## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354268.sorted.bam --OUTPUT SRX7354268.markdup.sorted.bam --METRICS_FILE SRX7354268.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 20:08:30 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 46403 45177618 7358215 3522613 40643 27389900 0 0.60641 19814306 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 8939803 8939803 2.0 1.102279 4360656 4360656 3.0 1.11274 2019071 2019071 4.0 1.11381 947919 947919 5.0 1.113919 476336 476336 6.0 1.113931 263940 263940 7.0 1.113932 162454 162454 8.0 1.113932 108589 108589 9.0 1.113932 77939 77939 10.0 1.113932 58871 58871 11.0 1.113932 46275 46275 12.0 1.113932 37231 37231 13.0 1.113932 30375 30375 14.0 1.113932 25221 25221 15.0 1.113932 21201 21201 16.0 1.113932 18277 18277 17.0 1.113932 15644 15644 18.0 1.113932 13611 13611 19.0 1.113932 12169 12169 20.0 1.113932 10683 10683 21.0 1.113932 9502 9502 22.0 1.113932 8354 8354 23.0 1.113932 7557 7557 24.0 1.113932 6757 6757 25.0 1.113932 6162 6162 26.0 1.113932 5695 5695 27.0 1.113932 5205 5205 28.0 1.113932 4778 4778 29.0 1.113932 4405 4405 30.0 1.113932 4020 4020 31.0 1.113932 3773 3773 32.0 1.113932 3465 3465 33.0 1.113932 3260 3260 34.0 1.113932 2997 2997 35.0 1.113932 2656 2656 36.0 1.113932 2581 2581 37.0 1.113932 2410 2410 38.0 1.113932 2217 2217 39.0 1.113932 2146 2146 40.0 1.113932 1998 1998 41.0 1.113932 1876 1876 42.0 1.113932 1788 1788 43.0 1.113932 1701 1701 44.0 1.113932 1646 1646 45.0 1.113932 1507 1507 46.0 1.113932 1508 1508 47.0 1.113932 1364 1364 48.0 1.113932 1263 1263 49.0 1.113932 1239 1239 50.0 1.113932 1209 1209 51.0 1.113932 1063 1063 52.0 1.113932 1031 1031 53.0 1.113932 1069 1069 54.0 1.113932 967 967 55.0 1.113932 896 896 56.0 1.113932 861 861 57.0 1.113932 874 874 58.0 1.113932 797 797 59.0 1.113932 777 777 60.0 1.113932 750 750 61.0 1.113932 731 731 62.0 1.113932 687 687 63.0 1.113932 609 609 64.0 1.113932 630 630 65.0 1.113932 629 629 66.0 1.113932 539 539 67.0 1.113932 579 579 68.0 1.113932 546 546 69.0 1.113932 537 537 70.0 1.113932 516 516 71.0 1.113932 543 543 72.0 1.113932 500 500 73.0 1.113932 468 468 74.0 1.113932 436 436 75.0 1.113932 415 415 76.0 1.113932 399 399 77.0 1.113932 370 370 78.0 1.113932 373 373 79.0 1.113932 411 411 80.0 1.113932 352 352 81.0 1.113932 375 375 82.0 1.113932 351 351 83.0 1.113932 337 337 84.0 1.113932 315 315 85.0 1.113932 302 302 86.0 1.113932 330 330 87.0 1.113932 287 287 88.0 1.113932 266 266 89.0 1.113932 295 295 90.0 1.113932 259 259 91.0 1.113932 253 253 92.0 1.113932 247 247 93.0 1.113932 263 263 94.0 1.113932 238 238 95.0 1.113932 249 249 96.0 1.113932 238 238 97.0 1.113932 203 203 98.0 1.113932 245 245 99.0 1.113932 211 211 100.0 1.113932 208 208 101.0 0 223 223 102.0 0 185 185 103.0 0 219 219 104.0 0 157 157 105.0 0 172 172 106.0 0 161 161 107.0 0 193 193 108.0 0 152 152 109.0 0 157 157 110.0 0 154 154 111.0 0 169 169 112.0 0 151 151 113.0 0 145 145 114.0 0 167 167 115.0 0 133 133 116.0 0 141 141 117.0 0 118 118 118.0 0 135 135 119.0 0 133 133 120.0 0 119 119 121.0 0 142 142 122.0 0 123 123 123.0 0 103 103 124.0 0 121 121 125.0 0 119 119 126.0 0 93 93 127.0 0 117 117 128.0 0 114 114 129.0 0 103 103 130.0 0 118 118 131.0 0 104 104 132.0 0 103 103 133.0 0 108 108 134.0 0 79 79 135.0 0 107 107 136.0 0 76 76 137.0 0 94 94 138.0 0 77 77 139.0 0 99 99 140.0 0 95 95 141.0 0 78 78 142.0 0 68 68 143.0 0 78 78 144.0 0 82 82 145.0 0 74 74 146.0 0 74 74 147.0 0 86 86 148.0 0 78 78 149.0 0 70 70 150.0 0 68 68 151.0 0 69 69 152.0 0 64 64 153.0 0 62 62 154.0 0 59 59 155.0 0 60 60 156.0 0 50 50 157.0 0 53 53 158.0 0 77 77 159.0 0 65 65 160.0 0 66 66 161.0 0 55 55 162.0 0 64 64 163.0 0 51 51 164.0 0 56 56 165.0 0 63 63 166.0 0 52 52 167.0 0 53 53 168.0 0 52 52 169.0 0 49 49 170.0 0 70 70 171.0 0 58 58 172.0 0 45 45 173.0 0 47 47 174.0 0 55 55 175.0 0 53 53 176.0 0 56 56 177.0 0 45 45 178.0 0 36 36 179.0 0 41 41 180.0 0 51 51 181.0 0 51 51 182.0 0 40 40 183.0 0 49 49 184.0 0 43 43 185.0 0 32 32 186.0 0 30 30 187.0 0 50 50 188.0 0 30 30 189.0 0 48 48 190.0 0 35 35 191.0 0 45 45 192.0 0 44 44 193.0 0 22 22 194.0 0 31 31 195.0 0 37 37 196.0 0 24 24 197.0 0 33 33 198.0 0 39 39 199.0 0 31 31 200.0 0 36 36 201.0 0 24 24 202.0 0 31 31 203.0 0 25 25 204.0 0 23 23 205.0 0 32 32 206.0 0 33 33 207.0 0 30 30 208.0 0 26 26 209.0 0 31 31 210.0 0 27 27 211.0 0 22 22 212.0 0 24 24 213.0 0 27 27 214.0 0 21 21 215.0 0 20 20 216.0 0 29 29 217.0 0 22 22 218.0 0 34 34 219.0 0 20 20 220.0 0 21 21 221.0 0 29 29 222.0 0 24 24 223.0 0 23 23 224.0 0 17 17 225.0 0 25 25 226.0 0 29 29 227.0 0 30 30 228.0 0 23 23 229.0 0 19 19 230.0 0 17 17 231.0 0 24 24 232.0 0 11 11 233.0 0 20 20 234.0 0 18 18 235.0 0 26 26 236.0 0 16 16 237.0 0 21 21 238.0 0 14 14 239.0 0 18 18 240.0 0 18 18 241.0 0 17 17 242.0 0 14 14 243.0 0 15 15 244.0 0 13 13 245.0 0 20 20 246.0 0 22 22 247.0 0 15 15 248.0 0 19 19 249.0 0 13 13 250.0 0 15 15 251.0 0 14 14 252.0 0 19 19 253.0 0 12 12 254.0 0 13 13 255.0 0 10 10 256.0 0 12 12 257.0 0 14 14 258.0 0 13 13 259.0 0 16 16 260.0 0 18 18 261.0 0 10 10 262.0 0 17 17 263.0 0 15 15 264.0 0 11 11 265.0 0 14 14 266.0 0 13 13 267.0 0 13 13 268.0 0 20 20 269.0 0 18 18 270.0 0 11 11 271.0 0 13 13 272.0 0 11 11 273.0 0 13 13 274.0 0 13 13 275.0 0 14 14 276.0 0 18 18 277.0 0 14 14 278.0 0 12 12 279.0 0 8 8 280.0 0 14 14 281.0 0 14 14 282.0 0 17 17 283.0 0 14 14 284.0 0 6 6 285.0 0 11 11 286.0 0 9 9 287.0 0 8 8 288.0 0 17 17 289.0 0 5 5 290.0 0 6 6 291.0 0 12 12 292.0 0 7 7 293.0 0 10 10 294.0 0 10 10 295.0 0 15 15 296.0 0 7 7 297.0 0 9 9 298.0 0 13 13 299.0 0 13 13 300.0 0 13 13 301.0 0 18 18 302.0 0 10 10 303.0 0 13 13 304.0 0 11 11 305.0 0 8 8 306.0 0 9 9 307.0 0 6 6 308.0 0 7 7 309.0 0 8 8 310.0 0 5 5 311.0 0 6 6 312.0 0 9 9 313.0 0 14 14 314.0 0 5 5 315.0 0 11 11 316.0 0 5 5 317.0 0 13 13 318.0 0 3 3 319.0 0 8 8 320.0 0 8 8 321.0 0 10 10 322.0 0 5 5 323.0 0 8 8 324.0 0 4 4 325.0 0 9 9 326.0 0 7 7 327.0 0 11 11 328.0 0 8 8 329.0 0 9 9 330.0 0 6 6 331.0 0 5 5 332.0 0 5 5 333.0 0 8 8 334.0 0 11 11 335.0 0 7 7 336.0 0 2 2 337.0 0 8 8 338.0 0 7 7 339.0 0 10 10 340.0 0 10 10 341.0 0 8 8 342.0 0 1 1 343.0 0 5 5 344.0 0 6 6 345.0 0 10 10 346.0 0 8 8 347.0 0 6 6 348.0 0 4 4 349.0 0 3 3 350.0 0 4 4 351.0 0 8 8 352.0 0 4 4 353.0 0 5 5 354.0 0 6 6 355.0 0 4 4 356.0 0 6 6 357.0 0 3 3 358.0 0 7 7 359.0 0 5 5 360.0 0 7 7 361.0 0 9 9 362.0 0 5 5 363.0 0 9 9 364.0 0 4 4 365.0 0 3 3 366.0 0 8 8 367.0 0 5 5 368.0 0 11 11 369.0 0 5 5 370.0 0 1 1 371.0 0 6 6 372.0 0 1 1 373.0 0 5 5 374.0 0 5 5 375.0 0 9 9 376.0 0 3 3 377.0 0 4 4 378.0 0 4 4 379.0 0 4 4 380.0 0 1 1 381.0 0 7 7 382.0 0 5 5 383.0 0 4 4 384.0 0 2 2 385.0 0 11 11 386.0 0 6 6 387.0 0 2 2 388.0 0 8 8 389.0 0 8 8 390.0 0 7 7 391.0 0 4 4 392.0 0 5 5 393.0 0 4 4 394.0 0 6 6 395.0 0 6 6 396.0 0 3 3 397.0 0 1 1 398.0 0 1 1 399.0 0 8 8 400.0 0 5 5 401.0 0 4 4 402.0 0 7 7 403.0 0 3 3 404.0 0 1 1 405.0 0 8 8 406.0 0 9 9 407.0 0 8 8 408.0 0 3 3 409.0 0 4 4 410.0 0 2 2 411.0 0 2 2 412.0 0 6 6 413.0 0 5 5 414.0 0 3 3 415.0 0 6 6 416.0 0 5 5 417.0 0 4 4 418.0 0 3 3 419.0 0 9 9 420.0 0 1 1 421.0 0 4 4 422.0 0 7 7 423.0 0 4 4 424.0 0 2 2 425.0 0 5 5 426.0 0 7 7 427.0 0 6 6 428.0 0 3 3 429.0 0 3 3 430.0 0 5 5 431.0 0 8 8 432.0 0 4 4 433.0 0 3 3 434.0 0 2 2 435.0 0 6 6 436.0 0 4 4 437.0 0 1 1 438.0 0 1 1 439.0 0 7 7 440.0 0 2 2 441.0 0 2 2 442.0 0 2 2 443.0 0 2 2 444.0 0 3 3 445.0 0 4 4 446.0 0 5 5 447.0 0 2 2 448.0 0 2 2 449.0 0 2 2 450.0 0 4 4 451.0 0 2 2 452.0 0 3 3 453.0 0 4 4 454.0 0 2 2 455.0 0 2 2 456.0 0 4 4 457.0 0 2 2 458.0 0 2 2 459.0 0 2 2 460.0 0 2 2 461.0 0 1 1 462.0 0 6 6 463.0 0 3 3 464.0 0 4 4 465.0 0 3 3 466.0 0 2 2 467.0 0 2 2 468.0 0 6 6 469.0 0 1 1 470.0 0 4 4 471.0 0 3 3 472.0 0 1 1 473.0 0 3 3 474.0 0 4 4 475.0 0 2 2 476.0 0 1 1 477.0 0 2 2 478.0 0 4 4 480.0 0 1 1 481.0 0 6 6 482.0 0 2 2 483.0 0 1 1 484.0 0 2 2 485.0 0 4 4 487.0 0 4 4 488.0 0 4 4 489.0 0 4 4 490.0 0 3 3 491.0 0 4 4 493.0 0 2 2 494.0 0 3 3 495.0 0 2 2 496.0 0 3 3 497.0 0 2 2 498.0 0 2 2 499.0 0 1 1 500.0 0 1 1 502.0 0 4 4 503.0 0 3 3 504.0 0 2 2 505.0 0 4 4 506.0 0 4 4 507.0 0 2 2 508.0 0 1 1 509.0 0 1 1 510.0 0 2 2 511.0 0 1 1 513.0 0 1 1 514.0 0 4 4 515.0 0 2 2 517.0 0 2 2 518.0 0 1 1 520.0 0 3 3 522.0 0 3 3 523.0 0 5 5 524.0 0 3 3 525.0 0 1 1 526.0 0 2 2 527.0 0 2 2 528.0 0 1 1 529.0 0 3 3 530.0 0 2 2 531.0 0 2 2 532.0 0 1 1 534.0 0 1 1 536.0 0 2 2 537.0 0 2 2 538.0 0 3 3 539.0 0 3 3 540.0 0 2 2 541.0 0 1 1 542.0 0 1 1 543.0 0 3 3 544.0 0 1 1 546.0 0 2 2 547.0 0 2 2 548.0 0 2 2 549.0 0 1 1 550.0 0 2 2 551.0 0 3 3 552.0 0 2 2 553.0 0 2 2 554.0 0 2 2 555.0 0 3 3 556.0 0 1 1 558.0 0 1 1 559.0 0 1 1 562.0 0 5 5 564.0 0 1 1 565.0 0 4 4 567.0 0 2 2 568.0 0 1 1 570.0 0 1 1 571.0 0 3 3 573.0 0 2 2 574.0 0 3 3 576.0 0 3 3 577.0 0 4 4 578.0 0 2 2 579.0 0 1 1 581.0 0 4 4 583.0 0 1 1 584.0 0 3 3 585.0 0 1 1 586.0 0 2 2 587.0 0 2 2 588.0 0 1 1 590.0 0 2 2 592.0 0 1 1 597.0 0 2 2 599.0 0 2 2 600.0 0 1 1 602.0 0 1 1 604.0 0 1 1 605.0 0 3 3 606.0 0 1 1 608.0 0 2 2 609.0 0 2 2 610.0 0 2 2 611.0 0 1 1 612.0 0 2 2 613.0 0 1 1 614.0 0 3 3 615.0 0 1 1 617.0 0 1 1 620.0 0 3 3 621.0 0 1 1 622.0 0 1 1 623.0 0 1 1 624.0 0 1 1 625.0 0 2 2 626.0 0 3 3 627.0 0 1 1 628.0 0 2 2 629.0 0 1 1 632.0 0 1 1 634.0 0 1 1 635.0 0 1 1 636.0 0 1 1 638.0 0 2 2 639.0 0 1 1 641.0 0 1 1 642.0 0 1 1 643.0 0 1 1 644.0 0 1 1 645.0 0 1 1 648.0 0 3 3 649.0 0 1 1 651.0 0 1 1 653.0 0 2 2 656.0 0 1 1 662.0 0 1 1 663.0 0 1 1 664.0 0 2 2 665.0 0 1 1 670.0 0 2 2 671.0 0 2 2 673.0 0 2 2 674.0 0 1 1 676.0 0 1 1 677.0 0 3 3 678.0 0 1 1 683.0 0 1 1 685.0 0 1 1 688.0 0 2 2 689.0 0 1 1 690.0 0 2 2 693.0 0 2 2 694.0 0 1 1 698.0 0 1 1 702.0 0 2 2 703.0 0 2 2 705.0 0 2 2 707.0 0 1 1 708.0 0 1 1 712.0 0 1 1 713.0 0 1 1 715.0 0 2 2 717.0 0 1 1 718.0 0 1 1 722.0 0 1 1 723.0 0 2 2 724.0 0 2 2 727.0 0 3 3 729.0 0 1 1 730.0 0 1 1 736.0 0 1 1 737.0 0 1 1 739.0 0 1 1 740.0 0 1 1 741.0 0 2 2 742.0 0 1 1 745.0 0 2 2 746.0 0 1 1 748.0 0 1 1 750.0 0 1 1 755.0 0 1 1 760.0 0 1 1 761.0 0 2 2 762.0 0 1 1 763.0 0 1 1 768.0 0 2 2 775.0 0 1 1 779.0 0 1 1 780.0 0 1 1 781.0 0 1 1 782.0 0 1 1 786.0 0 1 1 787.0 0 1 1 794.0 0 1 1 795.0 0 1 1 796.0 0 1 1 798.0 0 1 1 799.0 0 1 1 806.0 0 1 1 808.0 0 1 1 813.0 0 1 1 815.0 0 2 2 816.0 0 1 1 817.0 0 2 2 818.0 0 1 1 823.0 0 1 1 827.0 0 1 1 835.0 0 1 1 837.0 0 1 1 844.0 0 1 1 845.0 0 2 2 849.0 0 1 1 856.0 0 1 1 860.0 0 1 1 870.0 0 2 2 872.0 0 2 2 874.0 0 1 1 875.0 0 1 1 878.0 0 1 1 880.0 0 1 1 883.0 0 1 1 886.0 0 1 1 888.0 0 1 1 889.0 0 1 1 891.0 0 1 1 893.0 0 1 1 896.0 0 1 1 898.0 0 1 1 906.0 0 1 1 915.0 0 1 1 918.0 0 1 1 921.0 0 1 1 923.0 0 1 1 924.0 0 1 1 926.0 0 1 1 936.0 0 1 1 940.0 0 1 1 947.0 0 1 1 950.0 0 1 1 953.0 0 1 1 956.0 0 1 1 960.0 0 1 1 965.0 0 1 1 970.0 0 1 1 978.0 0 1 1 981.0 0 1 1 982.0 0 2 2 988.0 0 1 1 993.0 0 1 1 1013.0 0 1 1 1015.0 0 1 1 1025.0 0 1 1 1031.0 0 1 1 1059.0 0 1 1 1061.0 0 1 1 1067.0 0 1 1 1073.0 0 1 1 1081.0 0 1 1 1088.0 0 1 1 1096.0 0 1 1 1104.0 0 1 1 1105.0 0 1 1 1123.0 0 1 1 1124.0 0 1 1 1126.0 0 1 1 1149.0 0 1 1 1158.0 0 1 1 1169.0 0 2 2 1195.0 0 1 1 1217.0 0 1 1 1228.0 0 1 1 1246.0 0 1 1 1259.0 0 1 1 1260.0 0 1 1 1276.0 0 1 1 1277.0 0 1 1 1279.0 0 1 1 1298.0 0 1 1 1310.0 0 1 1 1312.0 0 1 1 1319.0 0 1 1 1358.0 0 1 1 1362.0 0 1 1 1364.0 0 1 1 1368.0 0 1 1 1372.0 0 1 1 1382.0 0 1 1 1386.0 0 1 1 1402.0 0 1 1 1409.0 0 1 1 1416.0 0 1 1 1449.0 0 1 1 1490.0 0 1 1 1509.0 0 1 1 1570.0 0 1 1 1616.0 0 1 1 1664.0 0 1 1 1672.0 0 1 1 1679.0 0 1 1 1763.0 0 1 1 1772.0 0 1 1 1785.0 0 1 1 2306.0 0 1 1 2341.0 0 1 1 2759.0 0 1 1