## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354091.sorted.bam --OUTPUT SRX7354091.markdup.sorted.bam --METRICS_FILE SRX7354091.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: Sat Oct 28 15:17:19 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 80413 67010929 9011114 5485655 68096 31446103 0 0.469495 46665894 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 24120671 24120671 2.0 1.237884 6971943 6971943 3.0 1.294473 2235561 2235561 4.0 1.307934 842580 842580 5.0 1.311137 386649 386649 6.0 1.311898 214670 214670 7.0 1.31208 138015 138015 8.0 1.312123 97578 97578 9.0 1.312133 73648 73648 10.0 1.312135 57444 57444 11.0 1.312136 46358 46358 12.0 1.312136 38387 38387 13.0 1.312136 32005 32005 14.0 1.312136 27273 27273 15.0 1.312136 23488 23488 16.0 1.312136 20116 20116 17.0 1.312136 18007 18007 18.0 1.312136 15681 15681 19.0 1.312136 13984 13984 20.0 1.312136 12291 12291 21.0 1.312136 11315 11315 22.0 1.312136 10072 10072 23.0 1.312136 9072 9072 24.0 1.312136 8266 8266 25.0 1.312136 7549 7549 26.0 1.312136 6962 6962 27.0 1.312136 6361 6361 28.0 1.312136 5804 5804 29.0 1.312136 5319 5319 30.0 1.312136 4894 4894 31.0 1.312136 4618 4618 32.0 1.312136 4263 4263 33.0 1.312136 4025 4025 34.0 1.312136 3753 3753 35.0 1.312136 3499 3499 36.0 1.312136 3250 3250 37.0 1.312136 3130 3130 38.0 1.312136 2925 2925 39.0 1.312136 2729 2729 40.0 1.312136 2537 2537 41.0 1.312136 2502 2502 42.0 1.312136 2353 2353 43.0 1.312136 2152 2152 44.0 1.312136 2097 2097 45.0 1.312136 2031 2031 46.0 1.312136 1889 1889 47.0 1.312136 1815 1815 48.0 1.312136 1684 1684 49.0 1.312136 1607 1607 50.0 1.312136 1476 1476 51.0 1.312136 1476 1476 52.0 1.312136 1398 1398 53.0 1.312136 1356 1356 54.0 1.312136 1256 1256 55.0 1.312136 1304 1304 56.0 1.312136 1161 1161 57.0 1.312136 1111 1111 58.0 1.312136 1094 1094 59.0 1.312136 1022 1022 60.0 1.312136 950 950 61.0 1.312136 983 983 62.0 1.312136 901 901 63.0 1.312136 880 880 64.0 1.312136 809 809 65.0 1.312136 786 786 66.0 1.312136 818 818 67.0 1.312136 737 737 68.0 1.312136 706 706 69.0 1.312136 687 687 70.0 1.312136 723 723 71.0 1.312136 640 640 72.0 1.312136 662 662 73.0 1.312136 611 611 74.0 1.312136 554 554 75.0 1.312136 611 611 76.0 1.312136 508 508 77.0 1.312136 550 550 78.0 1.312136 535 535 79.0 1.312136 533 533 80.0 1.312136 446 446 81.0 1.312136 501 501 82.0 1.312136 454 454 83.0 1.312136 434 434 84.0 1.312136 446 446 85.0 1.312136 409 409 86.0 1.312136 391 391 87.0 1.312136 393 393 88.0 1.312136 372 372 89.0 1.312136 348 348 90.0 1.312136 325 325 91.0 1.312136 373 373 92.0 1.312136 394 394 93.0 1.312136 363 363 94.0 1.312136 310 310 95.0 1.312136 324 324 96.0 1.312136 325 325 97.0 1.312136 288 288 98.0 1.312136 276 276 99.0 1.312136 286 286 100.0 1.312136 278 278 101.0 0 263 263 102.0 0 252 252 103.0 0 270 270 104.0 0 264 264 105.0 0 243 243 106.0 0 260 260 107.0 0 207 207 108.0 0 227 227 109.0 0 220 220 110.0 0 203 203 111.0 0 228 228 112.0 0 212 212 113.0 0 211 211 114.0 0 182 182 115.0 0 179 179 116.0 0 188 188 117.0 0 210 210 118.0 0 177 177 119.0 0 193 193 120.0 0 173 173 121.0 0 162 162 122.0 0 178 178 123.0 0 161 161 124.0 0 165 165 125.0 0 153 153 126.0 0 150 150 127.0 0 141 141 128.0 0 155 155 129.0 0 143 143 130.0 0 146 146 131.0 0 128 128 132.0 0 150 150 133.0 0 127 127 134.0 0 124 124 135.0 0 124 124 136.0 0 135 135 137.0 0 138 138 138.0 0 122 122 139.0 0 94 94 140.0 0 109 109 141.0 0 123 123 142.0 0 122 122 143.0 0 113 113 144.0 0 104 104 145.0 0 105 105 146.0 0 86 86 147.0 0 97 97 148.0 0 101 101 149.0 0 92 92 150.0 0 82 82 151.0 0 102 102 152.0 0 86 86 153.0 0 85 85 154.0 0 76 76 155.0 0 93 93 156.0 0 88 88 157.0 0 70 70 158.0 0 81 81 159.0 0 81 81 160.0 0 99 99 161.0 0 88 88 162.0 0 78 78 163.0 0 79 79 164.0 0 80 80 165.0 0 82 82 166.0 0 72 72 167.0 0 65 65 168.0 0 74 74 169.0 0 75 75 170.0 0 58 58 171.0 0 71 71 172.0 0 68 68 173.0 0 60 60 174.0 0 68 68 175.0 0 75 75 176.0 0 64 64 177.0 0 63 63 178.0 0 53 53 179.0 0 56 56 180.0 0 61 61 181.0 0 55 55 182.0 0 51 51 183.0 0 48 48 184.0 0 56 56 185.0 0 45 45 186.0 0 55 55 187.0 0 63 63 188.0 0 45 45 189.0 0 51 51 190.0 0 40 40 191.0 0 45 45 192.0 0 43 43 193.0 0 45 45 194.0 0 36 36 195.0 0 53 53 196.0 0 49 49 197.0 0 49 49 198.0 0 38 38 199.0 0 35 35 200.0 0 47 47 201.0 0 43 43 202.0 0 42 42 203.0 0 45 45 204.0 0 42 42 205.0 0 46 46 206.0 0 36 36 207.0 0 32 32 208.0 0 34 34 209.0 0 32 32 210.0 0 32 32 211.0 0 43 43 212.0 0 39 39 213.0 0 38 38 214.0 0 33 33 215.0 0 36 36 216.0 0 37 37 217.0 0 39 39 218.0 0 28 28 219.0 0 38 38 220.0 0 25 25 221.0 0 37 37 222.0 0 35 35 223.0 0 38 38 224.0 0 30 30 225.0 0 30 30 226.0 0 33 33 227.0 0 30 30 228.0 0 25 25 229.0 0 27 27 230.0 0 29 29 231.0 0 24 24 232.0 0 30 30 233.0 0 34 34 234.0 0 26 26 235.0 0 29 29 236.0 0 34 34 237.0 0 27 27 238.0 0 22 22 239.0 0 16 16 240.0 0 23 23 241.0 0 25 25 242.0 0 22 22 243.0 0 20 20 244.0 0 20 20 245.0 0 25 25 246.0 0 29 29 247.0 0 23 23 248.0 0 27 27 249.0 0 17 17 250.0 0 28 28 251.0 0 23 23 252.0 0 17 17 253.0 0 26 26 254.0 0 22 22 255.0 0 35 35 256.0 0 21 21 257.0 0 22 22 258.0 0 20 20 259.0 0 21 21 260.0 0 27 27 261.0 0 19 19 262.0 0 24 24 263.0 0 19 19 264.0 0 24 24 265.0 0 23 23 266.0 0 22 22 267.0 0 14 14 268.0 0 15 15 269.0 0 7 7 270.0 0 26 26 271.0 0 13 13 272.0 0 16 16 273.0 0 23 23 274.0 0 7 7 275.0 0 9 9 276.0 0 12 12 277.0 0 21 21 278.0 0 13 13 279.0 0 23 23 280.0 0 17 17 281.0 0 13 13 282.0 0 11 11 283.0 0 16 16 284.0 0 11 11 285.0 0 15 15 286.0 0 25 25 287.0 0 19 19 288.0 0 20 20 289.0 0 12 12 290.0 0 16 16 291.0 0 8 8 292.0 0 11 11 293.0 0 15 15 294.0 0 9 9 295.0 0 10 10 296.0 0 16 16 297.0 0 13 13 298.0 0 13 13 299.0 0 17 17 300.0 0 8 8 301.0 0 15 15 302.0 0 16 16 303.0 0 14 14 304.0 0 13 13 305.0 0 10 10 306.0 0 15 15 307.0 0 15 15 308.0 0 15 15 309.0 0 8 8 310.0 0 12 12 311.0 0 12 12 312.0 0 14 14 313.0 0 16 16 314.0 0 8 8 315.0 0 9 9 316.0 0 8 8 317.0 0 8 8 318.0 0 14 14 319.0 0 8 8 320.0 0 8 8 321.0 0 6 6 322.0 0 14 14 323.0 0 10 10 324.0 0 5 5 325.0 0 11 11 326.0 0 12 12 327.0 0 7 7 328.0 0 10 10 329.0 0 10 10 330.0 0 10 10 331.0 0 7 7 332.0 0 12 12 333.0 0 15 15 334.0 0 15 15 335.0 0 14 14 336.0 0 3 3 337.0 0 9 9 338.0 0 11 11 339.0 0 3 3 340.0 0 7 7 341.0 0 6 6 342.0 0 7 7 343.0 0 8 8 344.0 0 11 11 345.0 0 7 7 346.0 0 8 8 347.0 0 10 10 348.0 0 8 8 349.0 0 8 8 350.0 0 14 14 351.0 0 10 10 352.0 0 8 8 353.0 0 8 8 354.0 0 4 4 355.0 0 7 7 356.0 0 4 4 357.0 0 10 10 358.0 0 10 10 359.0 0 9 9 360.0 0 3 3 361.0 0 6 6 362.0 0 12 12 363.0 0 12 12 364.0 0 12 12 365.0 0 7 7 366.0 0 6 6 367.0 0 3 3 368.0 0 5 5 369.0 0 10 10 370.0 0 3 3 371.0 0 3 3 372.0 0 6 6 373.0 0 9 9 374.0 0 8 8 375.0 0 7 7 376.0 0 8 8 377.0 0 5 5 378.0 0 8 8 379.0 0 8 8 380.0 0 6 6 381.0 0 7 7 382.0 0 5 5 383.0 0 3 3 384.0 0 4 4 385.0 0 9 9 386.0 0 8 8 387.0 0 4 4 388.0 0 8 8 389.0 0 4 4 390.0 0 4 4 391.0 0 6 6 392.0 0 4 4 393.0 0 4 4 394.0 0 3 3 395.0 0 2 2 396.0 0 5 5 397.0 0 6 6 398.0 0 4 4 399.0 0 4 4 400.0 0 4 4 401.0 0 5 5 402.0 0 4 4 403.0 0 2 2 405.0 0 6 6 406.0 0 6 6 407.0 0 7 7 408.0 0 3 3 409.0 0 5 5 410.0 0 4 4 411.0 0 3 3 412.0 0 8 8 413.0 0 9 9 414.0 0 8 8 415.0 0 6 6 416.0 0 9 9 417.0 0 5 5 418.0 0 2 2 419.0 0 4 4 420.0 0 4 4 421.0 0 7 7 422.0 0 3 3 423.0 0 6 6 424.0 0 2 2 425.0 0 3 3 426.0 0 2 2 427.0 0 2 2 428.0 0 4 4 429.0 0 2 2 430.0 0 1 1 431.0 0 3 3 432.0 0 3 3 433.0 0 7 7 435.0 0 4 4 436.0 0 4 4 437.0 0 3 3 438.0 0 4 4 439.0 0 3 3 440.0 0 2 2 441.0 0 3 3 442.0 0 3 3 443.0 0 5 5 444.0 0 4 4 445.0 0 5 5 446.0 0 4 4 447.0 0 5 5 448.0 0 2 2 449.0 0 3 3 450.0 0 2 2 451.0 0 1 1 452.0 0 5 5 453.0 0 4 4 454.0 0 3 3 455.0 0 2 2 456.0 0 2 2 457.0 0 2 2 458.0 0 1 1 459.0 0 4 4 460.0 0 5 5 461.0 0 2 2 462.0 0 4 4 463.0 0 5 5 464.0 0 7 7 465.0 0 2 2 466.0 0 2 2 467.0 0 3 3 468.0 0 2 2 469.0 0 3 3 470.0 0 6 6 471.0 0 2 2 472.0 0 5 5 473.0 0 3 3 474.0 0 6 6 475.0 0 1 1 476.0 0 6 6 477.0 0 1 1 478.0 0 3 3 479.0 0 6 6 480.0 0 2 2 481.0 0 1 1 482.0 0 2 2 483.0 0 2 2 484.0 0 3 3 485.0 0 5 5 486.0 0 3 3 487.0 0 5 5 488.0 0 4 4 489.0 0 4 4 490.0 0 2 2 491.0 0 8 8 492.0 0 1 1 493.0 0 4 4 494.0 0 3 3 495.0 0 3 3 496.0 0 3 3 497.0 0 3 3 498.0 0 5 5 499.0 0 2 2 501.0 0 1 1 502.0 0 4 4 503.0 0 3 3 504.0 0 3 3 505.0 0 3 3 506.0 0 5 5 508.0 0 2 2 509.0 0 1 1 510.0 0 2 2 511.0 0 7 7 512.0 0 1 1 513.0 0 2 2 514.0 0 2 2 515.0 0 3 3 516.0 0 2 2 517.0 0 2 2 518.0 0 2 2 519.0 0 2 2 520.0 0 2 2 521.0 0 6 6 522.0 0 2 2 524.0 0 2 2 526.0 0 1 1 527.0 0 2 2 528.0 0 3 3 529.0 0 3 3 530.0 0 2 2 531.0 0 1 1 533.0 0 2 2 534.0 0 5 5 535.0 0 2 2 536.0 0 4 4 537.0 0 1 1 538.0 0 2 2 539.0 0 1 1 540.0 0 4 4 541.0 0 2 2 542.0 0 1 1 543.0 0 2 2 544.0 0 2 2 545.0 0 3 3 546.0 0 2 2 547.0 0 2 2 548.0 0 2 2 549.0 0 2 2 550.0 0 1 1 551.0 0 4 4 552.0 0 2 2 553.0 0 1 1 554.0 0 1 1 555.0 0 2 2 556.0 0 5 5 557.0 0 2 2 558.0 0 3 3 559.0 0 1 1 560.0 0 1 1 564.0 0 1 1 565.0 0 3 3 566.0 0 2 2 567.0 0 2 2 568.0 0 2 2 569.0 0 1 1 571.0 0 1 1 572.0 0 2 2 573.0 0 1 1 574.0 0 2 2 575.0 0 5 5 576.0 0 4 4 577.0 0 3 3 578.0 0 2 2 579.0 0 1 1 580.0 0 1 1 583.0 0 1 1 584.0 0 3 3 585.0 0 1 1 586.0 0 3 3 590.0 0 3 3 591.0 0 1 1 592.0 0 1 1 593.0 0 1 1 594.0 0 1 1 595.0 0 3 3 597.0 0 3 3 599.0 0 1 1 600.0 0 1 1 601.0 0 2 2 602.0 0 1 1 604.0 0 2 2 606.0 0 1 1 609.0 0 1 1 610.0 0 2 2 611.0 0 2 2 612.0 0 1 1 615.0 0 1 1 616.0 0 3 3 617.0 0 1 1 620.0 0 1 1 621.0 0 5 5 622.0 0 4 4 624.0 0 2 2 625.0 0 1 1 627.0 0 3 3 629.0 0 2 2 632.0 0 3 3 634.0 0 2 2 636.0 0 2 2 637.0 0 3 3 638.0 0 3 3 639.0 0 2 2 640.0 0 1 1 641.0 0 2 2 642.0 0 2 2 643.0 0 1 1 644.0 0 1 1 645.0 0 1 1 646.0 0 1 1 647.0 0 2 2 649.0 0 2 2 650.0 0 1 1 651.0 0 1 1 653.0 0 2 2 655.0 0 1 1 656.0 0 1 1 657.0 0 1 1 660.0 0 1 1 661.0 0 1 1 663.0 0 1 1 664.0 0 1 1 666.0 0 1 1 668.0 0 1 1 670.0 0 1 1 671.0 0 3 3 672.0 0 1 1 675.0 0 1 1 677.0 0 1 1 680.0 0 1 1 683.0 0 3 3 686.0 0 2 2 688.0 0 1 1 690.0 0 1 1 692.0 0 1 1 695.0 0 1 1 696.0 0 1 1 699.0 0 1 1 700.0 0 1 1 701.0 0 2 2 702.0 0 1 1 703.0 0 2 2 704.0 0 1 1 706.0 0 1 1 707.0 0 2 2 712.0 0 1 1 714.0 0 1 1 715.0 0 1 1 721.0 0 1 1 723.0 0 2 2 726.0 0 2 2 729.0 0 2 2 731.0 0 1 1 732.0 0 1 1 734.0 0 1 1 735.0 0 1 1 737.0 0 1 1 739.0 0 1 1 740.0 0 1 1 744.0 0 1 1 749.0 0 1 1 752.0 0 1 1 755.0 0 2 2 756.0 0 1 1 758.0 0 1 1 762.0 0 1 1 767.0 0 2 2 774.0 0 1 1 780.0 0 1 1 782.0 0 1 1 784.0 0 1 1 785.0 0 1 1 788.0 0 1 1 789.0 0 2 2 792.0 0 1 1 794.0 0 1 1 799.0 0 1 1 803.0 0 1 1 805.0 0 1 1 815.0 0 1 1 816.0 0 2 2 817.0 0 1 1 820.0 0 2 2 829.0 0 1 1 832.0 0 1 1 834.0 0 1 1 838.0 0 1 1 851.0 0 1 1 852.0 0 1 1 854.0 0 2 2 855.0 0 1 1 870.0 0 1 1 877.0 0 1 1 879.0 0 1 1 883.0 0 1 1 884.0 0 1 1 895.0 0 1 1 898.0 0 2 2 913.0 0 1 1 914.0 0 1 1 917.0 0 1 1 918.0 0 1 1 919.0 0 1 1 924.0 0 1 1 931.0 0 1 1 940.0 0 1 1 945.0 0 1 1 946.0 0 1 1 947.0 0 1 1 950.0 0 1 1 951.0 0 1 1 959.0 0 3 3 967.0 0 1 1 973.0 0 1 1 977.0 0 1 1 983.0 0 1 1 993.0 0 1 1 995.0 0 1 1 1002.0 0 1 1 1008.0 0 1 1 1009.0 0 1 1 1012.0 0 1 1 1015.0 0 2 2 1032.0 0 1 1 1042.0 0 2 2 1049.0 0 1 1 1073.0 0 1 1 1078.0 0 1 1 1082.0 0 1 1 1091.0 0 1 1 1109.0 0 1 1 1111.0 0 1 1 1125.0 0 1 1 1145.0 0 1 1 1164.0 0 1 1 1171.0 0 1 1 1184.0 0 1 1 1185.0 0 1 1 1188.0 0 1 1 1232.0 0 1 1 1246.0 0 1 1 1255.0 0 1 1 1274.0 0 1 1 1276.0 0 1 1 1293.0 0 1 1 1314.0 0 1 1 1322.0 0 1 1 1327.0 0 1 1 1346.0 0 1 1 1398.0 0 1 1 1403.0 0 1 1 1536.0 0 1 1 1590.0 0 1 1 1603.0 0 1 1 1631.0 0 1 1 1640.0 0 1 1 1641.0 0 1 1 1697.0 0 1 1 1711.0 0 1 1 1745.0 0 1 1 2040.0 0 1 1 2087.0 0 1 1 2451.0 0 1 1 2563.0 0 1 1 3290.0 0 1 1 4016.0 0 1 1