## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354350.sorted.bam --OUTPUT SRX7354350.markdup.sorted.bam --METRICS_FILE SRX7354350.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: Tue Oct 31 00:05:25 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 36155 36233555 5235112 3286887 25349 14615357 0 0.403514 31782071 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19009684 19009684 2.0 1.319799 1353165 1353165 3.0 1.42207 387527 387527 4.0 1.454777 196466 196466 5.0 1.465236 122799 122799 6.0 1.468581 84108 84108 7.0 1.469651 61763 61763 8.0 1.469993 47507 47507 9.0 1.470102 38002 38002 10.0 1.470137 31112 31112 11.0 1.470148 25790 25790 12.0 1.470152 21934 21934 13.0 1.470153 18791 18791 14.0 1.470153 16150 16150 15.0 1.470154 14182 14182 16.0 1.470154 12506 12506 17.0 1.470154 11245 11245 18.0 1.470154 10113 10113 19.0 1.470154 9059 9059 20.0 1.470154 8167 8167 21.0 1.470154 7503 7503 22.0 1.470154 6700 6700 23.0 1.470154 6212 6212 24.0 1.470154 5633 5633 25.0 1.470154 5224 5224 26.0 1.470154 4883 4883 27.0 1.470154 4461 4461 28.0 1.470154 4277 4277 29.0 1.470154 3899 3899 30.0 1.470154 3622 3622 31.0 1.470154 3352 3352 32.0 1.470154 3135 3135 33.0 1.470154 2911 2911 34.0 1.470154 2832 2832 35.0 1.470154 2685 2685 36.0 1.470154 2435 2435 37.0 1.470154 2431 2431 38.0 1.470154 2162 2162 39.0 1.470154 2127 2127 40.0 1.470154 1942 1942 41.0 1.470154 1891 1891 42.0 1.470154 1797 1797 43.0 1.470154 1796 1796 44.0 1.470154 1618 1618 45.0 1.470154 1583 1583 46.0 1.470154 1536 1536 47.0 1.470154 1398 1398 48.0 1.470154 1406 1406 49.0 1.470154 1291 1291 50.0 1.470154 1259 1259 51.0 1.470154 1181 1181 52.0 1.470154 1150 1150 53.0 1.470154 1131 1131 54.0 1.470154 1086 1086 55.0 1.470154 1012 1012 56.0 1.470154 1016 1016 57.0 1.470154 989 989 58.0 1.470154 876 876 59.0 1.470154 855 855 60.0 1.470154 853 853 61.0 1.470154 824 824 62.0 1.470154 772 772 63.0 1.470154 772 772 64.0 1.470154 709 709 65.0 1.470154 705 705 66.0 1.470154 687 687 67.0 1.470154 633 633 68.0 1.470154 653 653 69.0 1.470154 608 608 70.0 1.470154 595 595 71.0 1.470154 552 552 72.0 1.470154 560 560 73.0 1.470154 555 555 74.0 1.470154 522 522 75.0 1.470154 500 500 76.0 1.470154 482 482 77.0 1.470154 507 507 78.0 1.470154 476 476 79.0 1.470154 447 447 80.0 1.470154 442 442 81.0 1.470154 443 443 82.0 1.470154 415 415 83.0 1.470154 383 383 84.0 1.470154 393 393 85.0 1.470154 397 397 86.0 1.470154 390 390 87.0 1.470154 344 344 88.0 1.470154 347 347 89.0 1.470154 356 356 90.0 1.470154 334 334 91.0 1.470154 354 354 92.0 1.470154 309 309 93.0 1.470154 297 297 94.0 1.470154 301 301 95.0 1.470154 285 285 96.0 1.470154 290 290 97.0 1.470154 272 272 98.0 1.470154 288 288 99.0 1.470154 261 261 100.0 1.470154 256 256 101.0 0 277 277 102.0 0 265 265 103.0 0 240 240 104.0 0 238 238 105.0 0 213 213 106.0 0 233 233 107.0 0 220 220 108.0 0 204 204 109.0 0 230 230 110.0 0 197 197 111.0 0 188 188 112.0 0 187 187 113.0 0 176 176 114.0 0 176 176 115.0 0 183 183 116.0 0 176 176 117.0 0 178 178 118.0 0 184 184 119.0 0 172 172 120.0 0 170 170 121.0 0 162 162 122.0 0 165 165 123.0 0 169 169 124.0 0 154 154 125.0 0 150 150 126.0 0 144 144 127.0 0 127 127 128.0 0 146 146 129.0 0 117 117 130.0 0 132 132 131.0 0 125 125 132.0 0 119 119 133.0 0 117 117 134.0 0 154 154 135.0 0 127 127 136.0 0 126 126 137.0 0 134 134 138.0 0 107 107 139.0 0 108 108 140.0 0 121 121 141.0 0 108 108 142.0 0 120 120 143.0 0 103 103 144.0 0 90 90 145.0 0 87 87 146.0 0 87 87 147.0 0 99 99 148.0 0 106 106 149.0 0 92 92 150.0 0 101 101 151.0 0 93 93 152.0 0 93 93 153.0 0 110 110 154.0 0 91 91 155.0 0 85 85 156.0 0 72 72 157.0 0 76 76 158.0 0 83 83 159.0 0 90 90 160.0 0 80 80 161.0 0 61 61 162.0 0 81 81 163.0 0 72 72 164.0 0 79 79 165.0 0 71 71 166.0 0 87 87 167.0 0 74 74 168.0 0 63 63 169.0 0 52 52 170.0 0 71 71 171.0 0 63 63 172.0 0 61 61 173.0 0 66 66 174.0 0 66 66 175.0 0 52 52 176.0 0 56 56 177.0 0 75 75 178.0 0 69 69 179.0 0 58 58 180.0 0 66 66 181.0 0 59 59 182.0 0 47 47 183.0 0 59 59 184.0 0 47 47 185.0 0 61 61 186.0 0 55 55 187.0 0 65 65 188.0 0 57 57 189.0 0 42 42 190.0 0 45 45 191.0 0 50 50 192.0 0 49 49 193.0 0 41 41 194.0 0 60 60 195.0 0 50 50 196.0 0 43 43 197.0 0 55 55 198.0 0 40 40 199.0 0 39 39 200.0 0 41 41 201.0 0 53 53 202.0 0 40 40 203.0 0 45 45 204.0 0 39 39 205.0 0 49 49 206.0 0 39 39 207.0 0 43 43 208.0 0 31 31 209.0 0 25 25 210.0 0 30 30 211.0 0 40 40 212.0 0 35 35 213.0 0 25 25 214.0 0 36 36 215.0 0 42 42 216.0 0 28 28 217.0 0 38 38 218.0 0 29 29 219.0 0 34 34 220.0 0 32 32 221.0 0 39 39 222.0 0 26 26 223.0 0 36 36 224.0 0 32 32 225.0 0 26 26 226.0 0 39 39 227.0 0 25 25 228.0 0 43 43 229.0 0 42 42 230.0 0 33 33 231.0 0 34 34 232.0 0 30 30 233.0 0 29 29 234.0 0 31 31 235.0 0 33 33 236.0 0 29 29 237.0 0 21 21 238.0 0 20 20 239.0 0 19 19 240.0 0 19 19 241.0 0 27 27 242.0 0 32 32 243.0 0 25 25 244.0 0 18 18 245.0 0 22 22 246.0 0 33 33 247.0 0 16 16 248.0 0 29 29 249.0 0 22 22 250.0 0 16 16 251.0 0 25 25 252.0 0 21 21 253.0 0 26 26 254.0 0 16 16 255.0 0 21 21 256.0 0 30 30 257.0 0 19 19 258.0 0 24 24 259.0 0 22 22 260.0 0 16 16 261.0 0 16 16 262.0 0 24 24 263.0 0 17 17 264.0 0 17 17 265.0 0 23 23 266.0 0 20 20 267.0 0 22 22 268.0 0 17 17 269.0 0 24 24 270.0 0 25 25 271.0 0 31 31 272.0 0 19 19 273.0 0 14 14 274.0 0 20 20 275.0 0 22 22 276.0 0 20 20 277.0 0 14 14 278.0 0 11 11 279.0 0 17 17 280.0 0 16 16 281.0 0 17 17 282.0 0 22 22 283.0 0 18 18 284.0 0 18 18 285.0 0 17 17 286.0 0 11 11 287.0 0 14 14 288.0 0 8 8 289.0 0 13 13 290.0 0 16 16 291.0 0 18 18 292.0 0 11 11 293.0 0 18 18 294.0 0 14 14 295.0 0 16 16 296.0 0 13 13 297.0 0 24 24 298.0 0 7 7 299.0 0 11 11 300.0 0 15 15 301.0 0 15 15 302.0 0 13 13 303.0 0 14 14 304.0 0 11 11 305.0 0 11 11 306.0 0 15 15 307.0 0 15 15 308.0 0 11 11 309.0 0 15 15 310.0 0 11 11 311.0 0 11 11 312.0 0 8 8 313.0 0 10 10 314.0 0 11 11 315.0 0 13 13 316.0 0 11 11 317.0 0 10 10 318.0 0 7 7 319.0 0 9 9 320.0 0 19 19 321.0 0 8 8 322.0 0 6 6 323.0 0 12 12 324.0 0 7 7 325.0 0 9 9 326.0 0 12 12 327.0 0 10 10 328.0 0 11 11 329.0 0 11 11 330.0 0 11 11 331.0 0 10 10 332.0 0 7 7 333.0 0 15 15 334.0 0 17 17 335.0 0 3 3 336.0 0 11 11 337.0 0 7 7 338.0 0 6 6 339.0 0 9 9 340.0 0 15 15 341.0 0 12 12 342.0 0 12 12 343.0 0 9 9 344.0 0 4 4 345.0 0 9 9 346.0 0 7 7 347.0 0 9 9 348.0 0 8 8 349.0 0 6 6 350.0 0 9 9 351.0 0 10 10 352.0 0 7 7 353.0 0 7 7 354.0 0 8 8 355.0 0 8 8 356.0 0 8 8 357.0 0 6 6 358.0 0 11 11 359.0 0 13 13 360.0 0 9 9 361.0 0 5 5 362.0 0 8 8 363.0 0 8 8 364.0 0 8 8 365.0 0 9 9 366.0 0 8 8 367.0 0 8 8 368.0 0 6 6 369.0 0 6 6 370.0 0 6 6 371.0 0 9 9 372.0 0 10 10 373.0 0 6 6 374.0 0 7 7 375.0 0 12 12 376.0 0 5 5 377.0 0 4 4 378.0 0 3 3 379.0 0 8 8 380.0 0 6 6 381.0 0 5 5 382.0 0 5 5 383.0 0 1 1 384.0 0 5 5 385.0 0 5 5 386.0 0 4 4 387.0 0 6 6 388.0 0 9 9 389.0 0 4 4 390.0 0 7 7 391.0 0 7 7 392.0 0 6 6 393.0 0 9 9 394.0 0 3 3 395.0 0 3 3 396.0 0 6 6 397.0 0 4 4 398.0 0 11 11 399.0 0 4 4 400.0 0 5 5 401.0 0 10 10 402.0 0 2 2 403.0 0 6 6 404.0 0 5 5 405.0 0 2 2 406.0 0 7 7 407.0 0 5 5 408.0 0 3 3 409.0 0 2 2 410.0 0 5 5 411.0 0 6 6 412.0 0 3 3 413.0 0 4 4 414.0 0 6 6 415.0 0 9 9 416.0 0 3 3 417.0 0 3 3 418.0 0 4 4 419.0 0 4 4 420.0 0 4 4 421.0 0 6 6 422.0 0 4 4 423.0 0 7 7 424.0 0 7 7 425.0 0 5 5 426.0 0 5 5 427.0 0 3 3 428.0 0 2 2 429.0 0 7 7 430.0 0 5 5 431.0 0 7 7 432.0 0 4 4 433.0 0 5 5 434.0 0 2 2 435.0 0 3 3 436.0 0 6 6 437.0 0 8 8 438.0 0 3 3 439.0 0 4 4 440.0 0 3 3 441.0 0 4 4 442.0 0 3 3 443.0 0 4 4 444.0 0 4 4 445.0 0 2 2 446.0 0 2 2 447.0 0 5 5 448.0 0 4 4 449.0 0 2 2 450.0 0 3 3 451.0 0 2 2 452.0 0 4 4 453.0 0 1 1 454.0 0 2 2 455.0 0 8 8 456.0 0 2 2 457.0 0 6 6 458.0 0 2 2 459.0 0 3 3 460.0 0 8 8 461.0 0 7 7 462.0 0 4 4 463.0 0 3 3 464.0 0 3 3 465.0 0 3 3 466.0 0 4 4 467.0 0 3 3 468.0 0 1 1 469.0 0 6 6 470.0 0 3 3 471.0 0 6 6 472.0 0 5 5 473.0 0 3 3 474.0 0 1 1 475.0 0 3 3 476.0 0 2 2 477.0 0 5 5 478.0 0 1 1 479.0 0 1 1 480.0 0 3 3 481.0 0 1 1 482.0 0 2 2 483.0 0 7 7 484.0 0 5 5 485.0 0 2 2 486.0 0 6 6 487.0 0 5 5 488.0 0 4 4 489.0 0 7 7 490.0 0 5 5 491.0 0 2 2 492.0 0 2 2 493.0 0 4 4 494.0 0 3 3 495.0 0 5 5 497.0 0 2 2 498.0 0 1 1 499.0 0 2 2 500.0 0 5 5 501.0 0 2 2 502.0 0 3 3 503.0 0 1 1 504.0 0 2 2 505.0 0 3 3 506.0 0 2 2 507.0 0 1 1 508.0 0 2 2 509.0 0 4 4 510.0 0 1 1 511.0 0 2 2 512.0 0 3 3 513.0 0 5 5 514.0 0 2 2 515.0 0 2 2 516.0 0 3 3 518.0 0 1 1 519.0 0 4 4 520.0 0 1 1 521.0 0 1 1 522.0 0 2 2 523.0 0 5 5 525.0 0 10 10 526.0 0 3 3 527.0 0 1 1 528.0 0 1 1 529.0 0 4 4 531.0 0 2 2 532.0 0 2 2 534.0 0 2 2 535.0 0 2 2 536.0 0 1 1 537.0 0 3 3 538.0 0 2 2 539.0 0 1 1 540.0 0 4 4 541.0 0 1 1 543.0 0 2 2 544.0 0 1 1 545.0 0 2 2 546.0 0 4 4 547.0 0 3 3 548.0 0 1 1 551.0 0 6 6 552.0 0 1 1 553.0 0 5 5 554.0 0 1 1 555.0 0 1 1 556.0 0 1 1 557.0 0 2 2 558.0 0 1 1 559.0 0 2 2 560.0 0 3 3 561.0 0 1 1 562.0 0 2 2 563.0 0 1 1 564.0 0 4 4 565.0 0 2 2 566.0 0 2 2 567.0 0 2 2 568.0 0 1 1 570.0 0 3 3 571.0 0 2 2 573.0 0 3 3 574.0 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 1 583.0 0 2 2 586.0 0 3 3 587.0 0 2 2 589.0 0 2 2 590.0 0 3 3 591.0 0 1 1 592.0 0 2 2 593.0 0 2 2 594.0 0 1 1 596.0 0 1 1 597.0 0 2 2 598.0 0 4 4 602.0 0 4 4 605.0 0 3 3 606.0 0 3 3 607.0 0 3 3 608.0 0 1 1 610.0 0 1 1 612.0 0 1 1 613.0 0 1 1 614.0 0 1 1 615.0 0 3 3 616.0 0 1 1 617.0 0 1 1 618.0 0 1 1 619.0 0 3 3 620.0 0 1 1 621.0 0 1 1 622.0 0 3 3 623.0 0 2 2 624.0 0 1 1 626.0 0 2 2 627.0 0 2 2 628.0 0 2 2 634.0 0 3 3 635.0 0 5 5 636.0 0 1 1 637.0 0 1 1 639.0 0 2 2 640.0 0 2 2 641.0 0 1 1 642.0 0 3 3 643.0 0 2 2 644.0 0 4 4 645.0 0 2 2 646.0 0 2 2 647.0 0 1 1 648.0 0 1 1 649.0 0 1 1 650.0 0 1 1 651.0 0 3 3 653.0 0 2 2 656.0 0 1 1 658.0 0 2 2 660.0 0 1 1 661.0 0 1 1 662.0 0 2 2 664.0 0 1 1 665.0 0 1 1 668.0 0 3 3 669.0 0 1 1 670.0 0 1 1 671.0 0 1 1 673.0 0 2 2 675.0 0 1 1 676.0 0 2 2 677.0 0 3 3 681.0 0 1 1 686.0 0 1 1 687.0 0 3 3 690.0 0 1 1 691.0 0 1 1 693.0 0 1 1 695.0 0 2 2 697.0 0 1 1 698.0 0 4 4 699.0 0 1 1 700.0 0 2 2 701.0 0 1 1 704.0 0 1 1 705.0 0 1 1 709.0 0 1 1 710.0 0 1 1 711.0 0 1 1 713.0 0 2 2 714.0 0 2 2 716.0 0 1 1 718.0 0 2 2 719.0 0 2 2 724.0 0 1 1 725.0 0 2 2 726.0 0 1 1 727.0 0 2 2 728.0 0 1 1 731.0 0 1 1 740.0 0 2 2 743.0 0 2 2 744.0 0 1 1 745.0 0 2 2 748.0 0 1 1 749.0 0 1 1 750.0 0 2 2 751.0 0 1 1 753.0 0 1 1 756.0 0 1 1 757.0 0 1 1 760.0 0 1 1 761.0 0 2 2 763.0 0 2 2 768.0 0 1 1 771.0 0 1 1 777.0 0 1 1 779.0 0 1 1 781.0 0 1 1 785.0 0 1 1 787.0 0 1 1 792.0 0 1 1 794.0 0 1 1 796.0 0 1 1 797.0 0 2 2 800.0 0 1 1 802.0 0 1 1 807.0 0 4 4 808.0 0 1 1 811.0 0 1 1 818.0 0 1 1 820.0 0 1 1 821.0 0 1 1 823.0 0 1 1 825.0 0 1 1 826.0 0 1 1 827.0 0 1 1 828.0 0 1 1 829.0 0 1 1 835.0 0 1 1 836.0 0 1 1 838.0 0 1 1 843.0 0 1 1 844.0 0 1 1 847.0 0 2 2 848.0 0 1 1 855.0 0 1 1 859.0 0 1 1 861.0 0 2 2 862.0 0 2 2 866.0 0 1 1 868.0 0 1 1 875.0 0 1 1 878.0 0 1 1 879.0 0 2 2 882.0 0 1 1 885.0 0 1 1 887.0 0 1 1 891.0 0 1 1 893.0 0 1 1 898.0 0 2 2 900.0 0 1 1 913.0 0 1 1 914.0 0 1 1 915.0 0 1 1 916.0 0 1 1 921.0 0 1 1 926.0 0 1 1 937.0 0 1 1 938.0 0 1 1 949.0 0 1 1 955.0 0 1 1 959.0 0 1 1 960.0 0 1 1 964.0 0 1 1 970.0 0 1 1 974.0 0 2 2 975.0 0 1 1 987.0 0 1 1 994.0 0 1 1 1006.0 0 1 1 1008.0 0 1 1 1011.0 0 1 1 1014.0 0 1 1 1015.0 0 1 1 1019.0 0 1 1 1037.0 0 1 1 1042.0 0 1 1 1051.0 0 2 2 1054.0 0 1 1 1055.0 0 1 1 1060.0 0 1 1 1063.0 0 1 1 1064.0 0 1 1 1065.0 0 1 1 1072.0 0 1 1 1075.0 0 1 1 1076.0 0 1 1 1085.0 0 1 1 1089.0 0 1 1 1095.0 0 1 1 1099.0 0 1 1 1103.0 0 1 1 1111.0 0 1 1 1115.0 0 1 1 1120.0 0 1 1 1133.0 0 1 1 1151.0 0 1 1 1155.0 0 1 1 1160.0 0 1 1 1162.0 0 1 1 1163.0 0 1 1 1173.0 0 1 1 1206.0 0 1 1 1234.0 0 1 1 1235.0 0 1 1 1238.0 0 1 1 1245.0 0 1 1 1247.0 0 1 1 1255.0 0 1 1 1258.0 0 1 1 1260.0 0 1 1 1273.0 0 1 1 1286.0 0 1 1 1294.0 0 1 1 1321.0 0 1 1 1335.0 0 1 1 1347.0 0 1 1 1354.0 0 1 1 1355.0 0 1 1 1360.0 0 1 1 1362.0 0 1 1 1430.0 0 1 1 1443.0 0 1 1 1465.0 0 1 1 1501.0 0 1 1 1512.0 0 1 1 1571.0 0 1 1 1603.0 0 1 1 1625.0 0 1 1 1644.0 0 1 1 1667.0 0 1 1 1877.0 0 1 1 2192.0 0 1 1 2332.0 0 1 1 2722.0 0 1 1