## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354377.sorted.bam --OUTPUT SRX7354377.markdup.sorted.bam --METRICS_FILE SRX7354377.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 21:53:18 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 21817 30535503 3840814 1655197 14392 10334650 0 0.338562 34223562 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17829790 17829790 2.0 1.409738 1331404 1331404 3.0 1.577624 348783 348783 4.0 1.646413 169711 169711 5.0 1.674599 103316 103316 6.0 1.686147 70424 70424 7.0 1.690879 50990 50990 8.0 1.692818 38605 38605 9.0 1.693613 30535 30535 10.0 1.693938 24809 24809 11.0 1.694072 20286 20286 12.0 1.694126 17053 17053 13.0 1.694149 14469 14469 14.0 1.694158 12491 12491 15.0 1.694162 10919 10919 16.0 1.694163 9294 9294 17.0 1.694164 8275 8275 18.0 1.694164 7562 7562 19.0 1.694164 6548 6548 20.0 1.694164 6045 6045 21.0 1.694164 5361 5361 22.0 1.694164 4728 4728 23.0 1.694164 4432 4432 24.0 1.694164 4084 4084 25.0 1.694164 3726 3726 26.0 1.694164 3461 3461 27.0 1.694164 3131 3131 28.0 1.694164 2912 2912 29.0 1.694164 2767 2767 30.0 1.694164 2509 2509 31.0 1.694164 2432 2432 32.0 1.694164 2128 2128 33.0 1.694164 2025 2025 34.0 1.694164 1848 1848 35.0 1.694164 1762 1762 36.0 1.694164 1734 1734 37.0 1.694164 1523 1523 38.0 1.694164 1438 1438 39.0 1.694164 1463 1463 40.0 1.694164 1396 1396 41.0 1.694164 1243 1243 42.0 1.694164 1222 1222 43.0 1.694164 1133 1133 44.0 1.694164 1087 1087 45.0 1.694164 993 993 46.0 1.694164 930 930 47.0 1.694164 845 845 48.0 1.694164 851 851 49.0 1.694164 866 866 50.0 1.694164 763 763 51.0 1.694164 771 771 52.0 1.694164 702 702 53.0 1.694164 678 678 54.0 1.694164 654 654 55.0 1.694164 659 659 56.0 1.694164 592 592 57.0 1.694164 581 581 58.0 1.694164 560 560 59.0 1.694164 535 535 60.0 1.694164 471 471 61.0 1.694164 527 527 62.0 1.694164 472 472 63.0 1.694164 403 403 64.0 1.694164 476 476 65.0 1.694164 431 431 66.0 1.694164 396 396 67.0 1.694164 413 413 68.0 1.694164 385 385 69.0 1.694164 334 334 70.0 1.694164 373 373 71.0 1.694164 335 335 72.0 1.694164 348 348 73.0 1.694164 297 297 74.0 1.694164 329 329 75.0 1.694164 334 334 76.0 1.694164 277 277 77.0 1.694164 302 302 78.0 1.694164 233 233 79.0 1.694164 244 244 80.0 1.694164 235 235 81.0 1.694164 225 225 82.0 1.694164 250 250 83.0 1.694164 243 243 84.0 1.694164 196 196 85.0 1.694164 233 233 86.0 1.694164 189 189 87.0 1.694164 195 195 88.0 1.694164 198 198 89.0 1.694164 199 199 90.0 1.694164 197 197 91.0 1.694164 173 173 92.0 1.694164 179 179 93.0 1.694164 161 161 94.0 1.694164 161 161 95.0 1.694164 132 132 96.0 1.694164 157 157 97.0 1.694164 144 144 98.0 1.694164 163 163 99.0 1.694164 135 135 100.0 1.694164 149 149 101.0 0 136 136 102.0 0 130 130 103.0 0 145 145 104.0 0 142 142 105.0 0 123 123 106.0 0 118 118 107.0 0 121 121 108.0 0 115 115 109.0 0 119 119 110.0 0 110 110 111.0 0 93 93 112.0 0 112 112 113.0 0 109 109 114.0 0 100 100 115.0 0 108 108 116.0 0 102 102 117.0 0 99 99 118.0 0 70 70 119.0 0 91 91 120.0 0 107 107 121.0 0 97 97 122.0 0 90 90 123.0 0 92 92 124.0 0 87 87 125.0 0 76 76 126.0 0 83 83 127.0 0 74 74 128.0 0 63 63 129.0 0 73 73 130.0 0 63 63 131.0 0 57 57 132.0 0 82 82 133.0 0 61 61 134.0 0 60 60 135.0 0 63 63 136.0 0 61 61 137.0 0 65 65 138.0 0 69 69 139.0 0 70 70 140.0 0 63 63 141.0 0 59 59 142.0 0 55 55 143.0 0 64 64 144.0 0 59 59 145.0 0 59 59 146.0 0 57 57 147.0 0 49 49 148.0 0 55 55 149.0 0 55 55 150.0 0 42 42 151.0 0 46 46 152.0 0 41 41 153.0 0 40 40 154.0 0 51 51 155.0 0 45 45 156.0 0 37 37 157.0 0 34 34 158.0 0 38 38 159.0 0 34 34 160.0 0 36 36 161.0 0 39 39 162.0 0 44 44 163.0 0 40 40 164.0 0 31 31 165.0 0 39 39 166.0 0 16 16 167.0 0 29 29 168.0 0 40 40 169.0 0 28 28 170.0 0 38 38 171.0 0 25 25 172.0 0 25 25 173.0 0 31 31 174.0 0 24 24 175.0 0 35 35 176.0 0 28 28 177.0 0 23 23 178.0 0 37 37 179.0 0 28 28 180.0 0 25 25 181.0 0 25 25 182.0 0 31 31 183.0 0 24 24 184.0 0 24 24 185.0 0 37 37 186.0 0 27 27 187.0 0 31 31 188.0 0 23 23 189.0 0 22 22 190.0 0 28 28 191.0 0 22 22 192.0 0 20 20 193.0 0 32 32 194.0 0 20 20 195.0 0 20 20 196.0 0 27 27 197.0 0 26 26 198.0 0 24 24 199.0 0 21 21 200.0 0 23 23 201.0 0 20 20 202.0 0 19 19 203.0 0 21 21 204.0 0 11 11 205.0 0 25 25 206.0 0 26 26 207.0 0 19 19 208.0 0 21 21 209.0 0 16 16 210.0 0 19 19 211.0 0 14 14 212.0 0 19 19 213.0 0 16 16 214.0 0 14 14 215.0 0 15 15 216.0 0 17 17 217.0 0 13 13 218.0 0 14 14 219.0 0 10 10 220.0 0 12 12 221.0 0 20 20 222.0 0 15 15 223.0 0 20 20 224.0 0 14 14 225.0 0 19 19 226.0 0 20 20 227.0 0 15 15 228.0 0 17 17 229.0 0 19 19 230.0 0 14 14 231.0 0 18 18 232.0 0 12 12 233.0 0 11 11 234.0 0 12 12 235.0 0 11 11 236.0 0 11 11 237.0 0 13 13 238.0 0 11 11 239.0 0 14 14 240.0 0 13 13 241.0 0 10 10 242.0 0 16 16 243.0 0 11 11 244.0 0 11 11 245.0 0 4 4 246.0 0 15 15 247.0 0 14 14 248.0 0 11 11 249.0 0 11 11 250.0 0 7 7 251.0 0 13 13 252.0 0 9 9 253.0 0 16 16 254.0 0 12 12 255.0 0 5 5 256.0 0 9 9 257.0 0 11 11 258.0 0 7 7 259.0 0 11 11 260.0 0 13 13 261.0 0 13 13 262.0 0 11 11 263.0 0 8 8 264.0 0 10 10 265.0 0 11 11 266.0 0 5 5 267.0 0 8 8 268.0 0 14 14 269.0 0 11 11 270.0 0 6 6 271.0 0 6 6 272.0 0 14 14 273.0 0 11 11 274.0 0 11 11 275.0 0 8 8 276.0 0 6 6 277.0 0 4 4 278.0 0 8 8 279.0 0 5 5 280.0 0 11 11 281.0 0 10 10 282.0 0 13 13 283.0 0 2 2 284.0 0 9 9 285.0 0 9 9 286.0 0 7 7 287.0 0 6 6 288.0 0 6 6 289.0 0 9 9 290.0 0 12 12 291.0 0 11 11 292.0 0 5 5 293.0 0 3 3 294.0 0 4 4 295.0 0 9 9 296.0 0 2 2 297.0 0 7 7 298.0 0 5 5 299.0 0 6 6 300.0 0 6 6 301.0 0 7 7 302.0 0 8 8 303.0 0 6 6 304.0 0 6 6 305.0 0 5 5 306.0 0 6 6 307.0 0 4 4 308.0 0 7 7 309.0 0 9 9 310.0 0 8 8 311.0 0 1 1 312.0 0 1 1 313.0 0 11 11 314.0 0 8 8 315.0 0 7 7 316.0 0 6 6 317.0 0 2 2 318.0 0 8 8 319.0 0 4 4 320.0 0 5 5 321.0 0 6 6 322.0 0 8 8 323.0 0 4 4 324.0 0 3 3 326.0 0 6 6 327.0 0 3 3 328.0 0 5 5 329.0 0 2 2 330.0 0 5 5 331.0 0 6 6 332.0 0 4 4 333.0 0 5 5 334.0 0 4 4 335.0 0 6 6 336.0 0 2 2 337.0 0 5 5 338.0 0 5 5 339.0 0 4 4 340.0 0 5 5 341.0 0 1 1 342.0 0 3 3 343.0 0 6 6 344.0 0 5 5 345.0 0 6 6 346.0 0 4 4 347.0 0 5 5 349.0 0 2 2 350.0 0 3 3 351.0 0 4 4 352.0 0 2 2 353.0 0 2 2 354.0 0 3 3 355.0 0 8 8 357.0 0 3 3 358.0 0 6 6 359.0 0 5 5 360.0 0 4 4 361.0 0 2 2 362.0 0 6 6 363.0 0 3 3 365.0 0 5 5 366.0 0 5 5 367.0 0 1 1 368.0 0 4 4 369.0 0 4 4 370.0 0 2 2 371.0 0 3 3 372.0 0 3 3 373.0 0 7 7 374.0 0 4 4 375.0 0 3 3 376.0 0 1 1 378.0 0 4 4 379.0 0 3 3 380.0 0 2 2 381.0 0 2 2 382.0 0 4 4 383.0 0 1 1 384.0 0 4 4 385.0 0 2 2 386.0 0 3 3 387.0 0 5 5 388.0 0 2 2 389.0 0 1 1 390.0 0 1 1 391.0 0 6 6 392.0 0 1 1 393.0 0 1 1 394.0 0 4 4 395.0 0 2 2 396.0 0 3 3 397.0 0 4 4 398.0 0 2 2 399.0 0 6 6 400.0 0 2 2 401.0 0 1 1 402.0 0 6 6 403.0 0 2 2 404.0 0 4 4 405.0 0 4 4 407.0 0 3 3 408.0 0 5 5 409.0 0 5 5 410.0 0 1 1 411.0 0 4 4 412.0 0 5 5 413.0 0 3 3 414.0 0 4 4 415.0 0 2 2 416.0 0 1 1 417.0 0 2 2 418.0 0 4 4 419.0 0 2 2 420.0 0 5 5 421.0 0 2 2 422.0 0 1 1 423.0 0 2 2 424.0 0 6 6 425.0 0 2 2 426.0 0 1 1 428.0 0 4 4 429.0 0 1 1 430.0 0 1 1 431.0 0 3 3 432.0 0 1 1 434.0 0 1 1 435.0 0 3 3 436.0 0 2 2 437.0 0 1 1 438.0 0 3 3 439.0 0 1 1 440.0 0 2 2 441.0 0 1 1 442.0 0 2 2 443.0 0 3 3 444.0 0 2 2 445.0 0 1 1 447.0 0 1 1 448.0 0 3 3 449.0 0 1 1 450.0 0 4 4 451.0 0 1 1 452.0 0 7 7 453.0 0 2 2 456.0 0 1 1 457.0 0 3 3 458.0 0 1 1 461.0 0 1 1 462.0 0 1 1 464.0 0 2 2 465.0 0 1 1 467.0 0 1 1 468.0 0 1 1 470.0 0 1 1 471.0 0 1 1 473.0 0 1 1 474.0 0 1 1 476.0 0 2 2 477.0 0 5 5 478.0 0 1 1 479.0 0 3 3 480.0 0 3 3 482.0 0 1 1 483.0 0 1 1 484.0 0 2 2 485.0 0 1 1 486.0 0 2 2 487.0 0 1 1 489.0 0 1 1 490.0 0 1 1 492.0 0 1 1 496.0 0 1 1 497.0 0 1 1 498.0 0 1 1 499.0 0 2 2 500.0 0 1 1 501.0 0 1 1 503.0 0 1 1 504.0 0 1 1 505.0 0 1 1 506.0 0 3 3 507.0 0 3 3 508.0 0 1 1 509.0 0 1 1 510.0 0 3 3 511.0 0 2 2 514.0 0 2 2 515.0 0 2 2 517.0 0 1 1 518.0 0 3 3 519.0 0 1 1 521.0 0 2 2 523.0 0 2 2 524.0 0 2 2 525.0 0 2 2 527.0 0 3 3 530.0 0 4 4 531.0 0 1 1 532.0 0 3 3 533.0 0 1 1 534.0 0 1 1 535.0 0 2 2 537.0 0 1 1 538.0 0 2 2 539.0 0 2 2 542.0 0 1 1 544.0 0 1 1 545.0 0 1 1 548.0 0 1 1 550.0 0 1 1 552.0 0 2 2 555.0 0 1 1 560.0 0 1 1 563.0 0 2 2 564.0 0 1 1 570.0 0 1 1 571.0 0 1 1 573.0 0 1 1 575.0 0 2 2 577.0 0 1 1 582.0 0 1 1 583.0 0 1 1 584.0 0 1 1 590.0 0 2 2 592.0 0 1 1 593.0 0 2 2 595.0 0 2 2 596.0 0 1 1 598.0 0 1 1 599.0 0 1 1 602.0 0 1 1 606.0 0 2 2 613.0 0 1 1 614.0 0 3 3 617.0 0 1 1 621.0 0 1 1 622.0 0 1 1 627.0 0 1 1 628.0 0 1 1 630.0 0 1 1 632.0 0 1 1 639.0 0 1 1 641.0 0 1 1 642.0 0 1 1 646.0 0 1 1 647.0 0 1 1 651.0 0 1 1 652.0 0 1 1 654.0 0 1 1 657.0 0 1 1 660.0 0 1 1 662.0 0 1 1 666.0 0 1 1 668.0 0 2 2 675.0 0 1 1 676.0 0 1 1 677.0 0 2 2 680.0 0 1 1 681.0 0 1 1 685.0 0 1 1 694.0 0 1 1 699.0 0 1 1 702.0 0 1 1 704.0 0 1 1 709.0 0 1 1 713.0 0 2 2 719.0 0 2 2 720.0 0 2 2 721.0 0 1 1 723.0 0 1 1 726.0 0 1 1 736.0 0 1 1 737.0 0 1 1 739.0 0 1 1 750.0 0 1 1 773.0 0 1 1 774.0 0 3 3 776.0 0 1 1 781.0 0 1 1 783.0 0 1 1 785.0 0 2 2 790.0 0 1 1 813.0 0 1 1 818.0 0 1 1 825.0 0 1 1 828.0 0 1 1 829.0 0 1 1 835.0 0 1 1 843.0 0 1 1 846.0 0 1 1 849.0 0 1 1 850.0 0 1 1 852.0 0 1 1 859.0 0 1 1 873.0 0 1 1 874.0 0 1 1 891.0 0 1 1 894.0 0 1 1 902.0 0 1 1 904.0 0 1 1 908.0 0 1 1 920.0 0 1 1 922.0 0 1 1 956.0 0 2 2 966.0 0 1 1 977.0 0 1 1 978.0 0 1 1 986.0 0 1 1 1010.0 0 1 1 1022.0 0 1 1 1054.0 0 1 1 1057.0 0 1 1 1061.0 0 1 1 1082.0 0 1 1 1086.0 0 1 1 1125.0 0 1 1 1236.0 0 1 1 1704.0 0 1 1 1774.0 0 1 1 1791.0 0 1 1 3297.0 0 1 1