## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354168.sorted.bam --OUTPUT SRX7354168.markdup.sorted.bam --METRICS_FILE SRX7354168.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: Sun Oct 29 01:02:26 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 27631 39623385 5176607 2399353 20796 15249312 0 0.384985 37186446 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 20579382 20579382 2.0 1.344544 2229151 2229151 3.0 1.463255 565264 565264 4.0 1.504156 260829 260829 5.0 1.518248 154098 154098 6.0 1.523104 102471 102471 7.0 1.524776 73655 73655 8.0 1.525353 55336 55336 9.0 1.525551 43383 43383 10.0 1.52562 34441 34441 11.0 1.525643 28181 28181 12.0 1.525652 23428 23428 13.0 1.525654 19996 19996 14.0 1.525655 16957 16957 15.0 1.525656 14655 14655 16.0 1.525656 12993 12993 17.0 1.525656 11290 11290 18.0 1.525656 9884 9884 19.0 1.525656 8972 8972 20.0 1.525656 8114 8114 21.0 1.525656 7205 7205 22.0 1.525656 6523 6523 23.0 1.525656 5935 5935 24.0 1.525656 5503 5503 25.0 1.525656 5051 5051 26.0 1.525656 4566 4566 27.0 1.525656 4142 4142 28.0 1.525656 3886 3886 29.0 1.525656 3633 3633 30.0 1.525656 3392 3392 31.0 1.525656 3060 3060 32.0 1.525656 2981 2981 33.0 1.525656 2703 2703 34.0 1.525656 2438 2438 35.0 1.525656 2357 2357 36.0 1.525656 2197 2197 37.0 1.525656 2105 2105 38.0 1.525656 1944 1944 39.0 1.525656 1980 1980 40.0 1.525656 1766 1766 41.0 1.525656 1696 1696 42.0 1.525656 1572 1572 43.0 1.525656 1413 1413 44.0 1.525656 1379 1379 45.0 1.525656 1386 1386 46.0 1.525656 1313 1313 47.0 1.525656 1250 1250 48.0 1.525656 1140 1140 49.0 1.525656 1106 1106 50.0 1.525656 1098 1098 51.0 1.525656 985 985 52.0 1.525656 968 968 53.0 1.525656 940 940 54.0 1.525656 922 922 55.0 1.525656 821 821 56.0 1.525656 809 809 57.0 1.525656 770 770 58.0 1.525656 720 720 59.0 1.525656 720 720 60.0 1.525656 701 701 61.0 1.525656 627 627 62.0 1.525656 689 689 63.0 1.525656 639 639 64.0 1.525656 636 636 65.0 1.525656 547 547 66.0 1.525656 556 556 67.0 1.525656 510 510 68.0 1.525656 518 518 69.0 1.525656 487 487 70.0 1.525656 473 473 71.0 1.525656 463 463 72.0 1.525656 448 448 73.0 1.525656 461 461 74.0 1.525656 436 436 75.0 1.525656 424 424 76.0 1.525656 391 391 77.0 1.525656 375 375 78.0 1.525656 372 372 79.0 1.525656 394 394 80.0 1.525656 364 364 81.0 1.525656 318 318 82.0 1.525656 326 326 83.0 1.525656 322 322 84.0 1.525656 295 295 85.0 1.525656 292 292 86.0 1.525656 296 296 87.0 1.525656 271 271 88.0 1.525656 284 284 89.0 1.525656 279 279 90.0 1.525656 250 250 91.0 1.525656 271 271 92.0 1.525656 232 232 93.0 1.525656 247 247 94.0 1.525656 218 218 95.0 1.525656 225 225 96.0 1.525656 226 226 97.0 1.525656 202 202 98.0 1.525656 191 191 99.0 1.525656 209 209 100.0 1.525656 190 190 101.0 0 202 202 102.0 0 182 182 103.0 0 175 175 104.0 0 160 160 105.0 0 175 175 106.0 0 195 195 107.0 0 187 187 108.0 0 156 156 109.0 0 165 165 110.0 0 150 150 111.0 0 138 138 112.0 0 145 145 113.0 0 150 150 114.0 0 156 156 115.0 0 149 149 116.0 0 130 130 117.0 0 147 147 118.0 0 101 101 119.0 0 111 111 120.0 0 130 130 121.0 0 112 112 122.0 0 124 124 123.0 0 111 111 124.0 0 111 111 125.0 0 129 129 126.0 0 108 108 127.0 0 95 95 128.0 0 102 102 129.0 0 89 89 130.0 0 95 95 131.0 0 102 102 132.0 0 106 106 133.0 0 101 101 134.0 0 78 78 135.0 0 85 85 136.0 0 92 92 137.0 0 85 85 138.0 0 100 100 139.0 0 103 103 140.0 0 82 82 141.0 0 101 101 142.0 0 82 82 143.0 0 66 66 144.0 0 66 66 145.0 0 72 72 146.0 0 81 81 147.0 0 88 88 148.0 0 74 74 149.0 0 63 63 150.0 0 74 74 151.0 0 66 66 152.0 0 66 66 153.0 0 68 68 154.0 0 68 68 155.0 0 50 50 156.0 0 74 74 157.0 0 59 59 158.0 0 68 68 159.0 0 68 68 160.0 0 58 58 161.0 0 62 62 162.0 0 58 58 163.0 0 49 49 164.0 0 69 69 165.0 0 50 50 166.0 0 45 45 167.0 0 48 48 168.0 0 54 54 169.0 0 51 51 170.0 0 49 49 171.0 0 43 43 172.0 0 56 56 173.0 0 35 35 174.0 0 54 54 175.0 0 45 45 176.0 0 52 52 177.0 0 45 45 178.0 0 36 36 179.0 0 39 39 180.0 0 32 32 181.0 0 38 38 182.0 0 37 37 183.0 0 39 39 184.0 0 39 39 185.0 0 35 35 186.0 0 28 28 187.0 0 38 38 188.0 0 37 37 189.0 0 36 36 190.0 0 38 38 191.0 0 44 44 192.0 0 43 43 193.0 0 31 31 194.0 0 33 33 195.0 0 21 21 196.0 0 28 28 197.0 0 31 31 198.0 0 40 40 199.0 0 27 27 200.0 0 30 30 201.0 0 34 34 202.0 0 25 25 203.0 0 27 27 204.0 0 29 29 205.0 0 35 35 206.0 0 28 28 207.0 0 26 26 208.0 0 44 44 209.0 0 27 27 210.0 0 27 27 211.0 0 33 33 212.0 0 24 24 213.0 0 28 28 214.0 0 29 29 215.0 0 36 36 216.0 0 21 21 217.0 0 21 21 218.0 0 18 18 219.0 0 28 28 220.0 0 28 28 221.0 0 23 23 222.0 0 29 29 223.0 0 23 23 224.0 0 31 31 225.0 0 23 23 226.0 0 24 24 227.0 0 23 23 228.0 0 16 16 229.0 0 32 32 230.0 0 22 22 231.0 0 18 18 232.0 0 25 25 233.0 0 23 23 234.0 0 29 29 235.0 0 24 24 236.0 0 23 23 237.0 0 22 22 238.0 0 18 18 239.0 0 32 32 240.0 0 15 15 241.0 0 28 28 242.0 0 18 18 243.0 0 22 22 244.0 0 22 22 245.0 0 12 12 246.0 0 22 22 247.0 0 17 17 248.0 0 14 14 249.0 0 12 12 250.0 0 22 22 251.0 0 21 21 252.0 0 21 21 253.0 0 15 15 254.0 0 19 19 255.0 0 14 14 256.0 0 20 20 257.0 0 16 16 258.0 0 13 13 259.0 0 15 15 260.0 0 13 13 261.0 0 15 15 262.0 0 14 14 263.0 0 13 13 264.0 0 12 12 265.0 0 16 16 266.0 0 14 14 267.0 0 14 14 268.0 0 16 16 269.0 0 16 16 270.0 0 17 17 271.0 0 18 18 272.0 0 11 11 273.0 0 14 14 274.0 0 19 19 275.0 0 18 18 276.0 0 9 9 277.0 0 13 13 278.0 0 12 12 279.0 0 14 14 280.0 0 12 12 281.0 0 12 12 282.0 0 15 15 283.0 0 19 19 284.0 0 10 10 285.0 0 4 4 286.0 0 4 4 287.0 0 11 11 288.0 0 12 12 289.0 0 15 15 290.0 0 13 13 291.0 0 14 14 292.0 0 18 18 293.0 0 8 8 294.0 0 12 12 295.0 0 8 8 296.0 0 7 7 297.0 0 12 12 298.0 0 12 12 299.0 0 6 6 300.0 0 14 14 301.0 0 11 11 302.0 0 9 9 303.0 0 9 9 304.0 0 12 12 305.0 0 12 12 306.0 0 12 12 307.0 0 13 13 308.0 0 3 3 309.0 0 12 12 310.0 0 10 10 311.0 0 6 6 312.0 0 9 9 313.0 0 15 15 314.0 0 8 8 315.0 0 7 7 316.0 0 7 7 317.0 0 4 4 318.0 0 5 5 319.0 0 9 9 320.0 0 14 14 321.0 0 9 9 322.0 0 11 11 323.0 0 5 5 324.0 0 5 5 325.0 0 7 7 326.0 0 10 10 327.0 0 15 15 328.0 0 7 7 329.0 0 4 4 330.0 0 3 3 331.0 0 12 12 332.0 0 13 13 333.0 0 6 6 334.0 0 7 7 335.0 0 6 6 336.0 0 7 7 337.0 0 11 11 338.0 0 5 5 339.0 0 10 10 340.0 0 6 6 341.0 0 5 5 342.0 0 12 12 343.0 0 6 6 344.0 0 3 3 345.0 0 7 7 346.0 0 5 5 347.0 0 7 7 348.0 0 3 3 349.0 0 10 10 350.0 0 3 3 351.0 0 5 5 352.0 0 6 6 353.0 0 7 7 354.0 0 6 6 355.0 0 8 8 356.0 0 6 6 357.0 0 10 10 358.0 0 10 10 359.0 0 8 8 360.0 0 7 7 361.0 0 7 7 362.0 0 9 9 363.0 0 6 6 364.0 0 16 16 365.0 0 6 6 366.0 0 7 7 367.0 0 11 11 368.0 0 3 3 369.0 0 7 7 370.0 0 7 7 371.0 0 3 3 372.0 0 3 3 373.0 0 10 10 374.0 0 2 2 375.0 0 6 6 376.0 0 6 6 377.0 0 5 5 378.0 0 8 8 379.0 0 3 3 380.0 0 7 7 381.0 0 5 5 382.0 0 6 6 383.0 0 1 1 384.0 0 5 5 385.0 0 4 4 386.0 0 3 3 387.0 0 4 4 388.0 0 6 6 389.0 0 3 3 390.0 0 3 3 391.0 0 3 3 392.0 0 2 2 393.0 0 3 3 394.0 0 10 10 395.0 0 5 5 396.0 0 7 7 397.0 0 6 6 398.0 0 4 4 399.0 0 6 6 400.0 0 3 3 401.0 0 2 2 402.0 0 2 2 403.0 0 1 1 404.0 0 5 5 405.0 0 4 4 406.0 0 9 9 407.0 0 3 3 408.0 0 3 3 409.0 0 4 4 410.0 0 4 4 411.0 0 4 4 412.0 0 9 9 413.0 0 2 2 414.0 0 2 2 415.0 0 3 3 416.0 0 4 4 417.0 0 4 4 418.0 0 3 3 419.0 0 1 1 420.0 0 3 3 421.0 0 2 2 422.0 0 3 3 423.0 0 5 5 424.0 0 4 4 425.0 0 2 2 426.0 0 1 1 427.0 0 4 4 428.0 0 6 6 429.0 0 4 4 430.0 0 3 3 431.0 0 3 3 433.0 0 3 3 434.0 0 1 1 435.0 0 2 2 436.0 0 2 2 437.0 0 4 4 438.0 0 4 4 439.0 0 4 4 440.0 0 6 6 441.0 0 3 3 442.0 0 1 1 443.0 0 2 2 444.0 0 2 2 445.0 0 1 1 446.0 0 2 2 447.0 0 3 3 448.0 0 1 1 449.0 0 7 7 450.0 0 3 3 451.0 0 3 3 452.0 0 3 3 453.0 0 5 5 454.0 0 3 3 455.0 0 5 5 456.0 0 4 4 457.0 0 2 2 458.0 0 3 3 460.0 0 4 4 461.0 0 2 2 462.0 0 4 4 463.0 0 6 6 464.0 0 5 5 465.0 0 3 3 466.0 0 4 4 467.0 0 3 3 468.0 0 2 2 469.0 0 5 5 470.0 0 4 4 471.0 0 5 5 472.0 0 4 4 473.0 0 4 4 474.0 0 5 5 475.0 0 5 5 476.0 0 2 2 477.0 0 4 4 478.0 0 3 3 479.0 0 1 1 480.0 0 3 3 481.0 0 1 1 482.0 0 1 1 483.0 0 2 2 484.0 0 1 1 485.0 0 9 9 486.0 0 2 2 487.0 0 3 3 488.0 0 3 3 489.0 0 3 3 491.0 0 4 4 492.0 0 3 3 493.0 0 4 4 494.0 0 3 3 495.0 0 1 1 496.0 0 6 6 497.0 0 4 4 499.0 0 4 4 500.0 0 3 3 501.0 0 1 1 502.0 0 2 2 503.0 0 1 1 504.0 0 2 2 506.0 0 1 1 508.0 0 4 4 509.0 0 1 1 510.0 0 1 1 511.0 0 2 2 512.0 0 1 1 513.0 0 7 7 515.0 0 4 4 516.0 0 1 1 517.0 0 4 4 518.0 0 1 1 519.0 0 1 1 520.0 0 1 1 521.0 0 4 4 522.0 0 4 4 523.0 0 3 3 524.0 0 3 3 525.0 0 3 3 526.0 0 2 2 527.0 0 2 2 528.0 0 3 3 529.0 0 2 2 530.0 0 1 1 531.0 0 2 2 532.0 0 1 1 533.0 0 4 4 535.0 0 3 3 536.0 0 2 2 537.0 0 3 3 538.0 0 1 1 539.0 0 3 3 540.0 0 1 1 541.0 0 4 4 542.0 0 2 2 543.0 0 4 4 544.0 0 1 1 545.0 0 3 3 546.0 0 3 3 547.0 0 5 5 548.0 0 2 2 549.0 0 2 2 550.0 0 1 1 552.0 0 2 2 553.0 0 2 2 554.0 0 2 2 555.0 0 2 2 556.0 0 1 1 557.0 0 1 1 558.0 0 3 3 559.0 0 2 2 560.0 0 1 1 561.0 0 2 2 562.0 0 2 2 563.0 0 1 1 564.0 0 2 2 565.0 0 2 2 566.0 0 3 3 567.0 0 1 1 568.0 0 3 3 569.0 0 2 2 570.0 0 2 2 571.0 0 4 4 572.0 0 1 1 573.0 0 1 1 574.0 0 4 4 575.0 0 3 3 576.0 0 1 1 577.0 0 1 1 579.0 0 2 2 580.0 0 2 2 581.0 0 2 2 582.0 0 1 1 584.0 0 3 3 585.0 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 1 593.0 0 2 2 594.0 0 1 1 595.0 0 3 3 601.0 0 2 2 602.0 0 1 1 603.0 0 2 2 604.0 0 1 1 605.0 0 3 3 606.0 0 1 1 607.0 0 1 1 608.0 0 1 1 609.0 0 1 1 611.0 0 1 1 615.0 0 1 1 617.0 0 2 2 618.0 0 1 1 620.0 0 2 2 622.0 0 1 1 623.0 0 3 3 624.0 0 2 2 625.0 0 1 1 627.0 0 1 1 631.0 0 3 3 632.0 0 1 1 633.0 0 1 1 634.0 0 1 1 635.0 0 1 1 641.0 0 1 1 646.0 0 2 2 651.0 0 1 1 652.0 0 3 3 654.0 0 1 1 656.0 0 1 1 657.0 0 1 1 659.0 0 1 1 660.0 0 1 1 662.0 0 1 1 664.0 0 1 1 668.0 0 2 2 671.0 0 2 2 673.0 0 1 1 674.0 0 2 2 676.0 0 1 1 677.0 0 1 1 678.0 0 1 1 679.0 0 1 1 685.0 0 1 1 686.0 0 1 1 688.0 0 2 2 690.0 0 2 2 691.0 0 1 1 692.0 0 1 1 693.0 0 1 1 695.0 0 1 1 697.0 0 1 1 698.0 0 2 2 701.0 0 1 1 703.0 0 1 1 704.0 0 1 1 707.0 0 1 1 713.0 0 2 2 714.0 0 1 1 715.0 0 2 2 716.0 0 1 1 717.0 0 2 2 718.0 0 1 1 721.0 0 2 2 722.0 0 1 1 725.0 0 1 1 726.0 0 1 1 731.0 0 1 1 732.0 0 1 1 733.0 0 1 1 735.0 0 1 1 738.0 0 1 1 739.0 0 1 1 743.0 0 1 1 744.0 0 1 1 746.0 0 2 2 747.0 0 2 2 748.0 0 1 1 749.0 0 2 2 750.0 0 1 1 751.0 0 1 1 752.0 0 1 1 755.0 0 2 2 759.0 0 3 3 762.0 0 2 2 767.0 0 2 2 768.0 0 1 1 772.0 0 1 1 773.0 0 5 5 775.0 0 1 1 779.0 0 1 1 783.0 0 1 1 784.0 0 1 1 785.0 0 1 1 786.0 0 1 1 788.0 0 1 1 789.0 0 1 1 790.0 0 1 1 797.0 0 1 1 799.0 0 1 1 801.0 0 1 1 802.0 0 1 1 805.0 0 4 4 809.0 0 1 1 810.0 0 2 2 811.0 0 1 1 818.0 0 1 1 838.0 0 1 1 848.0 0 1 1 850.0 0 1 1 856.0 0 1 1 857.0 0 3 3 858.0 0 2 2 861.0 0 1 1 863.0 0 3 3 876.0 0 1 1 884.0 0 1 1 890.0 0 1 1 891.0 0 1 1 894.0 0 1 1 895.0 0 1 1 899.0 0 2 2 904.0 0 2 2 909.0 0 1 1 920.0 0 1 1 929.0 0 1 1 938.0 0 1 1 945.0 0 1 1 946.0 0 1 1 947.0 0 1 1 953.0 0 1 1 955.0 0 1 1 963.0 0 1 1 967.0 0 1 1 972.0 0 1 1 982.0 0 1 1 994.0 0 1 1 995.0 0 1 1 1004.0 0 1 1 1009.0 0 1 1 1013.0 0 1 1 1015.0 0 1 1 1024.0 0 1 1 1025.0 0 1 1 1027.0 0 1 1 1029.0 0 1 1 1041.0 0 1 1 1052.0 0 1 1 1053.0 0 1 1 1058.0 0 1 1 1062.0 0 1 1 1073.0 0 1 1 1077.0 0 1 1 1084.0 0 1 1 1093.0 0 2 2 1109.0 0 1 1 1113.0 0 1 1 1129.0 0 1 1 1133.0 0 1 1 1140.0 0 2 2 1153.0 0 1 1 1179.0 0 1 1 1182.0 0 1 1 1184.0 0 1 1 1207.0 0 1 1 1212.0 0 1 1 1214.0 0 1 1 1215.0 0 2 2 1245.0 0 1 1 1256.0 0 1 1 1276.0 0 1 1 1281.0 0 1 1 1294.0 0 2 2 1319.0 0 1 1 1324.0 0 1 1 1331.0 0 1 1 1343.0 0 1 1 1350.0 0 1 1 1426.0 0 1 1 1459.0 0 1 1 1467.0 0 1 1 1480.0 0 1 1 1530.0 0 1 1 1572.0 0 1 1 1605.0 0 1 1 1639.0 0 1 1 1651.0 0 1 1 1671.0 0 1 1 1687.0 0 1 1 1788.0 0 1 1 1797.0 0 1 1 1879.0 0 1 1 1923.0 0 1 1 1972.0 0 1 1 2367.0 0 1 1 2525.0 0 1 1 2607.0 0 1 1 3146.0 0 1 1