2 547.0 0 3 3 548.0 0 1 1 549.0 0 1 1 550.0 0 3 3 551.0 0 3 3 552.0 0 2 2 553.0 0 2 2 554.0 0 5 5 556.0 0 3 3 559.0 0 1 1 560.0 0 3 3 561.0 0 1 1 563.0 0 2 2 565.0 0 1 1 566.0 0 3 3 567.0 0 2 2 568.0 0 1 1 569.0 0 3 3 570.0 0 2 2 571.0 0 1 1 572.0 0 1 1 573.0 0 2 2 574.0 0 1 1 577.0 0 1 1 580.0 0 2 2 581.0 0 1 1 582.0 0 2 2 584.0 0 3 3 585.0 0 1 1 586.0 0 2 2 587.0 0 1 1 588.0 0 3 3 589.0 0 1 1 590.0 0 3 3 594.0 0 1 1 595.0 0 6 6 598.0 0 2 2 599.0 0 6 6 602.0 0 3 3 608.0 0 1 1 609.0 0 3 3 610.0 0 2 2 611.0 0 1 1 612.0 0 1 1 613.0 0 2 2 615.0 0 1 1 616.0 0 2 2 617.0 0 1 1 618.0 0 2 2 619.0 0 3 3 621.0 0 1 1 623.0 0 3 3 624.0 0 2 2 625.0 0 1 1 626.0 0 1 1 627.0 0 4 4 628.0 0 2 2 629.0 0 1 1 631.0 0 4 4 632.0 0 2 2 633.0 0 1 1 634.0 0 3 3 635.0 0 1 1 636.0 0 2 2 637.0 0 2 2 638.0 0 2 2 639.0 0 1 1 640.0 0 2 2 642.0 0 5 5 643.0 0 1 1 644.0 0 1 1 646.0 0 1 1 647.0 0 1 1 648.0 0 2 2 652.0 0 3 3 653.0 0 1 1 654.0 0 1 1 655.0 0 3 3 656.0 0 1 1 657.0 0 1 1 658.0 0 1 1 659.0 0 2 2 661.0 0 1 1 663.0 0 2 2 664.0 0 1 1 665.0 0 1 1 669.0 0 1 1 670.0 0 2 2 672.0 0 2 2 673.0 0 2 2 674.0 0 1 1 675.0 0 1 1 676.0 0 1 1 677.0 0 1 1 678.0 0 1 1 684.0 0 1 1 685.0 0 1 1 686.0 0 1 1 687.0 0 1 1 690.0 0 2 2 691.0 0 1 1 692.0 0 1 1 693.0 0 1 1 695.0 0 2 2 697.0 0 2 2 698.0 0 1 1 699.0 0 2 2 706.0 0 2 2 707.0 0 2 2 710.0 0 2 2 711.0 0 1 1 715.0 0 2 2 717.0 0 2 2 719.0 0 1 1 727.0 0 1 1 729.0 0 2 2 730.0 0 2 2 731.0 0 1 1 732.0 0 1 1 733.0 0 2 2 734.0 0 2 2 735.0 0 2 2 737.0 0 1 1 738.0 0 1 1 739.0 0 2 2 741.0 0 1 1 742.0 0 1 1 744.0 0 1 1 747.0 0 1 1 748.0 0 2 2 750.0 0 1 1 752.0 0 1 1 760.0 0 1 1 763.0 0 3 3 767.0 0 1 1 769.0 0 1 1 770.0 0 1 1 773.0 0 1 1 774.0 0 1 1 775.0 0 1 1 777.0 0 1 1 789.0 0 2 2 795.0 0 1 1 796.0 0 1 1 797.0 0 1 1 800.0 0 1 1 802.0 0 2 2 804.0 0 1 1 805.0 0 1 1 807.0 0 1 1 813.0 0 1 1 816.0 0 1 1 817.0 0 1 1 820.0 0 1 1 821.0 0 1 1 822.0 0 1 1 823.0 0 2 2 825.0 0 1 1 826.0 0 1 1 831.0 0 1 1 837.0 0 1 1 839.0 0 1 1 841.0 0 1 1 845.0 0 1 1 847.0 0 1 1 848.0 0 1 1 853.0 0 3 3 854.0 0 1 1 856.0 0 2 2 859.0 0 1 1 863.0 0 1 1 869.0 0 1 1 881.0 0 2 2 887.0 0 1 1 890.0 0 1 1 893.0 0 1 1 897.0 0 1 1 904.0 0 1 1 905.0 0 1 1 907.0 0 1 1 908.0 0 2 2 909.0 0 1 1 917.0 0 1 1 919.0 0 1 1 925.0 0 1 1 932.0 0 1 1 936.0 0 2 2 941.0 0 1 1 942.0 0 1 1 943.0 0 1 1 947.0 0 2 2 949.0 0 2 2 952.0 0 1 1 959.0 0 1 1 961.0 0 1 1 975.0 0 2 2 980.0 0 2 2 981.0 0 1 1 983.0 0 1 1 987.0 0 1 1 988.0 0 2 2 989.0 0 1 1 990.0 0 2 2 1002.0 0 1 1 1005.0 0 1 1 1006.0 0 1 1 1007.0 0 1 1 1008.0 0 2 2 1047.0 0 1 1 1050.0 0 1 1 1054.0 0 1 1 1055.0 0 1 1 1057.0 0 1 1 1058.0 0 1 1 1070.0 0 1 1 1085.0 0 1 1 1092.0 0 1 1 1093.0 0 1 1 1108.0 0 1 1 1110.0 0 1 1 1113.0 0 1 1 1127.0 0 1 1 1129.0 0 1 1 1148.0 0 1 1 1158.0 0 1 1 1167.0 0 1 1 1171.0 0 1 1 1173.0 0 1 1 1180.0 0 1 1 1182.0 0 1 1 1185.0 0 1 1 1190.0 0 1 1 1203.0 0 1 1 1216.0 0 1 1 1222.0 0 2 2 1237.0 0 1 1 1241.0 0 1 1 1264.0 0 1 1 1270.0 0 1 1 1283.0 0 1 1 1287.0 0 1 1 1362.0 0 1 1 1366.0 0 1 1 1442.0 0 1 1 1445.0 0 1 1 1476.0 0 1 1 1491.0 0 1 1 1606.0 0 1 1 1701.0 0 1 1 1777.0 0 1 1 1816.0 0 1 1 1992.0 0 1 1 2022.0 0 1 1 2040.0 0 1 1 2173.0 0 1 1 2283.0 0 1 1 2740.0 0 1 1 2773.0 0 1 1 2855.0 0 1 1 2898.0 0 1 1 3097.0 0 1 1 4783.0 0 1 1 7364.0 0 1 1