## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354363.sorted.bam --OUTPUT SRX7354363.markdup.sorted.bam --METRICS_FILE SRX7354363.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 23:37:03 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 42430 34704178 4580021 4389570 30806 14042147 0 0.40482 30302577 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17645137 17645137 2.0 1.318143 1706423 1706423 3.0 1.419358 427784 427784 4.0 1.451558 206689 206689 5.0 1.461803 127381 127381 6.0 1.465062 87719 87719 7.0 1.466099 64409 64409 8.0 1.466429 49691 49691 9.0 1.466534 39323 39323 10.0 1.466567 31770 31770 11.0 1.466578 26270 26270 12.0 1.466581 22365 22365 13.0 1.466582 19266 19266 14.0 1.466583 16354 16354 15.0 1.466583 14275 14275 16.0 1.466583 12481 12481 17.0 1.466583 11203 11203 18.0 1.466583 10039 10039 19.0 1.466583 8857 8857 20.0 1.466583 7958 7958 21.0 1.466583 7280 7280 22.0 1.466583 6598 6598 23.0 1.466583 6166 6166 24.0 1.466583 5594 5594 25.0 1.466583 5108 5108 26.0 1.466583 4695 4695 27.0 1.466583 4394 4394 28.0 1.466583 3939 3939 29.0 1.466583 3762 3762 30.0 1.466583 3428 3428 31.0 1.466583 3228 3228 32.0 1.466583 2981 2981 33.0 1.466583 2807 2807 34.0 1.466583 2595 2595 35.0 1.466583 2427 2427 36.0 1.466583 2404 2404 37.0 1.466583 2142 2142 38.0 1.466583 2031 2031 39.0 1.466583 2031 2031 40.0 1.466583 1953 1953 41.0 1.466583 1726 1726 42.0 1.466583 1685 1685 43.0 1.466583 1574 1574 44.0 1.466583 1482 1482 45.0 1.466583 1460 1460 46.0 1.466583 1420 1420 47.0 1.466583 1301 1301 48.0 1.466583 1271 1271 49.0 1.466583 1195 1195 50.0 1.466583 1109 1109 51.0 1.466583 1066 1066 52.0 1.466583 998 998 53.0 1.466583 969 969 54.0 1.466583 947 947 55.0 1.466583 877 877 56.0 1.466583 897 897 57.0 1.466583 845 845 58.0 1.466583 796 796 59.0 1.466583 784 784 60.0 1.466583 760 760 61.0 1.466583 747 747 62.0 1.466583 655 655 63.0 1.466583 677 677 64.0 1.466583 677 677 65.0 1.466583 609 609 66.0 1.466583 596 596 67.0 1.466583 587 587 68.0 1.466583 579 579 69.0 1.466583 546 546 70.0 1.466583 544 544 71.0 1.466583 509 509 72.0 1.466583 466 466 73.0 1.466583 496 496 74.0 1.466583 473 473 75.0 1.466583 434 434 76.0 1.466583 425 425 77.0 1.466583 365 365 78.0 1.466583 399 399 79.0 1.466583 362 362 80.0 1.466583 371 371 81.0 1.466583 375 375 82.0 1.466583 359 359 83.0 1.466583 325 325 84.0 1.466583 292 292 85.0 1.466583 282 282 86.0 1.466583 301 301 87.0 1.466583 321 321 88.0 1.466583 303 303 89.0 1.466583 304 304 90.0 1.466583 262 262 91.0 1.466583 266 266 92.0 1.466583 249 249 93.0 1.466583 225 225 94.0 1.466583 273 273 95.0 1.466583 237 237 96.0 1.466583 232 232 97.0 1.466583 246 246 98.0 1.466583 236 236 99.0 1.466583 215 215 100.0 1.466583 204 204 101.0 0 205 205 102.0 0 198 198 103.0 0 209 209 104.0 0 200 200 105.0 0 186 186 106.0 0 197 197 107.0 0 195 195 108.0 0 169 169 109.0 0 149 149 110.0 0 160 160 111.0 0 154 154 112.0 0 162 162 113.0 0 162 162 114.0 0 141 141 115.0 0 167 167 116.0 0 132 132 117.0 0 152 152 118.0 0 143 143 119.0 0 139 139 120.0 0 138 138 121.0 0 127 127 122.0 0 135 135 123.0 0 115 115 124.0 0 133 133 125.0 0 120 120 126.0 0 119 119 127.0 0 98 98 128.0 0 136 136 129.0 0 102 102 130.0 0 108 108 131.0 0 106 106 132.0 0 111 111 133.0 0 92 92 134.0 0 103 103 135.0 0 102 102 136.0 0 89 89 137.0 0 87 87 138.0 0 97 97 139.0 0 72 72 140.0 0 96 96 141.0 0 64 64 142.0 0 79 79 143.0 0 78 78 144.0 0 106 106 145.0 0 81 81 146.0 0 78 78 147.0 0 85 85 148.0 0 80 80 149.0 0 68 68 150.0 0 76 76 151.0 0 72 72 152.0 0 80 80 153.0 0 67 67 154.0 0 65 65 155.0 0 69 69 156.0 0 83 83 157.0 0 66 66 158.0 0 62 62 159.0 0 58 58 160.0 0 64 64 161.0 0 54 54 162.0 0 63 63 163.0 0 61 61 164.0 0 52 52 165.0 0 56 56 166.0 0 55 55 167.0 0 58 58 168.0 0 58 58 169.0 0 61 61 170.0 0 47 47 171.0 0 59 59 172.0 0 38 38 173.0 0 42 42 174.0 0 56 56 175.0 0 37 37 176.0 0 54 54 177.0 0 33 33 178.0 0 53 53 179.0 0 60 60 180.0 0 42 42 181.0 0 40 40 182.0 0 42 42 183.0 0 38 38 184.0 0 39 39 185.0 0 36 36 186.0 0 31 31 187.0 0 31 31 188.0 0 32 32 189.0 0 38 38 190.0 0 42 42 191.0 0 38 38 192.0 0 41 41 193.0 0 39 39 194.0 0 33 33 195.0 0 36 36 196.0 0 31 31 197.0 0 23 23 198.0 0 28 28 199.0 0 42 42 200.0 0 42 42 201.0 0 26 26 202.0 0 36 36 203.0 0 40 40 204.0 0 27 27 205.0 0 41 41 206.0 0 30 30 207.0 0 25 25 208.0 0 25 25 209.0 0 24 24 210.0 0 30 30 211.0 0 25 25 212.0 0 32 32 213.0 0 30 30 214.0 0 28 28 215.0 0 25 25 216.0 0 29 29 217.0 0 25 25 218.0 0 29 29 219.0 0 25 25 220.0 0 22 22 221.0 0 21 21 222.0 0 28 28 223.0 0 26 26 224.0 0 27 27 225.0 0 19 19 226.0 0 16 16 227.0 0 28 28 228.0 0 20 20 229.0 0 24 24 230.0 0 15 15 231.0 0 19 19 232.0 0 20 20 233.0 0 14 14 234.0 0 20 20 235.0 0 30 30 236.0 0 19 19 237.0 0 16 16 238.0 0 20 20 239.0 0 18 18 240.0 0 17 17 241.0 0 16 16 242.0 0 16 16 243.0 0 21 21 244.0 0 18 18 245.0 0 20 20 246.0 0 13 13 247.0 0 22 22 248.0 0 17 17 249.0 0 21 21 250.0 0 16 16 251.0 0 13 13 252.0 0 25 25 253.0 0 23 23 254.0 0 21 21 255.0 0 14 14 256.0 0 14 14 257.0 0 19 19 258.0 0 17 17 259.0 0 18 18 260.0 0 17 17 261.0 0 23 23 262.0 0 28 28 263.0 0 12 12 264.0 0 11 11 265.0 0 21 21 266.0 0 15 15 267.0 0 12 12 268.0 0 20 20 269.0 0 14 14 270.0 0 16 16 271.0 0 10 10 272.0 0 15 15 273.0 0 15 15 274.0 0 11 11 275.0 0 9 9 276.0 0 18 18 277.0 0 10 10 278.0 0 17 17 279.0 0 13 13 280.0 0 18 18 281.0 0 11 11 282.0 0 12 12 283.0 0 14 14 284.0 0 20 20 285.0 0 16 16 286.0 0 12 12 287.0 0 11 11 288.0 0 10 10 289.0 0 13 13 290.0 0 3 3 291.0 0 8 8 292.0 0 13 13 293.0 0 6 6 294.0 0 9 9 295.0 0 12 12 296.0 0 7 7 297.0 0 11 11 298.0 0 8 8 299.0 0 10 10 300.0 0 6 6 301.0 0 6 6 302.0 0 12 12 303.0 0 9 9 304.0 0 9 9 305.0 0 7 7 306.0 0 13 13 307.0 0 8 8 308.0 0 16 16 309.0 0 7 7 310.0 0 11 11 311.0 0 11 11 312.0 0 11 11 313.0 0 7 7 314.0 0 8 8 315.0 0 14 14 316.0 0 9 9 317.0 0 10 10 318.0 0 6 6 319.0 0 7 7 320.0 0 7 7 321.0 0 5 5 322.0 0 11 11 323.0 0 9 9 324.0 0 6 6 325.0 0 8 8 326.0 0 2 2 327.0 0 7 7 328.0 0 6 6 329.0 0 5 5 330.0 0 5 5 331.0 0 4 4 332.0 0 11 11 333.0 0 7 7 334.0 0 6 6 335.0 0 5 5 336.0 0 7 7 337.0 0 6 6 338.0 0 5 5 339.0 0 7 7 340.0 0 8 8 341.0 0 8 8 342.0 0 6 6 343.0 0 4 4 344.0 0 2 2 345.0 0 7 7 346.0 0 9 9 347.0 0 9 9 348.0 0 13 13 349.0 0 7 7 350.0 0 9 9 351.0 0 5 5 352.0 0 15 15 353.0 0 8 8 354.0 0 3 3 355.0 0 3 3 356.0 0 2 2 357.0 0 8 8 358.0 0 1 1 359.0 0 4 4 360.0 0 4 4 361.0 0 3 3 362.0 0 8 8 363.0 0 3 3 364.0 0 5 5 365.0 0 8 8 366.0 0 2 2 367.0 0 4 4 368.0 0 4 4 369.0 0 6 6 370.0 0 3 3 371.0 0 5 5 372.0 0 6 6 373.0 0 8 8 374.0 0 5 5 375.0 0 4 4 376.0 0 5 5 377.0 0 1 1 378.0 0 2 2 379.0 0 6 6 380.0 0 7 7 381.0 0 6 6 382.0 0 3 3 383.0 0 10 10 384.0 0 5 5 385.0 0 7 7 386.0 0 7 7 387.0 0 5 5 388.0 0 3 3 389.0 0 5 5 390.0 0 5 5 391.0 0 5 5 392.0 0 2 2 393.0 0 4 4 394.0 0 3 3 395.0 0 7 7 396.0 0 3 3 397.0 0 4 4 398.0 0 6 6 399.0 0 1 1 400.0 0 6 6 401.0 0 2 2 402.0 0 1 1 403.0 0 1 1 404.0 0 6 6 405.0 0 3 3 406.0 0 7 7 407.0 0 7 7 408.0 0 8 8 409.0 0 4 4 410.0 0 3 3 411.0 0 3 3 412.0 0 4 4 413.0 0 2 2 414.0 0 2 2 415.0 0 5 5 416.0 0 5 5 417.0 0 5 5 418.0 0 7 7 420.0 0 1 1 421.0 0 1 1 422.0 0 1 1 423.0 0 2 2 424.0 0 1 1 425.0 0 2 2 426.0 0 7 7 427.0 0 6 6 428.0 0 2 2 429.0 0 3 3 431.0 0 7 7 432.0 0 2 2 433.0 0 1 1 434.0 0 6 6 435.0 0 5 5 436.0 0 2 2 437.0 0 2 2 438.0 0 4 4 439.0 0 6 6 440.0 0 4 4 441.0 0 2 2 442.0 0 4 4 443.0 0 3 3 444.0 0 1 1 445.0 0 3 3 446.0 0 5 5 447.0 0 1 1 448.0 0 1 1 449.0 0 2 2 450.0 0 3 3 451.0 0 3 3 452.0 0 4 4 453.0 0 2 2 454.0 0 2 2 455.0 0 4 4 456.0 0 4 4 457.0 0 1 1 459.0 0 2 2 460.0 0 2 2 461.0 0 2 2 462.0 0 3 3 463.0 0 3 3 464.0 0 5 5 465.0 0 4 4 466.0 0 4 4 468.0 0 3 3 469.0 0 2 2 470.0 0 5 5 471.0 0 3 3 472.0 0 1 1 473.0 0 6 6 474.0 0 1 1 475.0 0 2 2 476.0 0 2 2 477.0 0 1 1 478.0 0 1 1 479.0 0 3 3 480.0 0 1 1 482.0 0 4 4 483.0 0 8 8 484.0 0 3 3 486.0 0 5 5 487.0 0 1 1 488.0 0 5 5 491.0 0 3 3 492.0 0 4 4 493.0 0 3 3 494.0 0 1 1 495.0 0 6 6 496.0 0 1 1 497.0 0 3 3 498.0 0 4 4 499.0 0 3 3 500.0 0 4 4 501.0 0 1 1 502.0 0 1 1 503.0 0 1 1 504.0 0 2 2 505.0 0 2 2 506.0 0 1 1 508.0 0 2 2 509.0 0 1 1 510.0 0 2 2 511.0 0 1 1 512.0 0 1 1 513.0 0 4 4 514.0 0 2 2 515.0 0 3 3 516.0 0 2 2 517.0 0 4 4 518.0 0 3 3 519.0 0 3 3 520.0 0 1 1 521.0 0 2 2 522.0 0 1 1 525.0 0 2 2 526.0 0 2 2 527.0 0 5 5 529.0 0 3 3 530.0 0 3 3 531.0 0 1 1 533.0 0 2 2 534.0 0 1 1 535.0 0 3 3 537.0 0 3 3 538.0 0 1 1 539.0 0 2 2 540.0 0 1 1 541.0 0 1 1 542.0 0 1 1 543.0 0 1 1 545.0 0 2 2 546.0 0 3 3 547.0 0 1 1 549.0 0 2 2 550.0 0 3 3 551.0 0 1 1 553.0 0 1 1 554.0 0 1 1 556.0 0 1 1 558.0 0 2 2 560.0 0 2 2 561.0 0 2 2 563.0 0 2 2 564.0 0 2 2 565.0 0 2 2 568.0 0 2 2 569.0 0 1 1 570.0 0 1 1 571.0 0 3 3 572.0 0 2 2 573.0 0 1 1 574.0 0 1 1 576.0 0 3 3 577.0 0 1 1 578.0 0 2 2 579.0 0 1 1 580.0 0 1 1 581.0 0 3 3 582.0 0 1 1 583.0 0 1 1 584.0 0 2 2 585.0 0 1 1 587.0 0 2 2 589.0 0 1 1 590.0 0 1 1 591.0 0 1 1 592.0 0 1 1 593.0 0 1 1 594.0 0 1 1 596.0 0 1 1 600.0 0 3 3 602.0 0 1 1 603.0 0 1 1 605.0 0 3 3 606.0 0 1 1 607.0 0 2 2 608.0 0 3 3 609.0 0 1 1 610.0 0 1 1 611.0 0 1 1 612.0 0 2 2 613.0 0 2 2 615.0 0 1 1 616.0 0 1 1 618.0 0 2 2 619.0 0 3 3 620.0 0 1 1 622.0 0 1 1 625.0 0 2 2 626.0 0 1 1 627.0 0 1 1 630.0 0 3 3 631.0 0 1 1 632.0 0 1 1 634.0 0 2 2 636.0 0 1 1 638.0 0 1 1 639.0 0 1 1 641.0 0 1 1 644.0 0 1 1 646.0 0 1 1 651.0 0 1 1 652.0 0 2 2 653.0 0 1 1 655.0 0 1 1 657.0 0 3 3 659.0 0 1 1 660.0 0 1 1 663.0 0 2 2 664.0 0 3 3 665.0 0 2 2 666.0 0 1 1 669.0 0 1 1 671.0 0 3 3 673.0 0 1 1 674.0 0 1 1 676.0 0 1 1 677.0 0 1 1 678.0 0 2 2 683.0 0 1 1 684.0 0 1 1 688.0 0 1 1 692.0 0 2 2 699.0 0 1 1 704.0 0 2 2 707.0 0 1 1 708.0 0 2 2 712.0 0 3 3 713.0 0 2 2 714.0 0 2 2 717.0 0 3 3 719.0 0 1 1 723.0 0 2 2 726.0 0 1 1 727.0 0 1 1 728.0 0 1 1 729.0 0 1 1 731.0 0 2 2 733.0 0 2 2 735.0 0 1 1 736.0 0 2 2 755.0 0 1 1 756.0 0 1 1 757.0 0 1 1 762.0 0 1 1 764.0 0 1 1 766.0 0 1 1 771.0 0 1 1 777.0 0 1 1 778.0 0 1 1 789.0 0 2 2 790.0 0 1 1 796.0 0 2 2 797.0 0 2 2 804.0 0 1 1 807.0 0 1 1 808.0 0 1 1 810.0 0 1 1 812.0 0 2 2 820.0 0 1 1 825.0 0 2 2 829.0 0 1 1 838.0 0 1 1 842.0 0 1 1 856.0 0 1 1 862.0 0 2 2 864.0 0 1 1 869.0 0 2 2 882.0 0 1 1 888.0 0 1 1 896.0 0 1 1 899.0 0 1 1 911.0 0 1 1 912.0 0 1 1 918.0 0 1 1 923.0 0 1 1 924.0 0 1 1 936.0 0 1 1 940.0 0 1 1 948.0 0 1 1 950.0 0 1 1 951.0 0 1 1 953.0 0 1 1 965.0 0 1 1 987.0 0 1 1 993.0 0 1 1 995.0 0 1 1 997.0 0 1 1 1002.0 0 1 1 1006.0 0 2 2 1010.0 0 1 1 1012.0 0 1 1 1019.0 0 1 1 1023.0 0 1 1 1039.0 0 1 1 1053.0 0 1 1 1055.0 0 1 1 1059.0 0 1 1 1061.0 0 1 1 1064.0 0 1 1 1083.0 0 1 1 1085.0 0 1 1 1117.0 0 1 1 1123.0 0 1 1 1151.0 0 1 1 1158.0 0 1 1 1194.0 0 1 1 1229.0 0 1 1 1234.0 0 1 1 1278.0 0 1 1 1280.0 0 1 1 1290.0 0 1 1 1292.0 0 1 1 1321.0 0 1 1 1407.0 0 1 1 1494.0 0 1 1 1539.0 0 1 1 1636.0 0 1 1 1765.0 0 1 1 2371.0 0 1 1