## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354297.sorted.bam --OUTPUT SRX7354297.markdup.sorted.bam --METRICS_FILE SRX7354297.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 22:18:18 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 398489 179130875 34004418 14198237 366226 142306107 0 0.794564 37122620 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 7029873 7029873 2.0 1.008023 5640259 5640259 3.0 1.008088 5053866 5053866 4.0 1.008088 4333004 4333004 5.0 1.008088 3538686 3538686 6.0 1.008088 2789326 2789326 7.0 1.008088 2147891 2147891 8.0 1.008088 1621970 1621970 9.0 1.008088 1209185 1209185 10.0 1.008088 884278 884278 11.0 1.008088 636391 636391 12.0 1.008088 450257 450257 13.0 1.008088 317927 317927 14.0 1.008088 223768 223768 15.0 1.008088 159227 159227 16.0 1.008088 116113 116113 17.0 1.008088 87232 87232 18.0 1.008088 67679 67679 19.0 1.008088 54602 54602 20.0 1.008088 44395 44395 21.0 1.008088 37779 37779 22.0 1.008088 32042 32042 23.0 1.008088 27860 27860 24.0 1.008088 24324 24324 25.0 1.008088 21531 21531 26.0 1.008088 19072 19072 27.0 1.008088 16696 16696 28.0 1.008088 15269 15269 29.0 1.008088 13671 13671 30.0 1.008088 12606 12606 31.0 1.008088 11245 11245 32.0 1.008088 10316 10316 33.0 1.008088 9291 9291 34.0 1.008088 8737 8737 35.0 1.008088 7949 7949 36.0 1.008088 7206 7206 37.0 1.008088 6817 6817 38.0 1.008088 6413 6413 39.0 1.008088 5911 5911 40.0 1.008088 5635 5635 41.0 1.008088 5210 5210 42.0 1.008088 4815 4815 43.0 1.008088 4502 4502 44.0 1.008088 4254 4254 45.0 1.008088 3832 3832 46.0 1.008088 3736 3736 47.0 1.008088 3631 3631 48.0 1.008088 3397 3397 49.0 1.008088 3034 3034 50.0 1.008088 2943 2943 51.0 1.008088 2833 2833 52.0 1.008088 2741 2741 53.0 1.008088 2532 2532 54.0 1.008088 2395 2395 55.0 1.008088 2232 2232 56.0 1.008088 2178 2178 57.0 1.008088 2117 2117 58.0 1.008088 1946 1946 59.0 1.008088 1889 1889 60.0 1.008088 1808 1808 61.0 1.008088 1682 1682 62.0 1.008088 1598 1598 63.0 1.008088 1532 1532 64.0 1.008088 1535 1535 65.0 1.008088 1436 1436 66.0 1.008088 1331 1331 67.0 1.008088 1257 1257 68.0 1.008088 1336 1336 69.0 1.008088 1251 1251 70.0 1.008088 1180 1180 71.0 1.008088 1155 1155 72.0 1.008088 1069 1069 73.0 1.008088 1115 1115 74.0 1.008088 1011 1011 75.0 1.008088 993 993 76.0 1.008088 960 960 77.0 1.008088 929 929 78.0 1.008088 887 887 79.0 1.008088 890 890 80.0 1.008088 783 783 81.0 1.008088 738 738 82.0 1.008088 778 778 83.0 1.008088 752 752 84.0 1.008088 755 755 85.0 1.008088 701 701 86.0 1.008088 657 657 87.0 1.008088 611 611 88.0 1.008088 605 605 89.0 1.008088 587 587 90.0 1.008088 591 591 91.0 1.008088 528 528 92.0 1.008088 511 511 93.0 1.008088 527 527 94.0 1.008088 547 547 95.0 1.008088 505 505 96.0 1.008088 508 508 97.0 1.008088 501 501 98.0 1.008088 420 420 99.0 1.008088 494 494 100.0 1.008088 427 427 101.0 0 412 412 102.0 0 409 409 103.0 0 366 366 104.0 0 402 402 105.0 0 345 345 106.0 0 380 380 107.0 0 351 351 108.0 0 322 322 109.0 0 341 341 110.0 0 320 320 111.0 0 315 315 112.0 0 314 314 113.0 0 282 282 114.0 0 275 275 115.0 0 262 262 116.0 0 287 287 117.0 0 271 271 118.0 0 244 244 119.0 0 265 265 120.0 0 258 258 121.0 0 245 245 122.0 0 248 248 123.0 0 226 226 124.0 0 237 237 125.0 0 234 234 126.0 0 217 217 127.0 0 198 198 128.0 0 216 216 129.0 0 189 189 130.0 0 197 197 131.0 0 192 192 132.0 0 191 191 133.0 0 191 191 134.0 0 163 163 135.0 0 167 167 136.0 0 176 176 137.0 0 187 187 138.0 0 162 162 139.0 0 181 181 140.0 0 151 151 141.0 0 170 170 142.0 0 151 151 143.0 0 154 154 144.0 0 143 143 145.0 0 165 165 146.0 0 150 150 147.0 0 154 154 148.0 0 155 155 149.0 0 158 158 150.0 0 130 130 151.0 0 113 113 152.0 0 121 121 153.0 0 124 124 154.0 0 132 132 155.0 0 112 112 156.0 0 126 126 157.0 0 111 111 158.0 0 104 104 159.0 0 95 95 160.0 0 107 107 161.0 0 108 108 162.0 0 117 117 163.0 0 98 98 164.0 0 101 101 165.0 0 103 103 166.0 0 88 88 167.0 0 92 92 168.0 0 92 92 169.0 0 96 96 170.0 0 96 96 171.0 0 86 86 172.0 0 97 97 173.0 0 83 83 174.0 0 88 88 175.0 0 85 85 176.0 0 92 92 177.0 0 75 75 178.0 0 87 87 179.0 0 71 71 180.0 0 73 73 181.0 0 74 74 182.0 0 83 83 183.0 0 59 59 184.0 0 77 77 185.0 0 61 61 186.0 0 61 61 187.0 0 78 78 188.0 0 80 80 189.0 0 62 62 190.0 0 52 52 191.0 0 69 69 192.0 0 60 60 193.0 0 67 67 194.0 0 60 60 195.0 0 48 48 196.0 0 57 57 197.0 0 60 60 198.0 0 50 50 199.0 0 57 57 200.0 0 42 42 201.0 0 45 45 202.0 0 55 55 203.0 0 52 52 204.0 0 51 51 205.0 0 52 52 206.0 0 47 47 207.0 0 49 49 208.0 0 44 44 209.0 0 44 44 210.0 0 46 46 211.0 0 47 47 212.0 0 39 39 213.0 0 38 38 214.0 0 39 39 215.0 0 53 53 216.0 0 43 43 217.0 0 38 38 218.0 0 47 47 219.0 0 38 38 220.0 0 53 53 221.0 0 36 36 222.0 0 39 39 223.0 0 40 40 224.0 0 39 39 225.0 0 28 28 226.0 0 37 37 227.0 0 38 38 228.0 0 33 33 229.0 0 42 42 230.0 0 33 33 231.0 0 32 32 232.0 0 38 38 233.0 0 32 32 234.0 0 29 29 235.0 0 39 39 236.0 0 29 29 237.0 0 33 33 238.0 0 32 32 239.0 0 28 28 240.0 0 41 41 241.0 0 20 20 242.0 0 33 33 243.0 0 28 28 244.0 0 29 29 245.0 0 20 20 246.0 0 30 30 247.0 0 32 32 248.0 0 25 25 249.0 0 32 32 250.0 0 25 25 251.0 0 25 25 252.0 0 32 32 253.0 0 26 26 254.0 0 20 20 255.0 0 29 29 256.0 0 25 25 257.0 0 26 26 258.0 0 25 25 259.0 0 27 27 260.0 0 24 24 261.0 0 26 26 262.0 0 25 25 263.0 0 25 25 264.0 0 22 22 265.0 0 18 18 266.0 0 22 22 267.0 0 16 16 268.0 0 21 21 269.0 0 21 21 270.0 0 19 19 271.0 0 23 23 272.0 0 13 13 273.0 0 22 22 274.0 0 11 11 275.0 0 25 25 276.0 0 16 16 277.0 0 20 20 278.0 0 23 23 279.0 0 16 16 280.0 0 9 9 281.0 0 16 16 282.0 0 20 20 283.0 0 22 22 284.0 0 23 23 285.0 0 17 17 286.0 0 20 20 287.0 0 20 20 288.0 0 12 12 289.0 0 18 18 290.0 0 14 14 291.0 0 13 13 292.0 0 14 14 293.0 0 14 14 294.0 0 19 19 295.0 0 19 19 296.0 0 15 15 297.0 0 18 18 298.0 0 13 13 299.0 0 7 7 300.0 0 9 9 301.0 0 18 18 302.0 0 14 14 303.0 0 13 13 304.0 0 11 11 305.0 0 8 8 306.0 0 17 17 307.0 0 10 10 308.0 0 15 15 309.0 0 15 15 310.0 0 22 22 311.0 0 13 13 312.0 0 11 11 313.0 0 12 12 314.0 0 12 12 315.0 0 12 12 316.0 0 13 13 317.0 0 9 9 318.0 0 15 15 319.0 0 8 8 320.0 0 12 12 321.0 0 9 9 322.0 0 15 15 323.0 0 10 10 324.0 0 9 9 325.0 0 8 8 326.0 0 14 14 327.0 0 9 9 328.0 0 18 18 329.0 0 10 10 330.0 0 10 10 331.0 0 9 9 332.0 0 10 10 333.0 0 10 10 334.0 0 8 8 335.0 0 7 7 336.0 0 7 7 337.0 0 6 6 338.0 0 12 12 339.0 0 11 11 340.0 0 4 4 341.0 0 13 13 342.0 0 10 10 343.0 0 12 12 344.0 0 11 11 345.0 0 12 12 346.0 0 10 10 347.0 0 8 8 348.0 0 11 11 349.0 0 6 6 350.0 0 12 12 351.0 0 12 12 352.0 0 9 9 353.0 0 16 16 354.0 0 9 9 355.0 0 12 12 356.0 0 12 12 357.0 0 4 4 358.0 0 8 8 359.0 0 7 7 360.0 0 3 3 361.0 0 4 4 362.0 0 7 7 363.0 0 11 11 364.0 0 13 13 365.0 0 4 4 366.0 0 9 9 367.0 0 9 9 368.0 0 7 7 369.0 0 7 7 370.0 0 9 9 371.0 0 8 8 372.0 0 12 12 373.0 0 7 7 374.0 0 5 5 375.0 0 6 6 376.0 0 5 5 377.0 0 12 12 378.0 0 8 8 379.0 0 7 7 380.0 0 5 5 381.0 0 6 6 382.0 0 3 3 383.0 0 4 4 384.0 0 3 3 385.0 0 9 9 386.0 0 8 8 387.0 0 5 5 388.0 0 7 7 389.0 0 8 8 390.0 0 4 4 391.0 0 8 8 392.0 0 4 4 393.0 0 5 5 394.0 0 6 6 395.0 0 7 7 396.0 0 3 3 397.0 0 8 8 398.0 0 4 4 399.0 0 9 9 400.0 0 3 3 401.0 0 3 3 402.0 0 4 4 403.0 0 6 6 404.0 0 5 5 405.0 0 2 2 406.0 0 2 2 408.0 0 5 5 409.0 0 8 8 410.0 0 6 6 411.0 0 5 5 412.0 0 3 3 413.0 0 4 4 414.0 0 6 6 415.0 0 10 10 416.0 0 2 2 417.0 0 3 3 418.0 0 5 5 419.0 0 4 4 420.0 0 4 4 421.0 0 4 4 422.0 0 6 6 423.0 0 2 2 424.0 0 4 4 425.0 0 4 4 426.0 0 7 7 427.0 0 2 2 428.0 0 5 5 429.0 0 5 5 430.0 0 3 3 431.0 0 2 2 432.0 0 3 3 433.0 0 7 7 435.0 0 5 5 436.0 0 6 6 437.0 0 2 2 438.0 0 4 4 439.0 0 1 1 440.0 0 6 6 441.0 0 3 3 442.0 0 2 2 443.0 0 7 7 444.0 0 4 4 445.0 0 3 3 446.0 0 1 1 447.0 0 1 1 448.0 0 3 3 449.0 0 4 4 450.0 0 2 2 451.0 0 2 2 452.0 0 7 7 453.0 0 5 5 454.0 0 2 2 455.0 0 3 3 456.0 0 2 2 457.0 0 2 2 461.0 0 2 2 462.0 0 6 6 463.0 0 2 2 464.0 0 4 4 465.0 0 4 4 466.0 0 4 4 467.0 0 3 3 469.0 0 6 6 470.0 0 4 4 471.0 0 2 2 472.0 0 3 3 473.0 0 4 4 474.0 0 2 2 475.0 0 4 4 476.0 0 2 2 477.0 0 4 4 478.0 0 3 3 479.0 0 3 3 480.0 0 1 1 481.0 0 7 7 482.0 0 3 3 483.0 0 5 5 484.0 0 2 2 485.0 0 5 5 486.0 0 3 3 487.0 0 1 1 488.0 0 2 2 489.0 0 4 4 490.0 0 2 2 491.0 0 3 3 492.0 0 2 2 493.0 0 5 5 496.0 0 1 1 497.0 0 5 5 498.0 0 4 4 499.0 0 3 3 500.0 0 4 4 501.0 0 6 6 502.0 0 2 2 503.0 0 3 3 504.0 0 1 1 505.0 0 2 2 506.0 0 1 1 507.0 0 1 1 508.0 0 1 1 509.0 0 1 1 510.0 0 3 3 511.0 0 3 3 512.0 0 3 3 513.0 0 4 4 515.0 0 2 2 517.0 0 2 2 518.0 0 2 2 519.0 0 4 4 520.0 0 2 2 521.0 0 6 6 522.0 0 1 1 523.0 0 1 1 524.0 0 2 2 525.0 0 5 5 526.0 0 3 3 527.0 0 3 3 529.0 0 2 2 530.0 0 3 3 531.0 0 2 2 532.0 0 3 3 534.0 0 1 1 535.0 0 1 1 536.0 0 3 3 537.0 0 2 2 538.0 0 5 5 539.0 0 2 2 540.0 0 3 3 541.0 0 2 2 542.0 0 3 3 543.0 0 1 1 544.0 0 3 3 545.0 0 1 1 546.0 0 3 3 548.0 0 2 2 549.0 0 4 4 550.0 0 6 6 551.0 0 1 1 552.0 0 1 1 553.0 0 2 2 554.0 0 1 1 555.0 0 1 1 556.0 0 3 3 558.0 0 5 5 560.0 0 1 1 561.0 0 2 2 562.0 0 2 2 563.0 0 1 1 565.0 0 2 2 566.0 0 3 3 567.0 0 2 2 568.0 0 1 1 570.0 0 1 1 571.0 0 1 1 572.0 0 3 3 573.0 0 1 1 574.0 0 3 3 576.0 0 2 2 577.0 0 2 2 578.0 0 2 2 579.0 0 1 1 580.0 0 1 1 581.0 0 2 2 582.0 0 2 2 583.0 0 1 1 585.0 0 2 2 590.0 0 1 1 591.0 0 1 1 592.0 0 5 5 594.0 0 1 1 595.0 0 1 1 597.0 0 2 2 598.0 0 1 1 600.0 0 5 5 601.0 0 2 2 602.0 0 3 3 603.0 0 1 1 604.0 0 2 2 606.0 0 1 1 607.0 0 1 1 609.0 0 3 3 610.0 0 1 1 611.0 0 1 1 612.0 0 1 1 613.0 0 1 1 614.0 0 1 1 618.0 0 2 2 620.0 0 1 1 621.0 0 1 1 622.0 0 2 2 623.0 0 1 1 624.0 0 2 2 625.0 0 2 2 626.0 0 2 2 627.0 0 2 2 629.0 0 1 1 632.0 0 3 3 634.0 0 1 1 637.0 0 3 3 641.0 0 1 1 642.0 0 2 2 643.0 0 1 1 644.0 0 1 1 645.0 0 1 1 646.0 0 1 1 648.0 0 1 1 651.0 0 2 2 653.0 0 2 2 654.0 0 2 2 655.0 0 1 1 656.0 0 1 1 658.0 0 3 3 661.0 0 1 1 662.0 0 1 1 664.0 0 1 1 665.0 0 2 2 666.0 0 1 1 667.0 0 3 3 669.0 0 1 1 673.0 0 2 2 675.0 0 1 1 676.0 0 2 2 677.0 0 1 1 678.0 0 3 3 679.0 0 2 2 680.0 0 1 1 684.0 0 2 2 686.0 0 1 1 687.0 0 1 1 688.0 0 1 1 689.0 0 3 3 690.0 0 3 3 691.0 0 2 2 692.0 0 2 2 693.0 0 1 1 694.0 0 2 2 695.0 0 1 1 696.0 0 1 1 697.0 0 1 1 698.0 0 2 2 699.0 0 1 1 700.0 0 1 1 701.0 0 2 2 702.0 0 2 2 703.0 0 2 2 705.0 0 1 1 707.0 0 1 1 708.0 0 1 1 709.0 0 1 1 712.0 0 2 2 713.0 0 3 3 714.0 0 1 1 725.0 0 1 1 726.0 0 1 1 727.0 0 3 3 730.0 0 1 1 731.0 0 2 2 734.0 0 1 1 735.0 0 4 4 736.0 0 2 2 739.0 0 2 2 740.0 0 2 2 742.0 0 1 1 743.0 0 2 2 744.0 0 1 1 746.0 0 1 1 752.0 0 1 1 753.0 0 1 1 754.0 0 1 1 755.0 0 1 1 756.0 0 1 1 758.0 0 1 1 759.0 0 3 3 760.0 0 1 1 762.0 0 1 1 763.0 0 1 1 766.0 0 1 1 767.0 0 1 1 771.0 0 1 1 772.0 0 1 1 774.0 0 1 1 776.0 0 3 3 778.0 0 2 2 779.0 0 1 1 781.0 0 1 1 787.0 0 1 1 792.0 0 2 2 794.0 0 1 1 796.0 0 1 1 798.0 0 2 2 802.0 0 1 1 804.0 0 1 1 807.0 0 1 1 808.0 0 2 2 809.0 0 2 2 810.0 0 3 3 817.0 0 1 1 821.0 0 2 2 828.0 0 1 1 829.0 0 1 1 830.0 0 1 1 831.0 0 1 1 835.0 0 1 1 837.0 0 1 1 838.0 0 1 1 840.0 0 1 1 844.0 0 1 1 845.0 0 1 1 846.0 0 1 1 848.0 0 1 1 849.0 0 1 1 851.0 0 1 1 853.0 0 1 1 860.0 0 1 1 864.0 0 1 1 869.0 0 1 1 870.0 0 1 1 872.0 0 1 1 873.0 0 2 2 878.0 0 1 1 882.0 0 1 1 889.0 0 1 1 894.0 0 1 1 911.0 0 1 1 915.0 0 2 2 930.0 0 2 2 935.0 0 2 2 939.0 0 1 1 944.0 0 1 1 950.0 0 1 1 951.0 0 1 1 958.0 0 1 1 959.0 0 1 1 970.0 0 1 1 971.0 0 1 1 977.0 0 2 2 1000.0 0 1 1 1003.0 0 1 1 1016.0 0 1 1 1017.0 0 1 1 1019.0 0 1 1 1027.0 0 1 1 1031.0 0 1 1 1040.0 0 1 1 1044.0 0 1 1 1049.0 0 1 1 1052.0 0 1 1 1054.0 0 1 1 1059.0 0 1 1 1064.0 0 1 1 1073.0 0 1 1 1085.0 0 1 1 1090.0 0 1 1 1113.0 0 1 1 1122.0 0 1 1 1124.0 0 1 1 1126.0 0 1 1 1135.0 0 1 1 1138.0 0 1 1 1154.0 0 1 1 1166.0 0 1 1 1170.0 0 1 1 1181.0 0 1 1 1191.0 0 1 1 1196.0 0 1 1 1198.0 0 1 1 1203.0 0 1 1 1204.0 0 1 1 1254.0 0 1 1 1257.0 0 1 1 1261.0 0 1 1 1281.0 0 1 1 1292.0 0 1 1 1294.0 0 1 1 1306.0 0 1 1 1328.0 0 1 1 1329.0 0 1 1 1334.0 0 1 1 1344.0 0 1 1 1346.0 0 1 1 1429.0 0 1 1 1462.0 0 1 1 1464.0 0 1 1 1492.0 0 1 1 1510.0 0 1 1 1546.0 0 1 1 1568.0 0 1 1 1579.0 0 1 1 1582.0 0 1 1 1609.0 0 1 1 1744.0 0 1 1 1760.0 0 1 1 1767.0 0 1 1 1818.0 0 1 1 1820.0 0 1 1 1902.0 0 1 1 2029.0 0 1 1 2050.0 0 1 1 2153.0 0 1 1 2230.0 0 1 1 2239.0 0 1 1 2271.0 0 1 1 2640.0 0 1 1 3054.0 0 1 1 3230.0 0 1 1 4053.0 0 1 1 4814.0 0 1 1 5744.0 0 1 1