## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354054.sorted.bam --OUTPUT SRX7354054.markdup.sorted.bam --METRICS_FILE SRX7354054.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 17:41:52 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 25137 27810680 3299051 1993029 17923 10376133 0 0.373252 27268796 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14825940 14825940 2.0 1.360641 1508837 1508837 3.0 1.490703 385834 385834 4.0 1.537609 182174 182174 5.0 1.554525 109608 109608 6.0 1.560626 73847 73847 7.0 1.562826 53304 53304 8.0 1.563619 40515 40515 9.0 1.563905 31569 31569 10.0 1.564009 25227 25227 11.0 1.564046 20620 20620 12.0 1.564059 17231 17231 13.0 1.564064 14634 14634 14.0 1.564066 12471 12471 15.0 1.564066 10688 10688 16.0 1.564067 9383 9383 17.0 1.564067 8157 8157 18.0 1.564067 7319 7319 19.0 1.564067 6550 6550 20.0 1.564067 5830 5830 21.0 1.564067 5281 5281 22.0 1.564067 4737 4737 23.0 1.564067 4332 4332 24.0 1.564067 3940 3940 25.0 1.564067 3488 3488 26.0 1.564067 3400 3400 27.0 1.564067 2925 2925 28.0 1.564067 2709 2709 29.0 1.564067 2589 2589 30.0 1.564067 2371 2371 31.0 1.564067 2243 2243 32.0 1.564067 2112 2112 33.0 1.564067 2008 2008 34.0 1.564067 1800 1800 35.0 1.564067 1677 1677 36.0 1.564067 1596 1596 37.0 1.564067 1453 1453 38.0 1.564067 1368 1368 39.0 1.564067 1344 1344 40.0 1.564067 1279 1279 41.0 1.564067 1166 1166 42.0 1.564067 1096 1096 43.0 1.564067 1053 1053 44.0 1.564067 1018 1018 45.0 1.564067 957 957 46.0 1.564067 880 880 47.0 1.564067 847 847 48.0 1.564067 789 789 49.0 1.564067 734 734 50.0 1.564067 754 754 51.0 1.564067 676 676 52.0 1.564067 682 682 53.0 1.564067 610 610 54.0 1.564067 611 611 55.0 1.564067 582 582 56.0 1.564067 593 593 57.0 1.564067 519 519 58.0 1.564067 528 528 59.0 1.564067 475 475 60.0 1.564067 493 493 61.0 1.564067 455 455 62.0 1.564067 448 448 63.0 1.564067 416 416 64.0 1.564067 415 415 65.0 1.564067 409 409 66.0 1.564067 406 406 67.0 1.564067 373 373 68.0 1.564067 347 347 69.0 1.564067 334 334 70.0 1.564067 326 326 71.0 1.564067 295 295 72.0 1.564067 303 303 73.0 1.564067 328 328 74.0 1.564067 307 307 75.0 1.564067 281 281 76.0 1.564067 260 260 77.0 1.564067 246 246 78.0 1.564067 246 246 79.0 1.564067 239 239 80.0 1.564067 243 243 81.0 1.564067 211 211 82.0 1.564067 243 243 83.0 1.564067 214 214 84.0 1.564067 230 230 85.0 1.564067 211 211 86.0 1.564067 191 191 87.0 1.564067 193 193 88.0 1.564067 192 192 89.0 1.564067 185 185 90.0 1.564067 171 171 91.0 1.564067 179 179 92.0 1.564067 144 144 93.0 1.564067 148 148 94.0 1.564067 134 134 95.0 1.564067 139 139 96.0 1.564067 158 158 97.0 1.564067 137 137 98.0 1.564067 149 149 99.0 1.564067 142 142 100.0 1.564067 122 122 101.0 0 117 117 102.0 0 126 126 103.0 0 138 138 104.0 0 118 118 105.0 0 122 122 106.0 0 125 125 107.0 0 93 93 108.0 0 113 113 109.0 0 97 97 110.0 0 106 106 111.0 0 99 99 112.0 0 86 86 113.0 0 107 107 114.0 0 123 123 115.0 0 96 96 116.0 0 91 91 117.0 0 79 79 118.0 0 77 77 119.0 0 76 76 120.0 0 86 86 121.0 0 77 77 122.0 0 68 68 123.0 0 79 79 124.0 0 60 60 125.0 0 79 79 126.0 0 73 73 127.0 0 73 73 128.0 0 67 67 129.0 0 55 55 130.0 0 64 64 131.0 0 67 67 132.0 0 62 62 133.0 0 52 52 134.0 0 53 53 135.0 0 53 53 136.0 0 56 56 137.0 0 51 51 138.0 0 52 52 139.0 0 53 53 140.0 0 54 54 141.0 0 53 53 142.0 0 49 49 143.0 0 48 48 144.0 0 62 62 145.0 0 43 43 146.0 0 38 38 147.0 0 36 36 148.0 0 48 48 149.0 0 50 50 150.0 0 45 45 151.0 0 37 37 152.0 0 38 38 153.0 0 37 37 154.0 0 44 44 155.0 0 33 33 156.0 0 37 37 157.0 0 34 34 158.0 0 31 31 159.0 0 41 41 160.0 0 30 30 161.0 0 37 37 162.0 0 37 37 163.0 0 43 43 164.0 0 40 40 165.0 0 30 30 166.0 0 35 35 167.0 0 43 43 168.0 0 36 36 169.0 0 28 28 170.0 0 27 27 171.0 0 30 30 172.0 0 28 28 173.0 0 38 38 174.0 0 30 30 175.0 0 31 31 176.0 0 29 29 177.0 0 33 33 178.0 0 22 22 179.0 0 24 24 180.0 0 24 24 181.0 0 19 19 182.0 0 23 23 183.0 0 30 30 184.0 0 18 18 185.0 0 19 19 186.0 0 18 18 187.0 0 27 27 188.0 0 28 28 189.0 0 12 12 190.0 0 19 19 191.0 0 23 23 192.0 0 23 23 193.0 0 29 29 194.0 0 21 21 195.0 0 22 22 196.0 0 20 20 197.0 0 15 15 198.0 0 16 16 199.0 0 23 23 200.0 0 21 21 201.0 0 19 19 202.0 0 24 24 203.0 0 18 18 204.0 0 16 16 205.0 0 16 16 206.0 0 9 9 207.0 0 15 15 208.0 0 15 15 209.0 0 16 16 210.0 0 12 12 211.0 0 21 21 212.0 0 22 22 213.0 0 19 19 214.0 0 11 11 215.0 0 12 12 216.0 0 10 10 217.0 0 11 11 218.0 0 10 10 219.0 0 16 16 220.0 0 20 20 221.0 0 22 22 222.0 0 10 10 223.0 0 9 9 224.0 0 12 12 225.0 0 13 13 226.0 0 14 14 227.0 0 12 12 228.0 0 11 11 229.0 0 11 11 230.0 0 11 11 231.0 0 10 10 232.0 0 14 14 233.0 0 8 8 234.0 0 11 11 235.0 0 15 15 236.0 0 8 8 237.0 0 14 14 238.0 0 14 14 239.0 0 7 7 240.0 0 11 11 241.0 0 11 11 242.0 0 12 12 243.0 0 13 13 244.0 0 6 6 245.0 0 9 9 246.0 0 17 17 247.0 0 13 13 248.0 0 15 15 249.0 0 7 7 250.0 0 17 17 251.0 0 8 8 252.0 0 5 5 253.0 0 5 5 254.0 0 3 3 255.0 0 10 10 256.0 0 6 6 257.0 0 10 10 258.0 0 11 11 259.0 0 3 3 260.0 0 14 14 261.0 0 7 7 262.0 0 8 8 263.0 0 6 6 264.0 0 9 9 265.0 0 9 9 266.0 0 6 6 267.0 0 8 8 268.0 0 8 8 269.0 0 5 5 270.0 0 5 5 271.0 0 13 13 272.0 0 5 5 273.0 0 5 5 274.0 0 13 13 275.0 0 6 6 276.0 0 4 4 277.0 0 5 5 278.0 0 8 8 279.0 0 4 4 280.0 0 3 3 281.0 0 6 6 282.0 0 5 5 283.0 0 11 11 284.0 0 4 4 285.0 0 9 9 286.0 0 10 10 287.0 0 10 10 288.0 0 8 8 289.0 0 6 6 290.0 0 8 8 291.0 0 6 6 292.0 0 7 7 293.0 0 5 5 294.0 0 11 11 295.0 0 7 7 296.0 0 10 10 297.0 0 5 5 298.0 0 4 4 299.0 0 6 6 300.0 0 7 7 301.0 0 5 5 302.0 0 5 5 303.0 0 6 6 304.0 0 6 6 305.0 0 8 8 306.0 0 4 4 307.0 0 4 4 308.0 0 5 5 309.0 0 6 6 310.0 0 5 5 311.0 0 7 7 312.0 0 4 4 313.0 0 6 6 314.0 0 9 9 315.0 0 4 4 316.0 0 3 3 317.0 0 5 5 318.0 0 2 2 319.0 0 6 6 320.0 0 4 4 321.0 0 9 9 322.0 0 4 4 323.0 0 3 3 324.0 0 3 3 325.0 0 3 3 326.0 0 3 3 327.0 0 4 4 328.0 0 4 4 329.0 0 7 7 330.0 0 4 4 331.0 0 7 7 332.0 0 2 2 333.0 0 4 4 334.0 0 3 3 335.0 0 4 4 337.0 0 5 5 338.0 0 2 2 339.0 0 2 2 340.0 0 3 3 341.0 0 2 2 342.0 0 6 6 343.0 0 4 4 344.0 0 4 4 345.0 0 5 5 346.0 0 2 2 347.0 0 1 1 348.0 0 7 7 349.0 0 4 4 350.0 0 2 2 351.0 0 5 5 352.0 0 3 3 353.0 0 4 4 354.0 0 1 1 355.0 0 8 8 356.0 0 7 7 357.0 0 4 4 358.0 0 2 2 359.0 0 3 3 360.0 0 5 5 361.0 0 2 2 362.0 0 2 2 363.0 0 7 7 364.0 0 2 2 365.0 0 6 6 366.0 0 3 3 367.0 0 3 3 368.0 0 4 4 369.0 0 4 4 370.0 0 3 3 371.0 0 3 3 372.0 0 4 4 373.0 0 5 5 374.0 0 2 2 375.0 0 3 3 376.0 0 4 4 377.0 0 5 5 378.0 0 1 1 379.0 0 4 4 380.0 0 1 1 382.0 0 5 5 384.0 0 2 2 385.0 0 2 2 386.0 0 3 3 387.0 0 3 3 388.0 0 4 4 389.0 0 2 2 390.0 0 1 1 392.0 0 1 1 393.0 0 5 5 394.0 0 1 1 395.0 0 3 3 396.0 0 1 1 397.0 0 3 3 398.0 0 4 4 399.0 0 1 1 400.0 0 2 2 401.0 0 4 4 402.0 0 4 4 403.0 0 1 1 404.0 0 1 1 405.0 0 3 3 406.0 0 1 1 407.0 0 2 2 408.0 0 2 2 409.0 0 1 1 410.0 0 1 1 411.0 0 1 1 412.0 0 2 2 413.0 0 3 3 414.0 0 6 6 415.0 0 3 3 416.0 0 1 1 417.0 0 2 2 418.0 0 3 3 419.0 0 1 1 420.0 0 2 2 421.0 0 1 1 422.0 0 4 4 423.0 0 2 2 424.0 0 2 2 425.0 0 1 1 426.0 0 2 2 427.0 0 1 1 428.0 0 4 4 430.0 0 2 2 431.0 0 3 3 432.0 0 3 3 433.0 0 4 4 434.0 0 1 1 435.0 0 3 3 436.0 0 2 2 437.0 0 1 1 438.0 0 4 4 439.0 0 1 1 440.0 0 1 1 441.0 0 2 2 442.0 0 3 3 444.0 0 2 2 445.0 0 3 3 446.0 0 3 3 448.0 0 3 3 449.0 0 2 2 452.0 0 1 1 453.0 0 1 1 455.0 0 2 2 456.0 0 2 2 457.0 0 1 1 458.0 0 1 1 459.0 0 1 1 463.0 0 1 1 464.0 0 6 6 465.0 0 2 2 466.0 0 4 4 467.0 0 2 2 468.0 0 2 2 469.0 0 2 2 471.0 0 1 1 472.0 0 2 2 473.0 0 2 2 476.0 0 2 2 478.0 0 2 2 479.0 0 2 2 480.0 0 1 1 481.0 0 2 2 482.0 0 1 1 483.0 0 3 3 484.0 0 2 2 485.0 0 2 2 486.0 0 3 3 487.0 0 1 1 488.0 0 2 2 490.0 0 2 2 491.0 0 2 2 492.0 0 1 1 493.0 0 1 1 495.0 0 1 1 496.0 0 1 1 497.0 0 1 1 498.0 0 1 1 501.0 0 2 2 503.0 0 1 1 507.0 0 1 1 510.0 0 1 1 512.0 0 1 1 513.0 0 2 2 514.0 0 1 1 516.0 0 1 1 520.0 0 1 1 521.0 0 2 2 522.0 0 1 1 523.0 0 1 1 525.0 0 1 1 526.0 0 1 1 528.0 0 2 2 529.0 0 2 2 530.0 0 2 2 533.0 0 2 2 534.0 0 1 1 535.0 0 1 1 539.0 0 2 2 544.0 0 1 1 546.0 0 1 1 547.0 0 1 1 549.0 0 2 2 550.0 0 1 1 551.0 0 2 2 558.0 0 1 1 559.0 0 1 1 563.0 0 1 1 564.0 0 1 1 567.0 0 1 1 571.0 0 1 1 572.0 0 1 1 574.0 0 1 1 575.0 0 1 1 580.0 0 1 1 583.0 0 1 1 585.0 0 1 1 587.0 0 2 2 588.0 0 1 1 593.0 0 1 1 594.0 0 1 1 596.0 0 2 2 600.0 0 1 1 601.0 0 1 1 606.0 0 1 1 615.0 0 1 1 617.0 0 1 1 622.0 0 1 1 627.0 0 1 1 628.0 0 1 1 629.0 0 1 1 630.0 0 3 3 641.0 0 1 1 645.0 0 1 1 648.0 0 1 1 653.0 0 1 1 655.0 0 2 2 662.0 0 1 1 664.0 0 2 2 665.0 0 1 1 666.0 0 1 1 667.0 0 1 1 669.0 0 1 1 670.0 0 1 1 673.0 0 2 2 681.0 0 2 2 683.0 0 1 1 695.0 0 1 1 698.0 0 1 1 702.0 0 2 2 703.0 0 1 1 723.0 0 1 1 727.0 0 1 1 741.0 0 1 1 743.0 0 1 1 748.0 0 2 2 756.0 0 1 1 760.0 0 1 1 784.0 0 1 1 803.0 0 1 1 821.0 0 2 2 824.0 0 1 1 831.0 0 1 1 839.0 0 1 1 846.0 0 1 1 864.0 0 1 1 871.0 0 1 1 921.0 0 2 2 925.0 0 1 1 959.0 0 1 1 980.0 0 1 1 991.0 0 1 1 996.0 0 1 1 1001.0 0 2 2 1030.0 0 1 1 1066.0 0 1 1 1071.0 0 1 1 1074.0 0 1 1 1115.0 0 1 1 1151.0 0 1 1 1202.0 0 1 1 1239.0 0 1 1 1388.0 0 1 1 1394.0 0 1 1 3505.0 0 1 1