## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354125.sorted.bam --OUTPUT SRX7354125.markdup.sorted.bam --METRICS_FILE SRX7354125.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: Fri Oct 27 17:03:40 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 37406 33115303 4222472 7596120 27548 11324102 0 0.342182 36602390 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18813865 18813865 2.0 1.404651 1765765 1765765 3.0 1.568393 429509 429509 4.0 1.634652 201191 201191 5.0 1.661463 121194 121194 6.0 1.672313 80999 80999 7.0 1.676703 58349 58349 8.0 1.678479 44096 44096 9.0 1.679198 34435 34435 10.0 1.679489 27362 27362 11.0 1.679607 22675 22675 12.0 1.679654 18848 18848 13.0 1.679674 16088 16088 14.0 1.679681 13683 13683 15.0 1.679685 11708 11708 16.0 1.679686 10357 10357 17.0 1.679686 8971 8971 18.0 1.679687 8084 8084 19.0 1.679687 7001 7001 20.0 1.679687 6214 6214 21.0 1.679687 5588 5588 22.0 1.679687 5098 5098 23.0 1.679687 4704 4704 24.0 1.679687 4301 4301 25.0 1.679687 3866 3866 26.0 1.679687 3654 3654 27.0 1.679687 3300 3300 28.0 1.679687 3009 3009 29.0 1.679687 2830 2830 30.0 1.679687 2546 2546 31.0 1.679687 2414 2414 32.0 1.679687 2214 2214 33.0 1.679687 2120 2120 34.0 1.679687 1992 1992 35.0 1.679687 1853 1853 36.0 1.679687 1697 1697 37.0 1.679687 1527 1527 38.0 1.679687 1499 1499 39.0 1.679687 1418 1418 40.0 1.679687 1380 1380 41.0 1.679687 1296 1296 42.0 1.679687 1199 1199 43.0 1.679687 1206 1206 44.0 1.679687 1030 1030 45.0 1.679687 948 948 46.0 1.679687 973 973 47.0 1.679687 916 916 48.0 1.679687 915 915 49.0 1.679687 800 800 50.0 1.679687 797 797 51.0 1.679687 751 751 52.0 1.679687 715 715 53.0 1.679687 672 672 54.0 1.679687 683 683 55.0 1.679687 591 591 56.0 1.679687 566 566 57.0 1.679687 560 560 58.0 1.679687 567 567 59.0 1.679687 527 527 60.0 1.679687 498 498 61.0 1.679687 462 462 62.0 1.679687 461 461 63.0 1.679687 449 449 64.0 1.679687 419 419 65.0 1.679687 442 442 66.0 1.679687 415 415 67.0 1.679687 357 357 68.0 1.679687 363 363 69.0 1.679687 353 353 70.0 1.679687 346 346 71.0 1.679687 345 345 72.0 1.679687 294 294 73.0 1.679687 311 311 74.0 1.679687 295 295 75.0 1.679687 303 303 76.0 1.679687 285 285 77.0 1.679687 265 265 78.0 1.679687 256 256 79.0 1.679687 257 257 80.0 1.679687 243 243 81.0 1.679687 237 237 82.0 1.679687 231 231 83.0 1.679687 232 232 84.0 1.679687 245 245 85.0 1.679687 220 220 86.0 1.679687 205 205 87.0 1.679687 174 174 88.0 1.679687 206 206 89.0 1.679687 182 182 90.0 1.679687 168 168 91.0 1.679687 192 192 92.0 1.679687 173 173 93.0 1.679687 168 168 94.0 1.679687 160 160 95.0 1.679687 161 161 96.0 1.679687 143 143 97.0 1.679687 154 154 98.0 1.679687 146 146 99.0 1.679687 129 129 100.0 1.679687 142 142 101.0 0 141 141 102.0 0 129 129 103.0 0 107 107 104.0 0 113 113 105.0 0 114 114 106.0 0 104 104 107.0 0 105 105 108.0 0 100 100 109.0 0 102 102 110.0 0 95 95 111.0 0 93 93 112.0 0 103 103 113.0 0 108 108 114.0 0 91 91 115.0 0 87 87 116.0 0 95 95 117.0 0 85 85 118.0 0 85 85 119.0 0 85 85 120.0 0 63 63 121.0 0 72 72 122.0 0 75 75 123.0 0 83 83 124.0 0 92 92 125.0 0 60 60 126.0 0 77 77 127.0 0 69 69 128.0 0 70 70 129.0 0 71 71 130.0 0 63 63 131.0 0 63 63 132.0 0 71 71 133.0 0 56 56 134.0 0 54 54 135.0 0 64 64 136.0 0 68 68 137.0 0 64 64 138.0 0 61 61 139.0 0 52 52 140.0 0 49 49 141.0 0 47 47 142.0 0 56 56 143.0 0 42 42 144.0 0 47 47 145.0 0 49 49 146.0 0 42 42 147.0 0 55 55 148.0 0 32 32 149.0 0 49 49 150.0 0 52 52 151.0 0 36 36 152.0 0 37 37 153.0 0 43 43 154.0 0 39 39 155.0 0 40 40 156.0 0 45 45 157.0 0 39 39 158.0 0 40 40 159.0 0 40 40 160.0 0 26 26 161.0 0 30 30 162.0 0 31 31 163.0 0 29 29 164.0 0 38 38 165.0 0 37 37 166.0 0 43 43 167.0 0 40 40 168.0 0 31 31 169.0 0 30 30 170.0 0 23 23 171.0 0 22 22 172.0 0 29 29 173.0 0 45 45 174.0 0 22 22 175.0 0 24 24 176.0 0 32 32 177.0 0 28 28 178.0 0 21 21 179.0 0 23 23 180.0 0 29 29 181.0 0 36 36 182.0 0 24 24 183.0 0 30 30 184.0 0 26 26 185.0 0 27 27 186.0 0 21 21 187.0 0 17 17 188.0 0 29 29 189.0 0 26 26 190.0 0 22 22 191.0 0 24 24 192.0 0 14 14 193.0 0 26 26 194.0 0 33 33 195.0 0 20 20 196.0 0 14 14 197.0 0 24 24 198.0 0 21 21 199.0 0 16 16 200.0 0 21 21 201.0 0 9 9 202.0 0 20 20 203.0 0 12 12 204.0 0 19 19 205.0 0 25 25 206.0 0 17 17 207.0 0 21 21 208.0 0 16 16 209.0 0 16 16 210.0 0 14 14 211.0 0 13 13 212.0 0 19 19 213.0 0 20 20 214.0 0 19 19 215.0 0 14 14 216.0 0 8 8 217.0 0 12 12 218.0 0 11 11 219.0 0 12 12 220.0 0 16 16 221.0 0 19 19 222.0 0 9 9 223.0 0 11 11 224.0 0 11 11 225.0 0 17 17 226.0 0 16 16 227.0 0 3 3 228.0 0 8 8 229.0 0 15 15 230.0 0 18 18 231.0 0 11 11 232.0 0 4 4 233.0 0 15 15 234.0 0 8 8 235.0 0 15 15 236.0 0 13 13 237.0 0 20 20 238.0 0 15 15 239.0 0 14 14 240.0 0 13 13 241.0 0 7 7 242.0 0 9 9 243.0 0 10 10 244.0 0 8 8 245.0 0 13 13 246.0 0 15 15 247.0 0 15 15 248.0 0 10 10 249.0 0 6 6 250.0 0 5 5 251.0 0 10 10 252.0 0 10 10 253.0 0 14 14 254.0 0 10 10 255.0 0 3 3 256.0 0 6 6 257.0 0 11 11 258.0 0 10 10 259.0 0 9 9 260.0 0 11 11 261.0 0 7 7 262.0 0 15 15 263.0 0 8 8 264.0 0 6 6 265.0 0 10 10 266.0 0 8 8 267.0 0 5 5 268.0 0 9 9 269.0 0 5 5 270.0 0 9 9 271.0 0 8 8 272.0 0 6 6 273.0 0 10 10 274.0 0 9 9 275.0 0 5 5 276.0 0 5 5 277.0 0 2 2 278.0 0 6 6 279.0 0 6 6 280.0 0 9 9 281.0 0 9 9 282.0 0 8 8 283.0 0 9 9 284.0 0 9 9 285.0 0 4 4 286.0 0 5 5 287.0 0 7 7 288.0 0 9 9 289.0 0 12 12 290.0 0 7 7 291.0 0 6 6 292.0 0 7 7 293.0 0 7 7 294.0 0 6 6 295.0 0 4 4 296.0 0 3 3 297.0 0 4 4 298.0 0 10 10 299.0 0 11 11 300.0 0 6 6 301.0 0 4 4 302.0 0 4 4 303.0 0 10 10 304.0 0 14 14 305.0 0 4 4 306.0 0 9 9 307.0 0 5 5 308.0 0 3 3 309.0 0 7 7 310.0 0 4 4 311.0 0 7 7 312.0 0 4 4 313.0 0 8 8 314.0 0 5 5 315.0 0 3 3 316.0 0 6 6 317.0 0 6 6 318.0 0 4 4 319.0 0 4 4 320.0 0 4 4 321.0 0 6 6 322.0 0 5 5 323.0 0 4 4 324.0 0 5 5 325.0 0 4 4 327.0 0 1 1 328.0 0 2 2 329.0 0 1 1 330.0 0 5 5 331.0 0 4 4 332.0 0 5 5 333.0 0 2 2 334.0 0 3 3 335.0 0 2 2 336.0 0 6 6 337.0 0 4 4 338.0 0 2 2 340.0 0 3 3 341.0 0 6 6 342.0 0 5 5 343.0 0 8 8 344.0 0 3 3 345.0 0 2 2 346.0 0 3 3 347.0 0 2 2 348.0 0 4 4 349.0 0 3 3 350.0 0 4 4 351.0 0 1 1 352.0 0 3 3 353.0 0 3 3 354.0 0 1 1 355.0 0 6 6 356.0 0 7 7 357.0 0 1 1 358.0 0 1 1 359.0 0 6 6 360.0 0 2 2 361.0 0 2 2 362.0 0 1 1 363.0 0 3 3 364.0 0 2 2 365.0 0 9 9 366.0 0 3 3 367.0 0 2 2 368.0 0 4 4 369.0 0 3 3 370.0 0 3 3 371.0 0 2 2 372.0 0 8 8 373.0 0 3 3 374.0 0 2 2 375.0 0 1 1 376.0 0 1 1 377.0 0 3 3 378.0 0 3 3 379.0 0 3 3 380.0 0 4 4 381.0 0 4 4 382.0 0 1 1 383.0 0 1 1 384.0 0 3 3 385.0 0 7 7 386.0 0 3 3 387.0 0 2 2 388.0 0 4 4 389.0 0 4 4 390.0 0 1 1 391.0 0 2 2 392.0 0 3 3 393.0 0 4 4 394.0 0 1 1 395.0 0 1 1 396.0 0 1 1 397.0 0 2 2 398.0 0 2 2 399.0 0 2 2 400.0 0 4 4 401.0 0 2 2 402.0 0 4 4 405.0 0 6 6 406.0 0 2 2 407.0 0 1 1 408.0 0 3 3 409.0 0 5 5 410.0 0 3 3 411.0 0 4 4 412.0 0 3 3 413.0 0 1 1 414.0 0 2 2 415.0 0 2 2 416.0 0 5 5 417.0 0 5 5 418.0 0 3 3 419.0 0 1 1 420.0 0 2 2 421.0 0 2 2 422.0 0 2 2 423.0 0 1 1 424.0 0 2 2 425.0 0 1 1 426.0 0 1 1 428.0 0 1 1 429.0 0 1 1 430.0 0 1 1 431.0 0 2 2 432.0 0 1 1 433.0 0 2 2 434.0 0 2 2 435.0 0 2 2 436.0 0 1 1 437.0 0 1 1 438.0 0 1 1 439.0 0 1 1 441.0 0 1 1 442.0 0 2 2 443.0 0 2 2 445.0 0 2 2 446.0 0 2 2 447.0 0 2 2 448.0 0 2 2 450.0 0 1 1 451.0 0 1 1 453.0 0 1 1 454.0 0 1 1 455.0 0 1 1 457.0 0 1 1 458.0 0 1 1 459.0 0 1 1 460.0 0 1 1 461.0 0 2 2 462.0 0 2 2 465.0 0 2 2 468.0 0 3 3 470.0 0 1 1 472.0 0 1 1 476.0 0 2 2 477.0 0 1 1 478.0 0 3 3 480.0 0 2 2 481.0 0 3 3 483.0 0 2 2 484.0 0 1 1 485.0 0 1 1 486.0 0 2 2 487.0 0 2 2 488.0 0 1 1 489.0 0 1 1 491.0 0 2 2 492.0 0 2 2 493.0 0 1 1 494.0 0 2 2 496.0 0 1 1 498.0 0 1 1 500.0 0 3 3 501.0 0 2 2 506.0 0 2 2 508.0 0 3 3 509.0 0 1 1 510.0 0 1 1 513.0 0 1 1 515.0 0 1 1 516.0 0 1 1 518.0 0 1 1 520.0 0 1 1 522.0 0 1 1 523.0 0 3 3 524.0 0 1 1 528.0 0 2 2 530.0 0 2 2 531.0 0 1 1 532.0 0 1 1 534.0 0 1 1 535.0 0 1 1 538.0 0 1 1 540.0 0 3 3 541.0 0 1 1 543.0 0 2 2 544.0 0 2 2 545.0 0 1 1 548.0 0 2 2 549.0 0 2 2 550.0 0 2 2 551.0 0 1 1 552.0 0 1 1 553.0 0 2 2 554.0 0 3 3 557.0 0 1 1 559.0 0 2 2 562.0 0 1 1 564.0 0 1 1 565.0 0 2 2 567.0 0 1 1 570.0 0 2 2 571.0 0 1 1 572.0 0 2 2 573.0 0 1 1 574.0 0 1 1 575.0 0 1 1 576.0 0 1 1 577.0 0 1 1 579.0 0 1 1 586.0 0 2 2 587.0 0 1 1 588.0 0 1 1 589.0 0 1 1 590.0 0 1 1 594.0 0 1 1 598.0 0 2 2 601.0 0 1 1 604.0 0 1 1 610.0 0 1 1 617.0 0 2 2 620.0 0 1 1 621.0 0 1 1 624.0 0 1 1 626.0 0 1 1 627.0 0 1 1 628.0 0 2 2 635.0 0 2 2 637.0 0 1 1 640.0 0 2 2 643.0 0 2 2 644.0 0 1 1 647.0 0 1 1 649.0 0 1 1 657.0 0 2 2 662.0 0 1 1 663.0 0 2 2 664.0 0 1 1 669.0 0 1 1 674.0 0 1 1 686.0 0 1 1 692.0 0 2 2 694.0 0 1 1 698.0 0 1 1 700.0 0 1 1 707.0 0 1 1 710.0 0 1 1 712.0 0 1 1 716.0 0 1 1 719.0 0 1 1 720.0 0 1 1 724.0 0 1 1 725.0 0 1 1 733.0 0 1 1 736.0 0 1 1 739.0 0 1 1 742.0 0 1 1 756.0 0 1 1 757.0 0 1 1 759.0 0 1 1 762.0 0 1 1 767.0 0 1 1 768.0 0 1 1 781.0 0 1 1 783.0 0 1 1 785.0 0 1 1 789.0 0 1 1 800.0 0 1 1 808.0 0 2 2 813.0 0 1 1 821.0 0 2 2 825.0 0 1 1 844.0 0 1 1 866.0 0 1 1 873.0 0 1 1 887.0 0 2 2 930.0 0 1 1 943.0 0 1 1 961.0 0 1 1 988.0 0 1 1 989.0 0 1 1 996.0 0 1 1 1010.0 0 1 1 1123.0 0 1 1 1124.0 0 1 1 1152.0 0 1 1 1183.0 0 1 1 1239.0 0 1 1 1241.0 0 1 1 1367.0 0 1 1 1379.0 0 1 1 1607.0 0 1 1 1721.0 0 1 1