## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354371.sorted.bam --OUTPUT SRX7354371.markdup.sorted.bam --METRICS_FILE SRX7354371.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 22:35:44 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 40552 38726639 7224324 4452184 31225 15684935 0 0.405208 33767021 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19677904 19677904 2.0 1.317627 1882462 1882462 3.0 1.418514 485512 485512 4.0 1.450558 236600 236600 5.0 1.460736 144641 144641 6.0 1.463969 99437 99437 7.0 1.464996 72762 72762 8.0 1.465322 55747 55747 9.0 1.465426 43974 43974 10.0 1.465459 35511 35511 11.0 1.465469 29559 29559 12.0 1.465473 24695 24695 13.0 1.465474 21228 21228 14.0 1.465474 18212 18212 15.0 1.465474 15717 15717 16.0 1.465474 13813 13813 17.0 1.465474 12390 12390 18.0 1.465474 11250 11250 19.0 1.465474 9998 9998 20.0 1.465474 8923 8923 21.0 1.465474 8055 8055 22.0 1.465474 7333 7333 23.0 1.465474 6672 6672 24.0 1.465474 6172 6172 25.0 1.465474 5545 5545 26.0 1.465474 5194 5194 27.0 1.465474 4780 4780 28.0 1.465474 4516 4516 29.0 1.465474 4103 4103 30.0 1.465474 3820 3820 31.0 1.465474 3626 3626 32.0 1.465474 3417 3417 33.0 1.465474 3236 3236 34.0 1.465474 2920 2920 35.0 1.465474 2769 2769 36.0 1.465474 2680 2680 37.0 1.465474 2481 2481 38.0 1.465474 2362 2362 39.0 1.465474 2246 2246 40.0 1.465474 2049 2049 41.0 1.465474 2024 2024 42.0 1.465474 1813 1813 43.0 1.465474 1789 1789 44.0 1.465474 1714 1714 45.0 1.465474 1567 1567 46.0 1.465474 1541 1541 47.0 1.465474 1494 1494 48.0 1.465474 1376 1376 49.0 1.465474 1319 1319 50.0 1.465474 1245 1245 51.0 1.465474 1195 1195 52.0 1.465474 1161 1161 53.0 1.465474 1119 1119 54.0 1.465474 1006 1006 55.0 1.465474 1043 1043 56.0 1.465474 1013 1013 57.0 1.465474 962 962 58.0 1.465474 945 945 59.0 1.465474 903 903 60.0 1.465474 880 880 61.0 1.465474 780 780 62.0 1.465474 757 757 63.0 1.465474 729 729 64.0 1.465474 710 710 65.0 1.465474 684 684 66.0 1.465474 669 669 67.0 1.465474 661 661 68.0 1.465474 593 593 69.0 1.465474 582 582 70.0 1.465474 593 593 71.0 1.465474 592 592 72.0 1.465474 541 541 73.0 1.465474 511 511 74.0 1.465474 511 511 75.0 1.465474 502 502 76.0 1.465474 515 515 77.0 1.465474 409 409 78.0 1.465474 447 447 79.0 1.465474 439 439 80.0 1.465474 420 420 81.0 1.465474 407 407 82.0 1.465474 389 389 83.0 1.465474 392 392 84.0 1.465474 371 371 85.0 1.465474 357 357 86.0 1.465474 337 337 87.0 1.465474 331 331 88.0 1.465474 332 332 89.0 1.465474 314 314 90.0 1.465474 324 324 91.0 1.465474 315 315 92.0 1.465474 284 284 93.0 1.465474 275 275 94.0 1.465474 288 288 95.0 1.465474 266 266 96.0 1.465474 276 276 97.0 1.465474 273 273 98.0 1.465474 253 253 99.0 1.465474 256 256 100.0 1.465474 229 229 101.0 0 247 247 102.0 0 217 217 103.0 0 224 224 104.0 0 220 220 105.0 0 207 207 106.0 0 196 196 107.0 0 197 197 108.0 0 219 219 109.0 0 187 187 110.0 0 204 204 111.0 0 199 199 112.0 0 180 180 113.0 0 178 178 114.0 0 179 179 115.0 0 172 172 116.0 0 168 168 117.0 0 150 150 118.0 0 154 154 119.0 0 142 142 120.0 0 163 163 121.0 0 150 150 122.0 0 147 147 123.0 0 133 133 124.0 0 143 143 125.0 0 130 130 126.0 0 143 143 127.0 0 131 131 128.0 0 109 109 129.0 0 137 137 130.0 0 117 117 131.0 0 124 124 132.0 0 128 128 133.0 0 134 134 134.0 0 113 113 135.0 0 124 124 136.0 0 119 119 137.0 0 108 108 138.0 0 98 98 139.0 0 93 93 140.0 0 90 90 141.0 0 105 105 142.0 0 87 87 143.0 0 102 102 144.0 0 80 80 145.0 0 90 90 146.0 0 83 83 147.0 0 107 107 148.0 0 83 83 149.0 0 88 88 150.0 0 86 86 151.0 0 80 80 152.0 0 91 91 153.0 0 81 81 154.0 0 74 74 155.0 0 84 84 156.0 0 78 78 157.0 0 69 69 158.0 0 79 79 159.0 0 72 72 160.0 0 60 60 161.0 0 65 65 162.0 0 69 69 163.0 0 61 61 164.0 0 52 52 165.0 0 63 63 166.0 0 64 64 167.0 0 58 58 168.0 0 63 63 169.0 0 66 66 170.0 0 52 52 171.0 0 77 77 172.0 0 45 45 173.0 0 60 60 174.0 0 56 56 175.0 0 68 68 176.0 0 39 39 177.0 0 62 62 178.0 0 63 63 179.0 0 44 44 180.0 0 53 53 181.0 0 48 48 182.0 0 45 45 183.0 0 45 45 184.0 0 52 52 185.0 0 43 43 186.0 0 42 42 187.0 0 30 30 188.0 0 47 47 189.0 0 48 48 190.0 0 37 37 191.0 0 52 52 192.0 0 37 37 193.0 0 44 44 194.0 0 37 37 195.0 0 50 50 196.0 0 29 29 197.0 0 34 34 198.0 0 30 30 199.0 0 41 41 200.0 0 39 39 201.0 0 44 44 202.0 0 35 35 203.0 0 27 27 204.0 0 43 43 205.0 0 26 26 206.0 0 30 30 207.0 0 30 30 208.0 0 35 35 209.0 0 31 31 210.0 0 38 38 211.0 0 40 40 212.0 0 19 19 213.0 0 33 33 214.0 0 28 28 215.0 0 21 21 216.0 0 33 33 217.0 0 25 25 218.0 0 35 35 219.0 0 28 28 220.0 0 32 32 221.0 0 26 26 222.0 0 32 32 223.0 0 30 30 224.0 0 31 31 225.0 0 14 14 226.0 0 26 26 227.0 0 31 31 228.0 0 20 20 229.0 0 21 21 230.0 0 32 32 231.0 0 20 20 232.0 0 24 24 233.0 0 24 24 234.0 0 19 19 235.0 0 37 37 236.0 0 22 22 237.0 0 18 18 238.0 0 21 21 239.0 0 25 25 240.0 0 25 25 241.0 0 22 22 242.0 0 15 15 243.0 0 21 21 244.0 0 24 24 245.0 0 24 24 246.0 0 15 15 247.0 0 20 20 248.0 0 21 21 249.0 0 23 23 250.0 0 20 20 251.0 0 16 16 252.0 0 22 22 253.0 0 13 13 254.0 0 20 20 255.0 0 19 19 256.0 0 27 27 257.0 0 21 21 258.0 0 17 17 259.0 0 13 13 260.0 0 16 16 261.0 0 20 20 262.0 0 14 14 263.0 0 19 19 264.0 0 17 17 265.0 0 23 23 266.0 0 16 16 267.0 0 15 15 268.0 0 17 17 269.0 0 13 13 270.0 0 10 10 271.0 0 10 10 272.0 0 18 18 273.0 0 20 20 274.0 0 16 16 275.0 0 9 9 276.0 0 21 21 277.0 0 11 11 278.0 0 11 11 279.0 0 13 13 280.0 0 12 12 281.0 0 11 11 282.0 0 13 13 283.0 0 11 11 284.0 0 16 16 285.0 0 13 13 286.0 0 11 11 287.0 0 15 15 288.0 0 12 12 289.0 0 13 13 290.0 0 15 15 291.0 0 11 11 292.0 0 10 10 293.0 0 12 12 294.0 0 12 12 295.0 0 7 7 296.0 0 11 11 297.0 0 11 11 298.0 0 9 9 299.0 0 4 4 300.0 0 13 13 301.0 0 15 15 302.0 0 16 16 303.0 0 10 10 304.0 0 14 14 305.0 0 8 8 306.0 0 12 12 307.0 0 9 9 308.0 0 10 10 309.0 0 7 7 310.0 0 9 9 311.0 0 18 18 312.0 0 5 5 313.0 0 12 12 314.0 0 16 16 315.0 0 11 11 316.0 0 5 5 317.0 0 6 6 318.0 0 9 9 319.0 0 6 6 320.0 0 8 8 321.0 0 21 21 322.0 0 10 10 323.0 0 8 8 324.0 0 3 3 325.0 0 8 8 326.0 0 9 9 327.0 0 9 9 328.0 0 6 6 329.0 0 2 2 330.0 0 8 8 331.0 0 6 6 332.0 0 10 10 333.0 0 6 6 334.0 0 9 9 335.0 0 4 4 336.0 0 7 7 337.0 0 8 8 338.0 0 10 10 339.0 0 11 11 340.0 0 8 8 341.0 0 5 5 342.0 0 10 10 343.0 0 11 11 344.0 0 7 7 345.0 0 6 6 346.0 0 5 5 347.0 0 11 11 348.0 0 8 8 349.0 0 3 3 350.0 0 5 5 351.0 0 10 10 352.0 0 8 8 353.0 0 5 5 354.0 0 5 5 355.0 0 5 5 356.0 0 6 6 357.0 0 7 7 358.0 0 2 2 359.0 0 1 1 360.0 0 5 5 361.0 0 5 5 362.0 0 4 4 363.0 0 5 5 364.0 0 4 4 365.0 0 4 4 366.0 0 7 7 367.0 0 13 13 368.0 0 10 10 369.0 0 5 5 370.0 0 9 9 371.0 0 3 3 372.0 0 4 4 373.0 0 3 3 374.0 0 6 6 375.0 0 3 3 376.0 0 6 6 377.0 0 2 2 378.0 0 4 4 379.0 0 5 5 380.0 0 7 7 381.0 0 8 8 382.0 0 8 8 383.0 0 3 3 384.0 0 7 7 385.0 0 5 5 386.0 0 5 5 387.0 0 5 5 388.0 0 4 4 389.0 0 5 5 390.0 0 2 2 391.0 0 8 8 392.0 0 4 4 393.0 0 5 5 394.0 0 5 5 395.0 0 6 6 396.0 0 7 7 397.0 0 5 5 398.0 0 4 4 399.0 0 7 7 400.0 0 4 4 401.0 0 3 3 402.0 0 3 3 403.0 0 9 9 404.0 0 5 5 405.0 0 4 4 406.0 0 3 3 407.0 0 6 6 408.0 0 2 2 409.0 0 6 6 410.0 0 4 4 412.0 0 2 2 413.0 0 8 8 414.0 0 2 2 415.0 0 8 8 416.0 0 6 6 417.0 0 3 3 418.0 0 5 5 419.0 0 4 4 420.0 0 1 1 421.0 0 4 4 422.0 0 6 6 424.0 0 3 3 425.0 0 4 4 426.0 0 4 4 427.0 0 6 6 428.0 0 5 5 429.0 0 4 4 430.0 0 4 4 431.0 0 3 3 432.0 0 2 2 433.0 0 4 4 434.0 0 5 5 435.0 0 5 5 436.0 0 2 2 437.0 0 5 5 438.0 0 5 5 439.0 0 4 4 440.0 0 5 5 441.0 0 3 3 442.0 0 5 5 443.0 0 4 4 444.0 0 3 3 445.0 0 4 4 446.0 0 7 7 447.0 0 1 1 448.0 0 7 7 449.0 0 1 1 450.0 0 4 4 451.0 0 2 2 452.0 0 2 2 453.0 0 3 3 454.0 0 2 2 455.0 0 4 4 456.0 0 2 2 457.0 0 3 3 458.0 0 3 3 459.0 0 4 4 460.0 0 2 2 461.0 0 5 5 462.0 0 6 6 463.0 0 2 2 464.0 0 2 2 465.0 0 2 2 466.0 0 1 1 467.0 0 1 1 468.0 0 2 2 469.0 0 2 2 470.0 0 1 1 471.0 0 4 4 472.0 0 2 2 473.0 0 2 2 474.0 0 6 6 475.0 0 3 3 476.0 0 3 3 477.0 0 4 4 478.0 0 1 1 479.0 0 5 5 480.0 0 3 3 481.0 0 1 1 482.0 0 5 5 484.0 0 4 4 485.0 0 1 1 486.0 0 3 3 487.0 0 2 2 488.0 0 2 2 489.0 0 3 3 490.0 0 3 3 491.0 0 1 1 492.0 0 6 6 494.0 0 2 2 495.0 0 5 5 496.0 0 3 3 497.0 0 1 1 498.0 0 2 2 499.0 0 1 1 500.0 0 5 5 501.0 0 3 3 502.0 0 3 3 503.0 0 4 4 504.0 0 2 2 506.0 0 1 1 507.0 0 3 3 508.0 0 1 1 509.0 0 1 1 510.0 0 2 2 511.0 0 1 1 512.0 0 2 2 513.0 0 5 5 516.0 0 1 1 517.0 0 1 1 518.0 0 2 2 519.0 0 2 2 520.0 0 2 2 521.0 0 5 5 522.0 0 1 1 523.0 0 3 3 526.0 0 2 2 528.0 0 2 2 529.0 0 2 2 530.0 0 3 3 531.0 0 1 1 532.0 0 2 2 533.0 0 1 1 534.0 0 1 1 536.0 0 1 1 537.0 0 5 5 538.0 0 3 3 539.0 0 1 1 540.0 0 1 1 541.0 0 2 2 542.0 0 2 2 544.0 0 3 3 545.0 0 1 1 546.0 0 1 1 547.0 0 1 1 548.0 0 4 4 549.0 0 3 3 551.0 0 1 1 552.0 0 1 1 553.0 0 2 2 554.0 0 1 1 555.0 0 1 1 556.0 0 2 2 559.0 0 4 4 561.0 0 4 4 562.0 0 1 1 563.0 0 1 1 564.0 0 1 1 565.0 0 2 2 566.0 0 2 2 568.0 0 3 3 569.0 0 3 3 570.0 0 1 1 571.0 0 1 1 572.0 0 2 2 573.0 0 3 3 574.0 0 2 2 575.0 0 1 1 578.0 0 2 2 579.0 0 1 1 580.0 0 1 1 581.0 0 1 1 585.0 0 3 3 586.0 0 1 1 587.0 0 2 2 590.0 0 2 2 591.0 0 2 2 595.0 0 3 3 596.0 0 2 2 597.0 0 2 2 598.0 0 2 2 600.0 0 1 1 603.0 0 1 1 604.0 0 1 1 605.0 0 1 1 606.0 0 1 1 607.0 0 1 1 610.0 0 1 1 611.0 0 2 2 614.0 0 2 2 615.0 0 2 2 617.0 0 2 2 618.0 0 4 4 619.0 0 3 3 620.0 0 1 1 623.0 0 1 1 625.0 0 1 1 626.0 0 1 1 629.0 0 1 1 631.0 0 2 2 633.0 0 1 1 635.0 0 1 1 637.0 0 1 1 639.0 0 1 1 640.0 0 1 1 642.0 0 1 1 646.0 0 1 1 649.0 0 2 2 651.0 0 1 1 664.0 0 1 1 667.0 0 1 1 670.0 0 1 1 671.0 0 1 1 672.0 0 2 2 675.0 0 1 1 678.0 0 1 1 679.0 0 1 1 680.0 0 1 1 681.0 0 1 1 682.0 0 1 1 688.0 0 1 1 693.0 0 1 1 694.0 0 1 1 699.0 0 2 2 701.0 0 2 2 702.0 0 2 2 709.0 0 2 2 714.0 0 1 1 719.0 0 1 1 724.0 0 1 1 725.0 0 1 1 727.0 0 1 1 728.0 0 1 1 737.0 0 1 1 738.0 0 1 1 741.0 0 1 1 751.0 0 1 1 754.0 0 2 2 756.0 0 1 1 757.0 0 2 2 759.0 0 1 1 760.0 0 2 2 762.0 0 1 1 771.0 0 1 1 780.0 0 1 1 790.0 0 1 1 797.0 0 1 1 799.0 0 1 1 800.0 0 1 1 804.0 0 1 1 807.0 0 3 3 808.0 0 1 1 810.0 0 1 1 815.0 0 1 1 821.0 0 1 1 822.0 0 1 1 823.0 0 1 1 828.0 0 2 2 832.0 0 1 1 835.0 0 1 1 839.0 0 1 1 844.0 0 1 1 846.0 0 1 1 856.0 0 1 1 859.0 0 1 1 865.0 0 1 1 867.0 0 1 1 869.0 0 1 1 876.0 0 1 1 886.0 0 1 1 891.0 0 1 1 914.0 0 2 2 923.0 0 1 1 928.0 0 1 1 930.0 0 1 1 932.0 0 1 1 951.0 0 1 1 952.0 0 2 2 954.0 0 2 2 969.0 0 1 1 979.0 0 1 1 995.0 0 1 1 996.0 0 1 1 1002.0 0 1 1 1031.0 0 1 1 1033.0 0 1 1 1038.0 0 1 1 1039.0 0 1 1 1044.0 0 1 1 1060.0 0 1 1 1104.0 0 1 1 1106.0 0 1 1 1110.0 0 1 1 1118.0 0 1 1 1145.0 0 1 1 1162.0 0 1 1 1179.0 0 1 1 1194.0 0 1 1 1197.0 0 1 1 1209.0 0 1 1 1212.0 0 1 1 1234.0 0 1 1 1245.0 0 1 1 1263.0 0 1 1 1271.0 0 1 1 1305.0 0 1 1 1384.0 0 1 1 1536.0 0 1 1 1713.0 0 1 1 1887.0 0 1 1 1922.0 0 1 1