## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354098.sorted.bam --OUTPUT SRX7354098.markdup.sorted.bam --METRICS_FILE SRX7354098.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 01:04:06 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 54666 40903546 5870923 6518952 43380 17915530 0 0.438232 31730301 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19356448 19356448 2.0 1.275518 2061415 2061415 3.0 1.351429 511481 511481 4.0 1.372344 243364 243364 5.0 1.378106 148589 148589 6.0 1.379694 102967 102967 7.0 1.380131 76050 76050 8.0 1.380252 58302 58302 9.0 1.380285 46413 46413 10.0 1.380294 37729 37729 11.0 1.380297 31850 31850 12.0 1.380297 26784 26784 13.0 1.380297 22829 22829 14.0 1.380297 19917 19917 15.0 1.380297 17263 17263 16.0 1.380297 15443 15443 17.0 1.380297 13661 13661 18.0 1.380297 12280 12280 19.0 1.380297 11051 11051 20.0 1.380297 9928 9928 21.0 1.380297 9081 9081 22.0 1.380297 8226 8226 23.0 1.380297 7447 7447 24.0 1.380297 6941 6941 25.0 1.380297 6410 6410 26.0 1.380297 5869 5869 27.0 1.380297 5424 5424 28.0 1.380297 5084 5084 29.0 1.380297 4702 4702 30.0 1.380297 4420 4420 31.0 1.380297 3894 3894 32.0 1.380297 3837 3837 33.0 1.380297 3627 3627 34.0 1.380297 3430 3430 35.0 1.380297 3220 3220 36.0 1.380297 3023 3023 37.0 1.380297 2808 2808 38.0 1.380297 2679 2679 39.0 1.380297 2525 2525 40.0 1.380297 2445 2445 41.0 1.380297 2211 2211 42.0 1.380297 2148 2148 43.0 1.380297 2068 2068 44.0 1.380297 1845 1845 45.0 1.380297 1858 1858 46.0 1.380297 1782 1782 47.0 1.380297 1586 1586 48.0 1.380297 1661 1661 49.0 1.380297 1535 1535 50.0 1.380297 1450 1450 51.0 1.380297 1420 1420 52.0 1.380297 1353 1353 53.0 1.380297 1296 1296 54.0 1.380297 1311 1311 55.0 1.380297 1191 1191 56.0 1.380297 1231 1231 57.0 1.380297 1112 1112 58.0 1.380297 1065 1065 59.0 1.380297 1066 1066 60.0 1.380297 1006 1006 61.0 1.380297 932 932 62.0 1.380297 942 942 63.0 1.380297 907 907 64.0 1.380297 850 850 65.0 1.380297 773 773 66.0 1.380297 798 798 67.0 1.380297 735 735 68.0 1.380297 729 729 69.0 1.380297 710 710 70.0 1.380297 671 671 71.0 1.380297 622 622 72.0 1.380297 670 670 73.0 1.380297 653 653 74.0 1.380297 633 633 75.0 1.380297 597 597 76.0 1.380297 555 555 77.0 1.380297 589 589 78.0 1.380297 550 550 79.0 1.380297 516 516 80.0 1.380297 512 512 81.0 1.380297 513 513 82.0 1.380297 493 493 83.0 1.380297 494 494 84.0 1.380297 418 418 85.0 1.380297 447 447 86.0 1.380297 440 440 87.0 1.380297 415 415 88.0 1.380297 384 384 89.0 1.380297 383 383 90.0 1.380297 376 376 91.0 1.380297 387 387 92.0 1.380297 378 378 93.0 1.380297 332 332 94.0 1.380297 363 363 95.0 1.380297 336 336 96.0 1.380297 320 320 97.0 1.380297 362 362 98.0 1.380297 281 281 99.0 1.380297 323 323 100.0 1.380297 288 288 101.0 0 269 269 102.0 0 309 309 103.0 0 262 262 104.0 0 266 266 105.0 0 260 260 106.0 0 258 258 107.0 0 254 254 108.0 0 252 252 109.0 0 239 239 110.0 0 221 221 111.0 0 218 218 112.0 0 216 216 113.0 0 206 206 114.0 0 236 236 115.0 0 224 224 116.0 0 194 194 117.0 0 207 207 118.0 0 188 188 119.0 0 212 212 120.0 0 184 184 121.0 0 205 205 122.0 0 191 191 123.0 0 182 182 124.0 0 171 171 125.0 0 179 179 126.0 0 163 163 127.0 0 139 139 128.0 0 150 150 129.0 0 172 172 130.0 0 168 168 131.0 0 160 160 132.0 0 129 129 133.0 0 155 155 134.0 0 142 142 135.0 0 135 135 136.0 0 115 115 137.0 0 127 127 138.0 0 133 133 139.0 0 123 123 140.0 0 137 137 141.0 0 124 124 142.0 0 119 119 143.0 0 97 97 144.0 0 126 126 145.0 0 116 116 146.0 0 104 104 147.0 0 117 117 148.0 0 93 93 149.0 0 103 103 150.0 0 112 112 151.0 0 122 122 152.0 0 92 92 153.0 0 101 101 154.0 0 87 87 155.0 0 109 109 156.0 0 81 81 157.0 0 105 105 158.0 0 91 91 159.0 0 94 94 160.0 0 95 95 161.0 0 97 97 162.0 0 82 82 163.0 0 88 88 164.0 0 82 82 165.0 0 82 82 166.0 0 80 80 167.0 0 91 91 168.0 0 84 84 169.0 0 84 84 170.0 0 76 76 171.0 0 57 57 172.0 0 79 79 173.0 0 74 74 174.0 0 58 58 175.0 0 91 91 176.0 0 69 69 177.0 0 69 69 178.0 0 58 58 179.0 0 69 69 180.0 0 62 62 181.0 0 59 59 182.0 0 67 67 183.0 0 55 55 184.0 0 55 55 185.0 0 60 60 186.0 0 55 55 187.0 0 57 57 188.0 0 69 69 189.0 0 59 59 190.0 0 46 46 191.0 0 44 44 192.0 0 57 57 193.0 0 55 55 194.0 0 56 56 195.0 0 42 42 196.0 0 56 56 197.0 0 57 57 198.0 0 45 45 199.0 0 50 50 200.0 0 43 43 201.0 0 38 38 202.0 0 43 43 203.0 0 45 45 204.0 0 42 42 205.0 0 41 41 206.0 0 46 46 207.0 0 36 36 208.0 0 49 49 209.0 0 52 52 210.0 0 41 41 211.0 0 44 44 212.0 0 44 44 213.0 0 38 38 214.0 0 41 41 215.0 0 37 37 216.0 0 39 39 217.0 0 43 43 218.0 0 33 33 219.0 0 32 32 220.0 0 32 32 221.0 0 51 51 222.0 0 42 42 223.0 0 38 38 224.0 0 52 52 225.0 0 33 33 226.0 0 36 36 227.0 0 24 24 228.0 0 30 30 229.0 0 38 38 230.0 0 42 42 231.0 0 33 33 232.0 0 36 36 233.0 0 36 36 234.0 0 32 32 235.0 0 37 37 236.0 0 29 29 237.0 0 33 33 238.0 0 41 41 239.0 0 28 28 240.0 0 24 24 241.0 0 23 23 242.0 0 17 17 243.0 0 36 36 244.0 0 29 29 245.0 0 28 28 246.0 0 29 29 247.0 0 33 33 248.0 0 27 27 249.0 0 24 24 250.0 0 26 26 251.0 0 28 28 252.0 0 23 23 253.0 0 16 16 254.0 0 19 19 255.0 0 28 28 256.0 0 31 31 257.0 0 20 20 258.0 0 32 32 259.0 0 24 24 260.0 0 26 26 261.0 0 22 22 262.0 0 26 26 263.0 0 25 25 264.0 0 19 19 265.0 0 18 18 266.0 0 13 13 267.0 0 22 22 268.0 0 19 19 269.0 0 21 21 270.0 0 24 24 271.0 0 23 23 272.0 0 23 23 273.0 0 19 19 274.0 0 23 23 275.0 0 16 16 276.0 0 20 20 277.0 0 16 16 278.0 0 16 16 279.0 0 20 20 280.0 0 19 19 281.0 0 21 21 282.0 0 17 17 283.0 0 24 24 284.0 0 21 21 285.0 0 19 19 286.0 0 12 12 287.0 0 22 22 288.0 0 14 14 289.0 0 20 20 290.0 0 18 18 291.0 0 19 19 292.0 0 15 15 293.0 0 13 13 294.0 0 17 17 295.0 0 13 13 296.0 0 20 20 297.0 0 24 24 298.0 0 15 15 299.0 0 11 11 300.0 0 16 16 301.0 0 16 16 302.0 0 9 9 303.0 0 11 11 304.0 0 10 10 305.0 0 22 22 306.0 0 21 21 307.0 0 19 19 308.0 0 13 13 309.0 0 10 10 310.0 0 11 11 311.0 0 9 9 312.0 0 15 15 313.0 0 14 14 314.0 0 10 10 315.0 0 15 15 316.0 0 12 12 317.0 0 9 9 318.0 0 21 21 319.0 0 15 15 320.0 0 15 15 321.0 0 12 12 322.0 0 13 13 323.0 0 11 11 324.0 0 19 19 325.0 0 13 13 326.0 0 20 20 327.0 0 20 20 328.0 0 15 15 329.0 0 7 7 330.0 0 10 10 331.0 0 16 16 332.0 0 12 12 333.0 0 4 4 334.0 0 20 20 335.0 0 18 18 336.0 0 18 18 337.0 0 15 15 338.0 0 9 9 339.0 0 11 11 340.0 0 8 8 341.0 0 8 8 342.0 0 11 11 343.0 0 7 7 344.0 0 18 18 345.0 0 6 6 346.0 0 4 4 347.0 0 13 13 348.0 0 10 10 349.0 0 7 7 350.0 0 8 8 351.0 0 7 7 352.0 0 14 14 353.0 0 11 11 354.0 0 12 12 355.0 0 11 11 356.0 0 8 8 357.0 0 11 11 358.0 0 8 8 359.0 0 10 10 360.0 0 12 12 361.0 0 11 11 362.0 0 7 7 363.0 0 7 7 364.0 0 7 7 365.0 0 8 8 366.0 0 8 8 367.0 0 6 6 368.0 0 11 11 369.0 0 12 12 370.0 0 6 6 371.0 0 11 11 372.0 0 5 5 373.0 0 4 4 374.0 0 6 6 375.0 0 11 11 376.0 0 6 6 377.0 0 7 7 378.0 0 8 8 379.0 0 5 5 380.0 0 7 7 381.0 0 4 4 382.0 0 11 11 383.0 0 8 8 384.0 0 5 5 385.0 0 10 10 386.0 0 9 9 387.0 0 7 7 388.0 0 4 4 389.0 0 4 4 390.0 0 7 7 391.0 0 7 7 392.0 0 4 4 393.0 0 7 7 394.0 0 5 5 395.0 0 7 7 396.0 0 4 4 397.0 0 3 3 398.0 0 9 9 399.0 0 8 8 400.0 0 4 4 401.0 0 5 5 402.0 0 7 7 403.0 0 9 9 404.0 0 8 8 405.0 0 9 9 406.0 0 3 3 407.0 0 5 5 408.0 0 7 7 409.0 0 7 7 410.0 0 5 5 411.0 0 7 7 412.0 0 5 5 413.0 0 6 6 414.0 0 1 1 415.0 0 1 1 416.0 0 6 6 417.0 0 3 3 418.0 0 7 7 419.0 0 7 7 420.0 0 9 9 421.0 0 8 8 422.0 0 6 6 423.0 0 5 5 424.0 0 1 1 425.0 0 3 3 426.0 0 10 10 427.0 0 4 4 428.0 0 5 5 429.0 0 2 2 430.0 0 1 1 431.0 0 3 3 432.0 0 5 5 433.0 0 2 2 435.0 0 2 2 436.0 0 6 6 437.0 0 2 2 438.0 0 5 5 439.0 0 3 3 440.0 0 4 4 441.0 0 1 1 442.0 0 2 2 443.0 0 7 7 444.0 0 4 4 445.0 0 5 5 446.0 0 11 11 447.0 0 6 6 448.0 0 3 3 449.0 0 5 5 450.0 0 3 3 451.0 0 3 3 452.0 0 2 2 453.0 0 4 4 454.0 0 3 3 455.0 0 5 5 456.0 0 3 3 457.0 0 6 6 458.0 0 2 2 459.0 0 1 1 460.0 0 2 2 461.0 0 4 4 462.0 0 4 4 463.0 0 6 6 464.0 0 3 3 465.0 0 2 2 466.0 0 3 3 467.0 0 4 4 468.0 0 8 8 469.0 0 4 4 470.0 0 6 6 472.0 0 5 5 473.0 0 5 5 474.0 0 9 9 475.0 0 4 4 476.0 0 7 7 477.0 0 3 3 478.0 0 3 3 479.0 0 8 8 480.0 0 3 3 481.0 0 3 3 482.0 0 3 3 483.0 0 1 1 484.0 0 2 2 485.0 0 4 4 486.0 0 8 8 487.0 0 3 3 488.0 0 5 5 489.0 0 3 3 490.0 0 2 2 491.0 0 3 3 492.0 0 5 5 494.0 0 2 2 495.0 0 4 4 496.0 0 4 4 497.0 0 2 2 498.0 0 8 8 499.0 0 2 2 500.0 0 4 4 501.0 0 4 4 502.0 0 2 2 504.0 0 2 2 505.0 0 3 3 506.0 0 2 2 507.0 0 1 1 508.0 0 3 3 509.0 0 1 1 510.0 0 2 2 511.0 0 3 3 512.0 0 2 2 513.0 0 3 3 514.0 0 10 10 515.0 0 3 3 516.0 0 3 3 517.0 0 3 3 518.0 0 2 2 519.0 0 3 3 520.0 0 4 4 521.0 0 3 3 522.0 0 3 3 523.0 0 6 6 524.0 0 1 1 525.0 0 2 2 526.0 0 1 1 527.0 0 2 2 529.0 0 3 3 530.0 0 1 1 531.0 0 3 3 532.0 0 3 3 533.0 0 3 3 534.0 0 3 3 535.0 0 3 3 536.0 0 3 3 537.0 0 2 2 538.0 0 3 3 539.0 0 7 7 540.0 0 2 2 541.0 0 3 3 543.0 0 5 5 544.0 0 1 1 545.0 0 2 2 546.0 0 5 5 547.0 0 1 1 548.0 0 1 1 549.0 0 4 4 550.0 0 4 4 551.0 0 1 1 552.0 0 3 3 553.0 0 6 6 554.0 0 2 2 555.0 0 2 2 556.0 0 3 3 557.0 0 2 2 558.0 0 2 2 559.0 0 2 2 560.0 0 2 2 561.0 0 2 2 562.0 0 4 4 563.0 0 2 2 564.0 0 1 1 565.0 0 1 1 566.0 0 1 1 567.0 0 2 2 568.0 0 3 3 569.0 0 1 1 570.0 0 2 2 572.0 0 1 1 574.0 0 2 2 575.0 0 3 3 576.0 0 6 6 577.0 0 4 4 579.0 0 1 1 580.0 0 2 2 581.0 0 1 1 582.0 0 4 4 583.0 0 1 1 585.0 0 4 4 588.0 0 2 2 590.0 0 1 1 592.0 0 1 1 594.0 0 2 2 595.0 0 1 1 596.0 0 1 1 597.0 0 1 1 598.0 0 2 2 600.0 0 2 2 601.0 0 3 3 602.0 0 4 4 603.0 0 3 3 605.0 0 3 3 606.0 0 3 3 607.0 0 1 1 608.0 0 3 3 609.0 0 1 1 610.0 0 2 2 611.0 0 1 1 612.0 0 4 4 614.0 0 3 3 615.0 0 4 4 616.0 0 1 1 617.0 0 2 2 618.0 0 3 3 619.0 0 2 2 620.0 0 2 2 621.0 0 1 1 622.0 0 1 1 623.0 0 1 1 624.0 0 3 3 627.0 0 1 1 628.0 0 2 2 629.0 0 1 1 631.0 0 1 1 632.0 0 2 2 633.0 0 2 2 634.0 0 2 2 636.0 0 2 2 637.0 0 3 3 638.0 0 2 2 639.0 0 4 4 641.0 0 1 1 642.0 0 3 3 643.0 0 1 1 644.0 0 2 2 646.0 0 1 1 649.0 0 1 1 651.0 0 2 2 652.0 0 2 2 653.0 0 2 2 654.0 0 1 1 655.0 0 1 1 656.0 0 1 1 657.0 0 1 1 658.0 0 2 2 659.0 0 2 2 660.0 0 2 2 663.0 0 1 1 664.0 0 5 5 665.0 0 2 2 666.0 0 1 1 667.0 0 2 2 668.0 0 1 1 669.0 0 2 2 670.0 0 1 1 671.0 0 1 1 672.0 0 3 3 673.0 0 1 1 675.0 0 4 4 676.0 0 2 2 677.0 0 1 1 678.0 0 2 2 679.0 0 3 3 680.0 0 4 4 681.0 0 1 1 682.0 0 3 3 683.0 0 4 4 684.0 0 1 1 685.0 0 1 1 687.0 0 1 1 688.0 0 1 1 690.0 0 3 3 691.0 0 1 1 692.0 0 1 1 694.0 0 1 1 698.0 0 4 4 701.0 0 1 1 703.0 0 1 1 704.0 0 2 2 709.0 0 2 2 710.0 0 1 1 712.0 0 2 2 717.0 0 1 1 719.0 0 1 1 720.0 0 1 1 721.0 0 2 2 724.0 0 1 1 725.0 0 2 2 729.0 0 1 1 734.0 0 1 1 737.0 0 1 1 741.0 0 2 2 744.0 0 3 3 745.0 0 1 1 749.0 0 1 1 751.0 0 1 1 753.0 0 1 1 756.0 0 1 1 758.0 0 1 1 763.0 0 2 2 764.0 0 1 1 767.0 0 2 2 771.0 0 1 1 772.0 0 1 1 776.0 0 2 2 777.0 0 2 2 778.0 0 1 1 780.0 0 4 4 781.0 0 1 1 784.0 0 1 1 785.0 0 3 3 789.0 0 3 3 790.0 0 2 2 792.0 0 1 1 793.0 0 1 1 794.0 0 2 2 798.0 0 1 1 801.0 0 1 1 808.0 0 2 2 810.0 0 1 1 812.0 0 1 1 813.0 0 1 1 819.0 0 1 1 820.0 0 1 1 822.0 0 2 2 827.0 0 2 2 832.0 0 1 1 838.0 0 1 1 839.0 0 1 1 840.0 0 4 4 841.0 0 1 1 845.0 0 1 1 846.0 0 1 1 847.0 0 1 1 852.0 0 2 2 853.0 0 1 1 855.0 0 2 2 856.0 0 2 2 858.0 0 1 1 861.0 0 1 1 862.0 0 1 1 864.0 0 2 2 865.0 0 1 1 873.0 0 1 1 878.0 0 1 1 880.0 0 1 1 883.0 0 1 1 886.0 0 1 1 890.0 0 1 1 893.0 0 1 1 896.0 0 2 2 897.0 0 2 2 903.0 0 2 2 908.0 0 1 1 910.0 0 2 2 916.0 0 1 1 919.0 0 2 2 920.0 0 1 1 926.0 0 2 2 927.0 0 1 1 928.0 0 1 1 930.0 0 1 1 931.0 0 1 1 932.0 0 1 1 933.0 0 1 1 935.0 0 1 1 937.0 0 1 1 942.0 0 1 1 951.0 0 1 1 963.0 0 1 1 971.0 0 1 1 976.0 0 1 1 979.0 0 1 1 987.0 0 1 1 992.0 0 1 1 994.0 0 1 1 996.0 0 1 1 1000.0 0 1 1 1006.0 0 1 1 1013.0 0 1 1 1021.0 0 2 2 1024.0 0 1 1 1025.0 0 2 2 1033.0 0 1 1 1034.0 0 1 1 1044.0 0 1 1 1048.0 0 1 1 1066.0 0 1 1 1074.0 0 1 1 1078.0 0 1 1 1079.0 0 1 1 1081.0 0 1 1 1093.0 0 1 1 1099.0 0 1 1 1101.0 0 1 1 1107.0 0 1 1 1113.0 0 1 1 1114.0 0 1 1 1133.0 0 1 1 1135.0 0 1 1 1137.0 0 1 1 1142.0 0 1 1 1149.0 0 1 1 1160.0 0 1 1 1169.0 0 1 1 1178.0 0 1 1 1185.0 0 1 1 1212.0 0 1 1 1225.0 0 1 1 1251.0 0 1 1 1256.0 0 1 1 1259.0 0 1 1 1260.0 0 1 1 1288.0 0 1 1 1346.0 0 1 1 1365.0 0 1 1 1376.0 0 1 1 1459.0 0 1 1 1487.0 0 1 1 1504.0 0 1 1 1507.0 0 1 1 1701.0 0 1 1 1721.0 0 1 1 1974.0 0 1 1 2006.0 0 1 1 2039.0 0 1 1 2175.0 0 1 1 2599.0 0 1 1 3410.0 0 1 1