## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354160.sorted.bam --OUTPUT SRX7354160.markdup.sorted.bam --METRICS_FILE SRX7354160.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 17:06:35 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 28252 36975951 5742690 1950284 21936 15399949 0 0.416623 30942562 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17964861 17964861 2.0 1.302708 2101002 2101002 3.0 1.39434 529357 529357 4.0 1.422078 245383 245383 5.0 1.430474 146392 146392 6.0 1.433016 98756 98756 7.0 1.433785 71943 71943 8.0 1.434018 54036 54036 9.0 1.434089 42785 42785 10.0 1.43411 34284 34284 11.0 1.434117 28220 28220 12.0 1.434119 23868 23868 13.0 1.434119 20219 20219 14.0 1.434119 17081 17081 15.0 1.434119 15033 15033 16.0 1.434119 13007 13007 17.0 1.434119 11765 11765 18.0 1.434119 10314 10314 19.0 1.434119 9379 9379 20.0 1.434119 8425 8425 21.0 1.434119 7657 7657 22.0 1.434119 6938 6938 23.0 1.434119 6184 6184 24.0 1.434119 5647 5647 25.0 1.434119 5278 5278 26.0 1.434119 4744 4744 27.0 1.434119 4468 4468 28.0 1.434119 4092 4092 29.0 1.434119 3658 3658 30.0 1.434119 3451 3451 31.0 1.434119 3316 3316 32.0 1.434119 3039 3039 33.0 1.434119 2861 2861 34.0 1.434119 2729 2729 35.0 1.434119 2507 2507 36.0 1.434119 2330 2330 37.0 1.434119 2253 2253 38.0 1.434119 2137 2137 39.0 1.434119 1983 1983 40.0 1.434119 1913 1913 41.0 1.434119 1819 1819 42.0 1.434119 1684 1684 43.0 1.434119 1617 1617 44.0 1.434119 1518 1518 45.0 1.434119 1522 1522 46.0 1.434119 1428 1428 47.0 1.434119 1363 1363 48.0 1.434119 1223 1223 49.0 1.434119 1238 1238 50.0 1.434119 1200 1200 51.0 1.434119 1107 1107 52.0 1.434119 1027 1027 53.0 1.434119 1005 1005 54.0 1.434119 936 936 55.0 1.434119 968 968 56.0 1.434119 868 868 57.0 1.434119 809 809 58.0 1.434119 791 791 59.0 1.434119 798 798 60.0 1.434119 728 728 61.0 1.434119 722 722 62.0 1.434119 682 682 63.0 1.434119 630 630 64.0 1.434119 601 601 65.0 1.434119 642 642 66.0 1.434119 567 567 67.0 1.434119 584 584 68.0 1.434119 586 586 69.0 1.434119 544 544 70.0 1.434119 509 509 71.0 1.434119 521 521 72.0 1.434119 513 513 73.0 1.434119 475 475 74.0 1.434119 495 495 75.0 1.434119 452 452 76.0 1.434119 413 413 77.0 1.434119 398 398 78.0 1.434119 430 430 79.0 1.434119 408 408 80.0 1.434119 379 379 81.0 1.434119 364 364 82.0 1.434119 381 381 83.0 1.434119 337 337 84.0 1.434119 323 323 85.0 1.434119 345 345 86.0 1.434119 330 330 87.0 1.434119 293 293 88.0 1.434119 307 307 89.0 1.434119 300 300 90.0 1.434119 306 306 91.0 1.434119 278 278 92.0 1.434119 272 272 93.0 1.434119 239 239 94.0 1.434119 282 282 95.0 1.434119 256 256 96.0 1.434119 226 226 97.0 1.434119 244 244 98.0 1.434119 230 230 99.0 1.434119 239 239 100.0 1.434119 218 218 101.0 0 213 213 102.0 0 230 230 103.0 0 221 221 104.0 0 193 193 105.0 0 221 221 106.0 0 174 174 107.0 0 208 208 108.0 0 187 187 109.0 0 151 151 110.0 0 185 185 111.0 0 190 190 112.0 0 164 164 113.0 0 189 189 114.0 0 169 169 115.0 0 159 159 116.0 0 158 158 117.0 0 182 182 118.0 0 138 138 119.0 0 136 136 120.0 0 139 139 121.0 0 138 138 122.0 0 122 122 123.0 0 124 124 124.0 0 118 118 125.0 0 128 128 126.0 0 117 117 127.0 0 126 126 128.0 0 104 104 129.0 0 114 114 130.0 0 101 101 131.0 0 107 107 132.0 0 116 116 133.0 0 101 101 134.0 0 98 98 135.0 0 103 103 136.0 0 116 116 137.0 0 100 100 138.0 0 100 100 139.0 0 85 85 140.0 0 93 93 141.0 0 108 108 142.0 0 99 99 143.0 0 100 100 144.0 0 95 95 145.0 0 103 103 146.0 0 98 98 147.0 0 94 94 148.0 0 80 80 149.0 0 83 83 150.0 0 70 70 151.0 0 71 71 152.0 0 69 69 153.0 0 67 67 154.0 0 72 72 155.0 0 60 60 156.0 0 61 61 157.0 0 77 77 158.0 0 75 75 159.0 0 72 72 160.0 0 81 81 161.0 0 49 49 162.0 0 66 66 163.0 0 54 54 164.0 0 58 58 165.0 0 65 65 166.0 0 52 52 167.0 0 38 38 168.0 0 59 59 169.0 0 47 47 170.0 0 52 52 171.0 0 44 44 172.0 0 58 58 173.0 0 54 54 174.0 0 49 49 175.0 0 45 45 176.0 0 57 57 177.0 0 44 44 178.0 0 57 57 179.0 0 53 53 180.0 0 52 52 181.0 0 49 49 182.0 0 33 33 183.0 0 51 51 184.0 0 49 49 185.0 0 55 55 186.0 0 45 45 187.0 0 34 34 188.0 0 51 51 189.0 0 50 50 190.0 0 40 40 191.0 0 43 43 192.0 0 37 37 193.0 0 29 29 194.0 0 47 47 195.0 0 47 47 196.0 0 39 39 197.0 0 29 29 198.0 0 30 30 199.0 0 35 35 200.0 0 37 37 201.0 0 36 36 202.0 0 32 32 203.0 0 32 32 204.0 0 41 41 205.0 0 38 38 206.0 0 23 23 207.0 0 26 26 208.0 0 37 37 209.0 0 24 24 210.0 0 40 40 211.0 0 32 32 212.0 0 24 24 213.0 0 29 29 214.0 0 29 29 215.0 0 25 25 216.0 0 26 26 217.0 0 31 31 218.0 0 22 22 219.0 0 20 20 220.0 0 27 27 221.0 0 22 22 222.0 0 32 32 223.0 0 37 37 224.0 0 28 28 225.0 0 30 30 226.0 0 28 28 227.0 0 30 30 228.0 0 37 37 229.0 0 23 23 230.0 0 22 22 231.0 0 20 20 232.0 0 21 21 233.0 0 22 22 234.0 0 29 29 235.0 0 24 24 236.0 0 23 23 237.0 0 19 19 238.0 0 17 17 239.0 0 12 12 240.0 0 25 25 241.0 0 22 22 242.0 0 27 27 243.0 0 18 18 244.0 0 28 28 245.0 0 15 15 246.0 0 12 12 247.0 0 14 14 248.0 0 21 21 249.0 0 13 13 250.0 0 20 20 251.0 0 14 14 252.0 0 14 14 253.0 0 10 10 254.0 0 16 16 255.0 0 18 18 256.0 0 13 13 257.0 0 10 10 258.0 0 13 13 259.0 0 10 10 260.0 0 15 15 261.0 0 24 24 262.0 0 16 16 263.0 0 15 15 264.0 0 21 21 265.0 0 17 17 266.0 0 12 12 267.0 0 18 18 268.0 0 14 14 269.0 0 16 16 270.0 0 13 13 271.0 0 20 20 272.0 0 14 14 273.0 0 13 13 274.0 0 18 18 275.0 0 17 17 276.0 0 15 15 277.0 0 16 16 278.0 0 15 15 279.0 0 12 12 280.0 0 10 10 281.0 0 10 10 282.0 0 18 18 283.0 0 14 14 284.0 0 10 10 285.0 0 13 13 286.0 0 7 7 287.0 0 16 16 288.0 0 10 10 289.0 0 12 12 290.0 0 10 10 291.0 0 12 12 292.0 0 8 8 293.0 0 12 12 294.0 0 8 8 295.0 0 11 11 296.0 0 10 10 297.0 0 18 18 298.0 0 14 14 299.0 0 13 13 300.0 0 12 12 301.0 0 14 14 302.0 0 7 7 303.0 0 9 9 304.0 0 10 10 305.0 0 10 10 306.0 0 6 6 307.0 0 13 13 308.0 0 10 10 309.0 0 10 10 310.0 0 11 11 311.0 0 10 10 312.0 0 13 13 313.0 0 11 11 314.0 0 5 5 315.0 0 8 8 316.0 0 7 7 317.0 0 6 6 318.0 0 5 5 319.0 0 11 11 320.0 0 7 7 321.0 0 11 11 322.0 0 5 5 323.0 0 10 10 324.0 0 9 9 325.0 0 7 7 326.0 0 6 6 327.0 0 12 12 328.0 0 9 9 329.0 0 5 5 330.0 0 16 16 331.0 0 9 9 332.0 0 9 9 333.0 0 8 8 334.0 0 5 5 335.0 0 4 4 336.0 0 7 7 337.0 0 12 12 338.0 0 11 11 339.0 0 9 9 340.0 0 8 8 341.0 0 15 15 342.0 0 8 8 343.0 0 6 6 344.0 0 7 7 345.0 0 9 9 346.0 0 5 5 347.0 0 11 11 348.0 0 4 4 349.0 0 9 9 350.0 0 4 4 351.0 0 8 8 352.0 0 9 9 353.0 0 6 6 354.0 0 7 7 355.0 0 6 6 356.0 0 6 6 357.0 0 10 10 358.0 0 7 7 359.0 0 4 4 360.0 0 4 4 361.0 0 11 11 362.0 0 6 6 363.0 0 4 4 364.0 0 5 5 365.0 0 8 8 366.0 0 5 5 367.0 0 4 4 368.0 0 7 7 369.0 0 5 5 370.0 0 5 5 371.0 0 7 7 372.0 0 7 7 373.0 0 3 3 374.0 0 5 5 375.0 0 6 6 376.0 0 2 2 377.0 0 6 6 378.0 0 5 5 379.0 0 3 3 380.0 0 5 5 381.0 0 9 9 382.0 0 5 5 383.0 0 4 4 384.0 0 8 8 385.0 0 9 9 386.0 0 3 3 387.0 0 5 5 388.0 0 9 9 389.0 0 3 3 390.0 0 5 5 391.0 0 8 8 392.0 0 5 5 393.0 0 3 3 394.0 0 7 7 395.0 0 4 4 396.0 0 6 6 397.0 0 11 11 398.0 0 5 5 399.0 0 6 6 400.0 0 5 5 401.0 0 1 1 402.0 0 3 3 403.0 0 4 4 404.0 0 3 3 405.0 0 3 3 406.0 0 3 3 407.0 0 4 4 408.0 0 6 6 409.0 0 3 3 410.0 0 7 7 411.0 0 4 4 412.0 0 3 3 413.0 0 3 3 414.0 0 4 4 415.0 0 3 3 416.0 0 1 1 417.0 0 8 8 418.0 0 7 7 419.0 0 6 6 420.0 0 2 2 421.0 0 7 7 422.0 0 4 4 423.0 0 4 4 424.0 0 6 6 425.0 0 3 3 427.0 0 3 3 428.0 0 3 3 429.0 0 3 3 430.0 0 3 3 431.0 0 7 7 432.0 0 3 3 433.0 0 2 2 434.0 0 6 6 435.0 0 2 2 436.0 0 4 4 437.0 0 3 3 438.0 0 12 12 439.0 0 5 5 440.0 0 2 2 441.0 0 4 4 442.0 0 2 2 444.0 0 5 5 445.0 0 2 2 446.0 0 3 3 447.0 0 5 5 448.0 0 5 5 449.0 0 1 1 450.0 0 2 2 451.0 0 4 4 452.0 0 2 2 453.0 0 1 1 454.0 0 4 4 455.0 0 4 4 456.0 0 4 4 457.0 0 5 5 458.0 0 2 2 459.0 0 1 1 460.0 0 3 3 462.0 0 4 4 463.0 0 1 1 464.0 0 2 2 465.0 0 6 6 466.0 0 1 1 468.0 0 1 1 469.0 0 3 3 470.0 0 3 3 471.0 0 3 3 472.0 0 6 6 473.0 0 3 3 474.0 0 5 5 475.0 0 2 2 476.0 0 3 3 478.0 0 3 3 479.0 0 3 3 480.0 0 5 5 481.0 0 1 1 482.0 0 3 3 483.0 0 3 3 484.0 0 3 3 485.0 0 3 3 486.0 0 1 1 487.0 0 2 2 488.0 0 5 5 489.0 0 5 5 490.0 0 5 5 491.0 0 1 1 492.0 0 3 3 493.0 0 1 1 494.0 0 4 4 495.0 0 2 2 496.0 0 3 3 497.0 0 2 2 498.0 0 3 3 499.0 0 1 1 501.0 0 2 2 502.0 0 1 1 503.0 0 2 2 504.0 0 3 3 505.0 0 2 2 506.0 0 1 1 507.0 0 4 4 508.0 0 1 1 509.0 0 1 1 510.0 0 2 2 512.0 0 2 2 513.0 0 6 6 514.0 0 3 3 515.0 0 3 3 516.0 0 5 5 517.0 0 5 5 518.0 0 2 2 519.0 0 3 3 520.0 0 2 2 521.0 0 1 1 522.0 0 2 2 523.0 0 2 2 524.0 0 1 1 525.0 0 2 2 526.0 0 1 1 528.0 0 1 1 529.0 0 1 1 530.0 0 1 1 531.0 0 1 1 532.0 0 1 1 533.0 0 2 2 534.0 0 4 4 535.0 0 3 3 536.0 0 1 1 537.0 0 2 2 538.0 0 2 2 539.0 0 3 3 540.0 0 4 4 542.0 0 3 3 543.0 0 1 1 544.0 0 2 2 545.0 0 2 2 546.0 0 1 1 548.0 0 2 2 549.0 0 1 1 552.0 0 3 3 553.0 0 2 2 554.0 0 3 3 555.0 0 1 1 556.0 0 1 1 557.0 0 1 1 558.0 0 1 1 559.0 0 2 2 560.0 0 2 2 561.0 0 4 4 562.0 0 2 2 563.0 0 3 3 565.0 0 1 1 568.0 0 2 2 570.0 0 2 2 571.0 0 1 1 572.0 0 2 2 573.0 0 1 1 576.0 0 1 1 578.0 0 1 1 580.0 0 2 2 582.0 0 2 2 583.0 0 1 1 585.0 0 3 3 587.0 0 1 1 588.0 0 2 2 589.0 0 1 1 591.0 0 2 2 592.0 0 2 2 594.0 0 3 3 595.0 0 2 2 596.0 0 2 2 597.0 0 1 1 598.0 0 1 1 599.0 0 1 1 601.0 0 2 2 602.0 0 1 1 603.0 0 1 1 605.0 0 1 1 608.0 0 2 2 609.0 0 1 1 610.0 0 4 4 611.0 0 2 2 612.0 0 1 1 613.0 0 2 2 614.0 0 1 1 615.0 0 2 2 616.0 0 2 2 620.0 0 2 2 621.0 0 1 1 624.0 0 1 1 625.0 0 1 1 627.0 0 1 1 628.0 0 1 1 631.0 0 1 1 634.0 0 2 2 635.0 0 2 2 642.0 0 1 1 643.0 0 1 1 644.0 0 1 1 646.0 0 1 1 647.0 0 1 1 648.0 0 1 1 649.0 0 1 1 651.0 0 2 2 654.0 0 3 3 656.0 0 1 1 658.0 0 2 2 660.0 0 1 1 661.0 0 1 1 662.0 0 2 2 663.0 0 1 1 664.0 0 1 1 666.0 0 1 1 670.0 0 1 1 671.0 0 1 1 673.0 0 1 1 674.0 0 1 1 675.0 0 1 1 676.0 0 1 1 678.0 0 1 1 679.0 0 1 1 682.0 0 1 1 683.0 0 2 2 684.0 0 1 1 685.0 0 2 2 686.0 0 1 1 687.0 0 1 1 688.0 0 2 2 691.0 0 1 1 693.0 0 1 1 696.0 0 2 2 699.0 0 1 1 700.0 0 1 1 701.0 0 1 1 704.0 0 1 1 705.0 0 1 1 717.0 0 1 1 718.0 0 2 2 719.0 0 1 1 721.0 0 1 1 723.0 0 1 1 724.0 0 3 3 725.0 0 1 1 728.0 0 1 1 734.0 0 2 2 736.0 0 1 1 738.0 0 1 1 739.0 0 1 1 740.0 0 1 1 741.0 0 2 2 743.0 0 2 2 745.0 0 2 2 746.0 0 1 1 749.0 0 1 1 752.0 0 1 1 754.0 0 2 2 757.0 0 2 2 758.0 0 1 1 762.0 0 1 1 764.0 0 1 1 765.0 0 2 2 766.0 0 1 1 767.0 0 1 1 768.0 0 1 1 769.0 0 2 2 770.0 0 1 1 773.0 0 1 1 777.0 0 1 1 781.0 0 1 1 785.0 0 1 1 788.0 0 1 1 790.0 0 2 2 798.0 0 1 1 801.0 0 1 1 802.0 0 1 1 812.0 0 1 1 814.0 0 1 1 815.0 0 1 1 820.0 0 1 1 830.0 0 1 1 842.0 0 1 1 844.0 0 1 1 846.0 0 1 1 849.0 0 1 1 858.0 0 1 1 861.0 0 1 1 869.0 0 2 2 870.0 0 1 1 871.0 0 1 1 880.0 0 1 1 888.0 0 1 1 895.0 0 1 1 898.0 0 2 2 904.0 0 1 1 911.0 0 1 1 915.0 0 1 1 916.0 0 1 1 920.0 0 2 2 938.0 0 2 2 940.0 0 1 1 941.0 0 1 1 948.0 0 1 1 951.0 0 1 1 971.0 0 1 1 974.0 0 1 1 975.0 0 1 1 981.0 0 1 1 986.0 0 1 1 988.0 0 2 2 998.0 0 1 1 1009.0 0 1 1 1030.0 0 1 1 1033.0 0 1 1 1040.0 0 1 1 1061.0 0 1 1 1062.0 0 1 1 1066.0 0 1 1 1075.0 0 1 1 1089.0 0 1 1 1100.0 0 1 1 1102.0 0 1 1 1103.0 0 1 1 1119.0 0 1 1 1166.0 0 1 1 1176.0 0 1 1 1203.0 0 1 1 1204.0 0 1 1 1216.0 0 1 1 1225.0 0 1 1 1231.0 0 1 1 1233.0 0 1 1 1235.0 0 1 1 1309.0 0 1 1 1317.0 0 1 1 1321.0 0 1 1 1324.0 0 1 1 1337.0 0 1 1 1348.0 0 1 1 1355.0 0 1 1 1510.0 0 1 1 1541.0 0 1 1 1543.0 0 1 1 1544.0 0 1 1 1587.0 0 1 1 1648.0 0 1 1 1654.0 0 1 1 1753.0 0 1 1 1773.0 0 1 1 1898.0 0 1 1 1943.0 0 1 1 1995.0 0 1 1 2030.0 0 1 1 3729.0 0 1 1