## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354340.sorted.bam --OUTPUT SRX7354340.markdup.sorted.bam --METRICS_FILE SRX7354340.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 23:09:26 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 37363 38538312 5369376 5625105 29814 17248058 0 0.447726 28917926 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16818518 16818518 2.0 1.26377 2670554 2670554 3.0 1.333344 685468 685468 4.0 1.351696 297896 297896 5.0 1.356536 172549 172549 6.0 1.357813 114244 114244 7.0 1.35815 81129 81129 8.0 1.358239 61176 61176 9.0 1.358262 47551 47551 10.0 1.358268 37890 37890 11.0 1.35827 31063 31063 12.0 1.35827 25937 25937 13.0 1.358271 21882 21882 14.0 1.358271 18574 18574 15.0 1.358271 15983 15983 16.0 1.358271 14227 14227 17.0 1.358271 12565 12565 18.0 1.358271 11023 11023 19.0 1.358271 9775 9775 20.0 1.358271 8726 8726 21.0 1.358271 8009 8009 22.0 1.358271 7203 7203 23.0 1.358271 6496 6496 24.0 1.358271 5951 5951 25.0 1.358271 5316 5316 26.0 1.358271 4995 4995 27.0 1.358271 4591 4591 28.0 1.358271 4109 4109 29.0 1.358271 3810 3810 30.0 1.358271 3649 3649 31.0 1.358271 3341 3341 32.0 1.358271 3284 3284 33.0 1.358271 2940 2940 34.0 1.358271 2712 2712 35.0 1.358271 2637 2637 36.0 1.358271 2458 2458 37.0 1.358271 2344 2344 38.0 1.358271 2210 2210 39.0 1.358271 1989 1989 40.0 1.358271 1841 1841 41.0 1.358271 1828 1828 42.0 1.358271 1756 1756 43.0 1.358271 1677 1677 44.0 1.358271 1585 1585 45.0 1.358271 1518 1518 46.0 1.358271 1406 1406 47.0 1.358271 1388 1388 48.0 1.358271 1269 1269 49.0 1.358271 1229 1229 50.0 1.358271 1187 1187 51.0 1.358271 1091 1091 52.0 1.358271 1059 1059 53.0 1.358271 999 999 54.0 1.358271 1017 1017 55.0 1.358271 890 890 56.0 1.358271 880 880 57.0 1.358271 918 918 58.0 1.358271 811 811 59.0 1.358271 754 754 60.0 1.358271 761 761 61.0 1.358271 757 757 62.0 1.358271 680 680 63.0 1.358271 670 670 64.0 1.358271 623 623 65.0 1.358271 629 629 66.0 1.358271 643 643 67.0 1.358271 584 584 68.0 1.358271 574 574 69.0 1.358271 532 532 70.0 1.358271 561 561 71.0 1.358271 492 492 72.0 1.358271 533 533 73.0 1.358271 475 475 74.0 1.358271 434 434 75.0 1.358271 449 449 76.0 1.358271 450 450 77.0 1.358271 427 427 78.0 1.358271 402 402 79.0 1.358271 401 401 80.0 1.358271 360 360 81.0 1.358271 386 386 82.0 1.358271 375 375 83.0 1.358271 371 371 84.0 1.358271 346 346 85.0 1.358271 325 325 86.0 1.358271 333 333 87.0 1.358271 323 323 88.0 1.358271 293 293 89.0 1.358271 303 303 90.0 1.358271 312 312 91.0 1.358271 277 277 92.0 1.358271 296 296 93.0 1.358271 272 272 94.0 1.358271 236 236 95.0 1.358271 255 255 96.0 1.358271 260 260 97.0 1.358271 239 239 98.0 1.358271 249 249 99.0 1.358271 218 218 100.0 1.358271 195 195 101.0 0 230 230 102.0 0 211 211 103.0 0 222 222 104.0 0 190 190 105.0 0 204 204 106.0 0 181 181 107.0 0 174 174 108.0 0 179 179 109.0 0 156 156 110.0 0 196 196 111.0 0 197 197 112.0 0 170 170 113.0 0 163 163 114.0 0 146 146 115.0 0 156 156 116.0 0 174 174 117.0 0 142 142 118.0 0 128 128 119.0 0 126 126 120.0 0 137 137 121.0 0 146 146 122.0 0 128 128 123.0 0 116 116 124.0 0 143 143 125.0 0 130 130 126.0 0 127 127 127.0 0 113 113 128.0 0 135 135 129.0 0 95 95 130.0 0 129 129 131.0 0 115 115 132.0 0 115 115 133.0 0 114 114 134.0 0 102 102 135.0 0 90 90 136.0 0 95 95 137.0 0 109 109 138.0 0 107 107 139.0 0 110 110 140.0 0 75 75 141.0 0 87 87 142.0 0 88 88 143.0 0 78 78 144.0 0 74 74 145.0 0 98 98 146.0 0 59 59 147.0 0 95 95 148.0 0 64 64 149.0 0 74 74 150.0 0 67 67 151.0 0 88 88 152.0 0 76 76 153.0 0 60 60 154.0 0 82 82 155.0 0 67 67 156.0 0 63 63 157.0 0 68 68 158.0 0 62 62 159.0 0 72 72 160.0 0 49 49 161.0 0 70 70 162.0 0 66 66 163.0 0 58 58 164.0 0 58 58 165.0 0 53 53 166.0 0 59 59 167.0 0 62 62 168.0 0 56 56 169.0 0 57 57 170.0 0 46 46 171.0 0 52 52 172.0 0 58 58 173.0 0 50 50 174.0 0 63 63 175.0 0 52 52 176.0 0 54 54 177.0 0 50 50 178.0 0 39 39 179.0 0 44 44 180.0 0 57 57 181.0 0 45 45 182.0 0 54 54 183.0 0 56 56 184.0 0 44 44 185.0 0 56 56 186.0 0 52 52 187.0 0 52 52 188.0 0 48 48 189.0 0 37 37 190.0 0 41 41 191.0 0 35 35 192.0 0 40 40 193.0 0 34 34 194.0 0 46 46 195.0 0 54 54 196.0 0 35 35 197.0 0 37 37 198.0 0 38 38 199.0 0 35 35 200.0 0 44 44 201.0 0 29 29 202.0 0 47 47 203.0 0 29 29 204.0 0 39 39 205.0 0 32 32 206.0 0 28 28 207.0 0 43 43 208.0 0 36 36 209.0 0 34 34 210.0 0 33 33 211.0 0 34 34 212.0 0 35 35 213.0 0 26 26 214.0 0 29 29 215.0 0 26 26 216.0 0 29 29 217.0 0 39 39 218.0 0 29 29 219.0 0 21 21 220.0 0 35 35 221.0 0 23 23 222.0 0 38 38 223.0 0 34 34 224.0 0 26 26 225.0 0 33 33 226.0 0 35 35 227.0 0 25 25 228.0 0 18 18 229.0 0 31 31 230.0 0 21 21 231.0 0 36 36 232.0 0 26 26 233.0 0 15 15 234.0 0 19 19 235.0 0 19 19 236.0 0 22 22 237.0 0 19 19 238.0 0 16 16 239.0 0 27 27 240.0 0 23 23 241.0 0 21 21 242.0 0 25 25 243.0 0 28 28 244.0 0 24 24 245.0 0 17 17 246.0 0 26 26 247.0 0 15 15 248.0 0 11 11 249.0 0 21 21 250.0 0 21 21 251.0 0 18 18 252.0 0 19 19 253.0 0 27 27 254.0 0 12 12 255.0 0 17 17 256.0 0 21 21 257.0 0 19 19 258.0 0 18 18 259.0 0 18 18 260.0 0 14 14 261.0 0 20 20 262.0 0 22 22 263.0 0 24 24 264.0 0 17 17 265.0 0 17 17 266.0 0 18 18 267.0 0 16 16 268.0 0 15 15 269.0 0 17 17 270.0 0 23 23 271.0 0 18 18 272.0 0 14 14 273.0 0 6 6 274.0 0 14 14 275.0 0 10 10 276.0 0 15 15 277.0 0 9 9 278.0 0 19 19 279.0 0 15 15 280.0 0 18 18 281.0 0 16 16 282.0 0 11 11 283.0 0 16 16 284.0 0 15 15 285.0 0 10 10 286.0 0 8 8 287.0 0 17 17 288.0 0 10 10 289.0 0 14 14 290.0 0 9 9 291.0 0 10 10 292.0 0 16 16 293.0 0 15 15 294.0 0 11 11 295.0 0 15 15 296.0 0 20 20 297.0 0 19 19 298.0 0 8 8 299.0 0 11 11 300.0 0 12 12 301.0 0 14 14 302.0 0 13 13 303.0 0 10 10 304.0 0 10 10 305.0 0 16 16 306.0 0 7 7 307.0 0 15 15 308.0 0 6 6 309.0 0 15 15 310.0 0 12 12 311.0 0 12 12 312.0 0 18 18 313.0 0 12 12 314.0 0 13 13 315.0 0 12 12 316.0 0 8 8 317.0 0 12 12 318.0 0 11 11 319.0 0 13 13 320.0 0 11 11 321.0 0 11 11 322.0 0 10 10 323.0 0 7 7 324.0 0 9 9 325.0 0 10 10 326.0 0 5 5 327.0 0 12 12 328.0 0 8 8 329.0 0 6 6 330.0 0 10 10 331.0 0 10 10 332.0 0 6 6 333.0 0 6 6 334.0 0 10 10 335.0 0 17 17 336.0 0 4 4 337.0 0 7 7 338.0 0 14 14 339.0 0 3 3 340.0 0 5 5 341.0 0 9 9 342.0 0 6 6 343.0 0 14 14 344.0 0 5 5 345.0 0 10 10 346.0 0 9 9 347.0 0 12 12 348.0 0 15 15 349.0 0 2 2 350.0 0 9 9 351.0 0 8 8 352.0 0 7 7 353.0 0 7 7 354.0 0 10 10 355.0 0 8 8 356.0 0 6 6 357.0 0 2 2 358.0 0 5 5 359.0 0 8 8 360.0 0 9 9 361.0 0 10 10 362.0 0 9 9 363.0 0 7 7 364.0 0 13 13 365.0 0 7 7 366.0 0 7 7 367.0 0 5 5 368.0 0 5 5 369.0 0 4 4 370.0 0 13 13 371.0 0 5 5 372.0 0 6 6 373.0 0 9 9 374.0 0 3 3 375.0 0 2 2 376.0 0 11 11 377.0 0 4 4 378.0 0 6 6 379.0 0 4 4 380.0 0 7 7 381.0 0 7 7 382.0 0 7 7 383.0 0 5 5 384.0 0 9 9 385.0 0 2 2 386.0 0 7 7 387.0 0 6 6 388.0 0 6 6 389.0 0 5 5 390.0 0 4 4 391.0 0 6 6 392.0 0 7 7 393.0 0 6 6 394.0 0 9 9 395.0 0 8 8 396.0 0 4 4 397.0 0 5 5 398.0 0 2 2 399.0 0 6 6 400.0 0 3 3 401.0 0 8 8 402.0 0 7 7 403.0 0 3 3 404.0 0 4 4 405.0 0 4 4 406.0 0 6 6 407.0 0 7 7 408.0 0 5 5 409.0 0 7 7 410.0 0 11 11 411.0 0 2 2 412.0 0 6 6 413.0 0 5 5 414.0 0 4 4 415.0 0 10 10 416.0 0 2 2 417.0 0 3 3 418.0 0 4 4 419.0 0 1 1 420.0 0 6 6 421.0 0 5 5 422.0 0 1 1 423.0 0 6 6 424.0 0 3 3 425.0 0 5 5 426.0 0 6 6 427.0 0 3 3 428.0 0 6 6 429.0 0 4 4 430.0 0 2 2 431.0 0 8 8 432.0 0 7 7 433.0 0 5 5 434.0 0 4 4 435.0 0 2 2 436.0 0 3 3 437.0 0 7 7 438.0 0 5 5 439.0 0 2 2 440.0 0 3 3 441.0 0 2 2 442.0 0 4 4 443.0 0 8 8 444.0 0 4 4 445.0 0 7 7 446.0 0 4 4 447.0 0 3 3 448.0 0 4 4 449.0 0 1 1 450.0 0 1 1 451.0 0 3 3 452.0 0 4 4 453.0 0 4 4 454.0 0 1 1 455.0 0 5 5 456.0 0 5 5 457.0 0 2 2 458.0 0 7 7 459.0 0 6 6 460.0 0 2 2 461.0 0 6 6 462.0 0 5 5 463.0 0 4 4 464.0 0 2 2 465.0 0 3 3 466.0 0 3 3 467.0 0 1 1 468.0 0 2 2 469.0 0 2 2 470.0 0 1 1 471.0 0 1 1 472.0 0 3 3 473.0 0 3 3 474.0 0 2 2 475.0 0 2 2 476.0 0 3 3 477.0 0 2 2 478.0 0 2 2 479.0 0 2 2 480.0 0 4 4 481.0 0 5 5 482.0 0 4 4 483.0 0 4 4 484.0 0 4 4 485.0 0 2 2 486.0 0 7 7 487.0 0 2 2 488.0 0 5 5 489.0 0 3 3 490.0 0 2 2 491.0 0 3 3 492.0 0 4 4 493.0 0 3 3 494.0 0 3 3 495.0 0 3 3 496.0 0 4 4 497.0 0 1 1 498.0 0 2 2 499.0 0 2 2 500.0 0 3 3 501.0 0 1 1 502.0 0 4 4 503.0 0 1 1 504.0 0 5 5 505.0 0 6 6 506.0 0 2 2 507.0 0 3 3 508.0 0 1 1 509.0 0 6 6 510.0 0 1 1 512.0 0 3 3 513.0 0 1 1 514.0 0 2 2 515.0 0 5 5 516.0 0 1 1 517.0 0 3 3 519.0 0 1 1 521.0 0 1 1 522.0 0 2 2 523.0 0 3 3 524.0 0 3 3 526.0 0 2 2 527.0 0 1 1 528.0 0 4 4 529.0 0 2 2 530.0 0 3 3 531.0 0 3 3 532.0 0 2 2 533.0 0 1 1 534.0 0 2 2 535.0 0 3 3 536.0 0 2 2 540.0 0 3 3 541.0 0 1 1 542.0 0 2 2 543.0 0 4 4 544.0 0 1 1 545.0 0 1 1 548.0 0 4 4 549.0 0 2 2 551.0 0 1 1 552.0 0 2 2 553.0 0 3 3 554.0 0 1 1 555.0 0 2 2 556.0 0 6 6 558.0 0 1 1 559.0 0 2 2 560.0 0 3 3 561.0 0 2 2 562.0 0 1 1 563.0 0 1 1 564.0 0 3 3 565.0 0 4 4 566.0 0 1 1 568.0 0 1 1 571.0 0 4 4 572.0 0 1 1 574.0 0 2 2 575.0 0 2 2 576.0 0 3 3 577.0 0 1 1 579.0 0 2 2 583.0 0 1 1 584.0 0 3 3 586.0 0 3 3 587.0 0 3 3 588.0 0 3 3 589.0 0 2 2 592.0 0 1 1 593.0 0 2 2 594.0 0 4 4 596.0 0 1 1 597.0 0 1 1 598.0 0 1 1 599.0 0 1 1 600.0 0 1 1 601.0 0 1 1 602.0 0 1 1 603.0 0 1 1 604.0 0 1 1 607.0 0 2 2 609.0 0 2 2 610.0 0 1 1 611.0 0 1 1 612.0 0 1 1 613.0 0 2 2 614.0 0 1 1 615.0 0 1 1 616.0 0 2 2 619.0 0 1 1 620.0 0 2 2 621.0 0 2 2 623.0 0 1 1 624.0 0 2 2 625.0 0 1 1 627.0 0 2 2 628.0 0 1 1 630.0 0 2 2 632.0 0 1 1 633.0 0 6 6 634.0 0 1 1 637.0 0 1 1 638.0 0 1 1 641.0 0 2 2 642.0 0 1 1 645.0 0 1 1 646.0 0 1 1 651.0 0 1 1 653.0 0 2 2 655.0 0 2 2 656.0 0 1 1 658.0 0 1 1 659.0 0 2 2 660.0 0 2 2 661.0 0 4 4 664.0 0 3 3 667.0 0 2 2 668.0 0 2 2 669.0 0 1 1 670.0 0 3 3 671.0 0 1 1 672.0 0 3 3 673.0 0 1 1 674.0 0 1 1 675.0 0 1 1 676.0 0 1 1 677.0 0 1 1 680.0 0 2 2 681.0 0 1 1 683.0 0 3 3 684.0 0 3 3 686.0 0 2 2 687.0 0 1 1 690.0 0 1 1 694.0 0 1 1 695.0 0 1 1 696.0 0 1 1 698.0 0 2 2 699.0 0 2 2 702.0 0 1 1 703.0 0 1 1 705.0 0 3 3 708.0 0 1 1 709.0 0 1 1 711.0 0 1 1 712.0 0 2 2 713.0 0 1 1 715.0 0 1 1 716.0 0 2 2 717.0 0 5 5 718.0 0 1 1 719.0 0 1 1 720.0 0 1 1 722.0 0 2 2 723.0 0 1 1 725.0 0 1 1 726.0 0 2 2 727.0 0 1 1 728.0 0 1 1 729.0 0 2 2 733.0 0 1 1 734.0 0 1 1 735.0 0 2 2 737.0 0 1 1 740.0 0 2 2 748.0 0 1 1 749.0 0 2 2 752.0 0 1 1 755.0 0 3 3 756.0 0 1 1 758.0 0 1 1 759.0 0 3 3 760.0 0 1 1 762.0 0 3 3 765.0 0 1 1 767.0 0 1 1 768.0 0 1 1 769.0 0 1 1 772.0 0 1 1 775.0 0 1 1 778.0 0 1 1 780.0 0 1 1 782.0 0 1 1 784.0 0 1 1 786.0 0 2 2 789.0 0 2 2 790.0 0 3 3 791.0 0 1 1 792.0 0 1 1 795.0 0 1 1 808.0 0 1 1 811.0 0 1 1 812.0 0 3 3 814.0 0 1 1 816.0 0 2 2 817.0 0 1 1 820.0 0 3 3 824.0 0 1 1 826.0 0 2 2 827.0 0 2 2 833.0 0 1 1 834.0 0 2 2 847.0 0 1 1 849.0 0 1 1 851.0 0 1 1 855.0 0 1 1 856.0 0 1 1 858.0 0 1 1 862.0 0 3 3 870.0 0 1 1 874.0 0 3 3 876.0 0 1 1 878.0 0 1 1 880.0 0 2 2 886.0 0 1 1 892.0 0 1 1 894.0 0 1 1 897.0 0 1 1 900.0 0 2 2 901.0 0 1 1 916.0 0 1 1 922.0 0 1 1 923.0 0 2 2 924.0 0 1 1 936.0 0 2 2 938.0 0 2 2 941.0 0 1 1 943.0 0 1 1 952.0 0 1 1 961.0 0 1 1 963.0 0 1 1 964.0 0 2 2 967.0 0 1 1 974.0 0 1 1 982.0 0 1 1 989.0 0 1 1 992.0 0 1 1 999.0 0 1 1 1000.0 0 1 1 1001.0 0 1 1 1002.0 0 1 1 1006.0 0 1 1 1007.0 0 1 1 1010.0 0 1 1 1014.0 0 1 1 1016.0 0 1 1 1018.0 0 1 1 1026.0 0 1 1 1038.0 0 1 1 1039.0 0 2 2 1046.0 0 1 1 1058.0 0 1 1 1072.0 0 1 1 1084.0 0 1 1 1085.0 0 1 1 1094.0 0 2 2 1102.0 0 1 1 1106.0 0 1 1 1109.0 0 3 3 1110.0 0 1 1 1111.0 0 1 1 1113.0 0 1 1 1122.0 0 1 1 1147.0 0 1 1 1155.0 0 1 1 1164.0 0 1 1 1198.0 0 1 1 1204.0 0 1 1 1222.0 0 1 1 1225.0 0 1 1 1226.0 0 1 1 1232.0 0 1 1 1245.0 0 1 1 1263.0 0 1 1 1266.0 0 1 1 1277.0 0 1 1 1281.0 0 1 1 1282.0 0 1 1 1292.0 0 1 1 1328.0 0 1 1 1329.0 0 1 1 1331.0 0 1 1 1333.0 0 1 1 1370.0 0 1 1 1387.0 0 1 1 1399.0 0 1 1 1406.0 0 1 1 1408.0 0 1 1 1442.0 0 1 1 1476.0 0 1 1 1480.0 0 1 1 1504.0 0 1 1 1518.0 0 1 1 1547.0 0 1 1 1549.0 0 1 1 1550.0 0 1 1 1592.0 0 1 1 1668.0 0 1 1 1713.0 0 1 1 1727.0 0 1 1 1750.0 0 1 1 1771.0 0 1 1 1801.0 0 1 1 1832.0 0 1 1 1886.0 0 1 1 1895.0 0 1 1 1925.0 0 1 1 2041.0 0 1 1 2287.0 0 1 1