## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354053.sorted.bam --OUTPUT SRX7354053.markdup.sorted.bam --METRICS_FILE SRX7354053.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 00:57:34 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 70502 50983671 6571399 11688798 53653 19069740 0 0.374304 49814704 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 26787418 26787418 2.0 1.359347 3247347 3247347 3.0 1.488478 709898 709898 4.0 1.53488 298142 298142 5.0 1.551555 173877 173877 6.0 1.557547 115637 115637 7.0 1.5597 84015 84015 8.0 1.560474 63469 63469 9.0 1.560752 49688 49688 10.0 1.560852 40371 40371 11.0 1.560888 33304 33304 12.0 1.560901 28204 28204 13.0 1.560905 23686 23686 14.0 1.560907 20399 20399 15.0 1.560907 17926 17926 16.0 1.560908 15721 15721 17.0 1.560908 13900 13900 18.0 1.560908 12348 12348 19.0 1.560908 11210 11210 20.0 1.560908 9889 9889 21.0 1.560908 9127 9127 22.0 1.560908 8281 8281 23.0 1.560908 7471 7471 24.0 1.560908 6999 6999 25.0 1.560908 6277 6277 26.0 1.560908 5706 5706 27.0 1.560908 5371 5371 28.0 1.560908 5017 5017 29.0 1.560908 4610 4610 30.0 1.560908 4207 4207 31.0 1.560908 4030 4030 32.0 1.560908 3789 3789 33.0 1.560908 3533 3533 34.0 1.560908 3399 3399 35.0 1.560908 3062 3062 36.0 1.560908 2925 2925 37.0 1.560908 2798 2798 38.0 1.560908 2638 2638 39.0 1.560908 2484 2484 40.0 1.560908 2266 2266 41.0 1.560908 2172 2172 42.0 1.560908 2110 2110 43.0 1.560908 2023 2023 44.0 1.560908 1846 1846 45.0 1.560908 1835 1835 46.0 1.560908 1738 1738 47.0 1.560908 1629 1629 48.0 1.560908 1550 1550 49.0 1.560908 1526 1526 50.0 1.560908 1416 1416 51.0 1.560908 1350 1350 52.0 1.560908 1300 1300 53.0 1.560908 1232 1232 54.0 1.560908 1206 1206 55.0 1.560908 1132 1132 56.0 1.560908 1083 1083 57.0 1.560908 1053 1053 58.0 1.560908 921 921 59.0 1.560908 936 936 60.0 1.560908 993 993 61.0 1.560908 944 944 62.0 1.560908 898 898 63.0 1.560908 877 877 64.0 1.560908 849 849 65.0 1.560908 741 741 66.0 1.560908 727 727 67.0 1.560908 689 689 68.0 1.560908 697 697 69.0 1.560908 647 647 70.0 1.560908 676 676 71.0 1.560908 616 616 72.0 1.560908 580 580 73.0 1.560908 588 588 74.0 1.560908 569 569 75.0 1.560908 559 559 76.0 1.560908 537 537 77.0 1.560908 537 537 78.0 1.560908 482 482 79.0 1.560908 470 470 80.0 1.560908 471 471 81.0 1.560908 438 438 82.0 1.560908 439 439 83.0 1.560908 400 400 84.0 1.560908 386 386 85.0 1.560908 438 438 86.0 1.560908 411 411 87.0 1.560908 398 398 88.0 1.560908 363 363 89.0 1.560908 315 315 90.0 1.560908 333 333 91.0 1.560908 351 351 92.0 1.560908 351 351 93.0 1.560908 347 347 94.0 1.560908 307 307 95.0 1.560908 338 338 96.0 1.560908 268 268 97.0 1.560908 300 300 98.0 1.560908 263 263 99.0 1.560908 278 278 100.0 1.560908 256 256 101.0 0 271 271 102.0 0 257 257 103.0 0 267 267 104.0 0 227 227 105.0 0 234 234 106.0 0 259 259 107.0 0 197 197 108.0 0 215 215 109.0 0 217 217 110.0 0 203 203 111.0 0 187 187 112.0 0 193 193 113.0 0 185 185 114.0 0 176 176 115.0 0 215 215 116.0 0 155 155 117.0 0 183 183 118.0 0 158 158 119.0 0 147 147 120.0 0 174 174 121.0 0 190 190 122.0 0 156 156 123.0 0 139 139 124.0 0 163 163 125.0 0 132 132 126.0 0 145 145 127.0 0 127 127 128.0 0 158 158 129.0 0 115 115 130.0 0 119 119 131.0 0 139 139 132.0 0 126 126 133.0 0 125 125 134.0 0 130 130 135.0 0 119 119 136.0 0 122 122 137.0 0 118 118 138.0 0 109 109 139.0 0 124 124 140.0 0 122 122 141.0 0 115 115 142.0 0 101 101 143.0 0 134 134 144.0 0 102 102 145.0 0 100 100 146.0 0 96 96 147.0 0 87 87 148.0 0 113 113 149.0 0 96 96 150.0 0 99 99 151.0 0 89 89 152.0 0 75 75 153.0 0 94 94 154.0 0 94 94 155.0 0 75 75 156.0 0 76 76 157.0 0 80 80 158.0 0 81 81 159.0 0 86 86 160.0 0 66 66 161.0 0 64 64 162.0 0 83 83 163.0 0 84 84 164.0 0 72 72 165.0 0 69 69 166.0 0 74 74 167.0 0 65 65 168.0 0 71 71 169.0 0 65 65 170.0 0 56 56 171.0 0 59 59 172.0 0 65 65 173.0 0 48 48 174.0 0 67 67 175.0 0 71 71 176.0 0 56 56 177.0 0 49 49 178.0 0 40 40 179.0 0 52 52 180.0 0 51 51 181.0 0 48 48 182.0 0 46 46 183.0 0 46 46 184.0 0 51 51 185.0 0 35 35 186.0 0 56 56 187.0 0 40 40 188.0 0 54 54 189.0 0 50 50 190.0 0 51 51 191.0 0 47 47 192.0 0 41 41 193.0 0 47 47 194.0 0 54 54 195.0 0 43 43 196.0 0 36 36 197.0 0 41 41 198.0 0 41 41 199.0 0 39 39 200.0 0 37 37 201.0 0 43 43 202.0 0 40 40 203.0 0 38 38 204.0 0 26 26 205.0 0 36 36 206.0 0 25 25 207.0 0 40 40 208.0 0 37 37 209.0 0 38 38 210.0 0 25 25 211.0 0 35 35 212.0 0 29 29 213.0 0 40 40 214.0 0 40 40 215.0 0 21 21 216.0 0 19 19 217.0 0 30 30 218.0 0 32 32 219.0 0 36 36 220.0 0 28 28 221.0 0 32 32 222.0 0 31 31 223.0 0 23 23 224.0 0 24 24 225.0 0 25 25 226.0 0 33 33 227.0 0 20 20 228.0 0 22 22 229.0 0 18 18 230.0 0 32 32 231.0 0 25 25 232.0 0 32 32 233.0 0 27 27 234.0 0 32 32 235.0 0 23 23 236.0 0 27 27 237.0 0 29 29 238.0 0 23 23 239.0 0 26 26 240.0 0 20 20 241.0 0 25 25 242.0 0 15 15 243.0 0 18 18 244.0 0 21 21 245.0 0 27 27 246.0 0 21 21 247.0 0 19 19 248.0 0 21 21 249.0 0 22 22 250.0 0 18 18 251.0 0 13 13 252.0 0 14 14 253.0 0 27 27 254.0 0 15 15 255.0 0 21 21 256.0 0 18 18 257.0 0 19 19 258.0 0 20 20 259.0 0 17 17 260.0 0 19 19 261.0 0 22 22 262.0 0 19 19 263.0 0 15 15 264.0 0 16 16 265.0 0 21 21 266.0 0 15 15 267.0 0 13 13 268.0 0 19 19 269.0 0 15 15 270.0 0 13 13 271.0 0 14 14 272.0 0 14 14 273.0 0 18 18 274.0 0 8 8 275.0 0 19 19 276.0 0 15 15 277.0 0 18 18 278.0 0 16 16 279.0 0 19 19 280.0 0 19 19 281.0 0 15 15 282.0 0 20 20 283.0 0 16 16 284.0 0 16 16 285.0 0 15 15 286.0 0 7 7 287.0 0 12 12 288.0 0 19 19 289.0 0 12 12 290.0 0 13 13 291.0 0 16 16 292.0 0 16 16 293.0 0 10 10 294.0 0 4 4 295.0 0 9 9 296.0 0 15 15 297.0 0 21 21 298.0 0 14 14 299.0 0 19 19 300.0 0 9 9 301.0 0 12 12 302.0 0 3 3 303.0 0 11 11 304.0 0 15 15 305.0 0 8 8 306.0 0 4 4 307.0 0 4 4 308.0 0 11 11 309.0 0 10 10 310.0 0 11 11 311.0 0 5 5 312.0 0 8 8 313.0 0 3 3 314.0 0 16 16 315.0 0 13 13 316.0 0 6 6 317.0 0 8 8 318.0 0 11 11 319.0 0 11 11 320.0 0 8 8 321.0 0 8 8 322.0 0 10 10 323.0 0 10 10 324.0 0 12 12 325.0 0 8 8 326.0 0 6 6 327.0 0 8 8 328.0 0 12 12 329.0 0 9 9 330.0 0 8 8 331.0 0 13 13 332.0 0 7 7 333.0 0 6 6 334.0 0 4 4 335.0 0 7 7 336.0 0 4 4 337.0 0 9 9 338.0 0 7 7 339.0 0 7 7 340.0 0 11 11 341.0 0 9 9 342.0 0 4 4 343.0 0 7 7 344.0 0 5 5 345.0 0 6 6 346.0 0 10 10 347.0 0 8 8 348.0 0 7 7 349.0 0 8 8 350.0 0 7 7 351.0 0 8 8 352.0 0 9 9 353.0 0 4 4 354.0 0 9 9 355.0 0 5 5 356.0 0 7 7 357.0 0 5 5 358.0 0 3 3 359.0 0 4 4 360.0 0 10 10 361.0 0 5 5 362.0 0 6 6 363.0 0 8 8 364.0 0 2 2 365.0 0 8 8 366.0 0 5 5 367.0 0 1 1 368.0 0 7 7 369.0 0 9 9 370.0 0 6 6 371.0 0 13 13 372.0 0 6 6 373.0 0 3 3 374.0 0 9 9 375.0 0 6 6 376.0 0 8 8 377.0 0 7 7 378.0 0 3 3 379.0 0 6 6 380.0 0 7 7 381.0 0 3 3 382.0 0 5 5 383.0 0 4 4 384.0 0 3 3 385.0 0 7 7 386.0 0 3 3 387.0 0 3 3 388.0 0 6 6 389.0 0 4 4 390.0 0 8 8 391.0 0 3 3 392.0 0 4 4 393.0 0 3 3 394.0 0 7 7 395.0 0 3 3 396.0 0 8 8 397.0 0 5 5 398.0 0 10 10 399.0 0 5 5 400.0 0 9 9 401.0 0 5 5 402.0 0 5 5 403.0 0 3 3 404.0 0 2 2 405.0 0 3 3 406.0 0 3 3 407.0 0 1 1 408.0 0 4 4 409.0 0 4 4 410.0 0 4 4 411.0 0 1 1 412.0 0 3 3 413.0 0 6 6 414.0 0 2 2 415.0 0 4 4 416.0 0 3 3 417.0 0 5 5 418.0 0 3 3 419.0 0 5 5 420.0 0 4 4 421.0 0 2 2 422.0 0 7 7 423.0 0 5 5 424.0 0 1 1 425.0 0 2 2 426.0 0 4 4 427.0 0 3 3 428.0 0 5 5 429.0 0 2 2 430.0 0 2 2 431.0 0 4 4 432.0 0 2 2 433.0 0 5 5 434.0 0 3 3 435.0 0 4 4 436.0 0 3 3 437.0 0 6 6 438.0 0 3 3 439.0 0 4 4 440.0 0 3 3 441.0 0 2 2 442.0 0 1 1 443.0 0 2 2 444.0 0 2 2 445.0 0 1 1 446.0 0 3 3 447.0 0 2 2 448.0 0 6 6 449.0 0 3 3 450.0 0 5 5 451.0 0 3 3 452.0 0 4 4 453.0 0 2 2 454.0 0 3 3 455.0 0 3 3 456.0 0 3 3 457.0 0 4 4 458.0 0 5 5 459.0 0 3 3 460.0 0 2 2 461.0 0 1 1 462.0 0 3 3 463.0 0 4 4 464.0 0 3 3 465.0 0 2 2 466.0 0 6 6 467.0 0 1 1 468.0 0 3 3 469.0 0 2 2 470.0 0 3 3 471.0 0 5 5 472.0 0 1 1 473.0 0 3 3 474.0 0 1 1 475.0 0 1 1 476.0 0 4 4 477.0 0 1 1 478.0 0 2 2 479.0 0 1 1 480.0 0 2 2 481.0 0 2 2 482.0 0 2 2 483.0 0 4 4 484.0 0 4 4 485.0 0 2 2 486.0 0 2 2 487.0 0 1 1 488.0 0 2 2 489.0 0 4 4 490.0 0 4 4 491.0 0 5 5 492.0 0 1 1 493.0 0 1 1 494.0 0 1 1 495.0 0 4 4 496.0 0 4 4 497.0 0 1 1 499.0 0 1 1 500.0 0 2 2 502.0 0 4 4 503.0 0 1 1 504.0 0 1 1 505.0 0 3 3 506.0 0 4 4 507.0 0 1 1 508.0 0 2 2 509.0 0 3 3 511.0 0 2 2 512.0 0 2 2 513.0 0 3 3 514.0 0 3 3 515.0 0 3 3 516.0 0 2 2 518.0 0 2 2 519.0 0 2 2 520.0 0 2 2 521.0 0 2 2 522.0 0 3 3 523.0 0 2 2 524.0 0 1 1 525.0 0 3 3 526.0 0 1 1 528.0 0 1 1 529.0 0 2 2 530.0 0 3 3 531.0 0 1 1 532.0 0 2 2 535.0 0 2 2 536.0 0 1 1 538.0 0 3 3 539.0 0 3 3 540.0 0 2 2 541.0 0 1 1 542.0 0 2 2 543.0 0 2 2 545.0 0 2 2 547.0 0 1 1 548.0 0 3 3 550.0 0 3 3 551.0 0 2 2 552.0 0 2 2 553.0 0 1 1 554.0 0 1 1 555.0 0 2 2 556.0 0 1 1 558.0 0 3 3 559.0 0 1 1 561.0 0 1 1 562.0 0 2 2 564.0 0 4 4 565.0 0 3 3 566.0 0 2 2 570.0 0 3 3 572.0 0 3 3 575.0 0 2 2 576.0 0 2 2 578.0 0 1 1 579.0 0 1 1 580.0 0 2 2 581.0 0 2 2 583.0 0 1 1 584.0 0 1 1 585.0 0 4 4 586.0 0 1 1 587.0 0 2 2 588.0 0 1 1 592.0 0 1 1 593.0 0 1 1 594.0 0 2 2 595.0 0 1 1 596.0 0 1 1 600.0 0 2 2 601.0 0 1 1 602.0 0 1 1 604.0 0 1 1 607.0 0 1 1 608.0 0 1 1 609.0 0 1 1 611.0 0 1 1 613.0 0 3 3 614.0 0 2 2 617.0 0 3 3 619.0 0 2 2 620.0 0 2 2 622.0 0 1 1 624.0 0 1 1 625.0 0 1 1 626.0 0 2 2 629.0 0 2 2 631.0 0 1 1 633.0 0 1 1 635.0 0 2 2 636.0 0 1 1 637.0 0 1 1 639.0 0 1 1 640.0 0 1 1 641.0 0 3 3 643.0 0 3 3 644.0 0 1 1 647.0 0 1 1 648.0 0 2 2 649.0 0 1 1 651.0 0 1 1 653.0 0 2 2 656.0 0 2 2 657.0 0 1 1 658.0 0 1 1 663.0 0 1 1 664.0 0 1 1 667.0 0 2 2 668.0 0 1 1 669.0 0 1 1 674.0 0 1 1 675.0 0 2 2 684.0 0 1 1 685.0 0 1 1 686.0 0 2 2 690.0 0 1 1 694.0 0 1 1 696.0 0 1 1 697.0 0 1 1 701.0 0 1 1 703.0 0 1 1 707.0 0 3 3 708.0 0 1 1 709.0 0 1 1 715.0 0 1 1 717.0 0 4 4 719.0 0 1 1 720.0 0 1 1 725.0 0 2 2 728.0 0 1 1 729.0 0 1 1 730.0 0 1 1 733.0 0 1 1 737.0 0 1 1 739.0 0 1 1 741.0 0 1 1 742.0 0 1 1 745.0 0 1 1 748.0 0 1 1 749.0 0 1 1 750.0 0 3 3 759.0 0 1 1 766.0 0 1 1 767.0 0 1 1 776.0 0 1 1 778.0 0 1 1 782.0 0 1 1 789.0 0 1 1 791.0 0 1 1 792.0 0 1 1 794.0 0 1 1 800.0 0 1 1 801.0 0 1 1 807.0 0 1 1 813.0 0 1 1 820.0 0 1 1 827.0 0 1 1 834.0 0 1 1 835.0 0 1 1 840.0 0 1 1 857.0 0 1 1 865.0 0 1 1 877.0 0 1 1 881.0 0 2 2 894.0 0 1 1 896.0 0 1 1 904.0 0 1 1 909.0 0 1 1 914.0 0 1 1 927.0 0 1 1 936.0 0 1 1 938.0 0 1 1 945.0 0 1 1 964.0 0 1 1 977.0 0 1 1 993.0 0 1 1 1007.0 0 1 1 1011.0 0 1 1 1023.0 0 1 1 1026.0 0 2 2 1035.0 0 1 1 1047.0 0 1 1 1056.0 0 1 1 1060.0 0 1 1 1081.0 0 1 1 1104.0 0 1 1 1107.0 0 1 1 1123.0 0 1 1 1126.0 0 1 1 1186.0 0 1 1 1200.0 0 1 1 1350.0 0 1 1 1355.0 0 1 1 1378.0 0 1 1 1481.0 0 1 1 1588.0 0 1 1 1805.0 0 1 1 1895.0 0 1 1 2029.0 0 1 1 2089.0 0 1 1 2225.0 0 1 1