## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354294.sorted.bam --OUTPUT SRX7354294.markdup.sorted.bam --METRICS_FILE SRX7354294.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 22:05:28 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 22114 34573819 4199652 1433794 15561 12606098 0 0.364722 35004785 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18141773 18141773 2.0 1.372437 2460489 2460489 3.0 1.511146 547238 547238 4.0 1.562806 224168 224168 5.0 1.582046 127109 127109 6.0 1.589212 83428 83428 7.0 1.591881 59586 59586 8.0 1.592875 44983 44983 9.0 1.593245 34939 34939 10.0 1.593383 27981 27981 11.0 1.593434 22630 22630 12.0 1.593453 18823 18823 13.0 1.59346 15786 15786 14.0 1.593463 13744 13744 15.0 1.593464 11677 11677 16.0 1.593464 10413 10413 17.0 1.593464 8891 8891 18.0 1.593465 7976 7976 19.0 1.593465 7124 7124 20.0 1.593465 6193 6193 21.0 1.593465 5590 5590 22.0 1.593465 5120 5120 23.0 1.593465 4661 4661 24.0 1.593465 4263 4263 25.0 1.593465 4012 4012 26.0 1.593465 3628 3628 27.0 1.593465 3348 3348 28.0 1.593465 3095 3095 29.0 1.593465 2655 2655 30.0 1.593465 2606 2606 31.0 1.593465 2531 2531 32.0 1.593465 2274 2274 33.0 1.593465 2062 2062 34.0 1.593465 1896 1896 35.0 1.593465 1857 1857 36.0 1.593465 1717 1717 37.0 1.593465 1586 1586 38.0 1.593465 1501 1501 39.0 1.593465 1416 1416 40.0 1.593465 1419 1419 41.0 1.593465 1300 1300 42.0 1.593465 1275 1275 43.0 1.593465 1164 1164 44.0 1.593465 1088 1088 45.0 1.593465 1012 1012 46.0 1.593465 939 939 47.0 1.593465 896 896 48.0 1.593465 889 889 49.0 1.593465 832 832 50.0 1.593465 846 846 51.0 1.593465 781 781 52.0 1.593465 735 735 53.0 1.593465 728 728 54.0 1.593465 700 700 55.0 1.593465 641 641 56.0 1.593465 628 628 57.0 1.593465 640 640 58.0 1.593465 540 540 59.0 1.593465 527 527 60.0 1.593465 501 501 61.0 1.593465 536 536 62.0 1.593465 494 494 63.0 1.593465 462 462 64.0 1.593465 439 439 65.0 1.593465 436 436 66.0 1.593465 400 400 67.0 1.593465 409 409 68.0 1.593465 346 346 69.0 1.593465 372 372 70.0 1.593465 349 349 71.0 1.593465 356 356 72.0 1.593465 330 330 73.0 1.593465 312 312 74.0 1.593465 303 303 75.0 1.593465 283 283 76.0 1.593465 320 320 77.0 1.593465 312 312 78.0 1.593465 259 259 79.0 1.593465 269 269 80.0 1.593465 271 271 81.0 1.593465 264 264 82.0 1.593465 244 244 83.0 1.593465 232 232 84.0 1.593465 237 237 85.0 1.593465 233 233 86.0 1.593465 188 188 87.0 1.593465 208 208 88.0 1.593465 216 216 89.0 1.593465 184 184 90.0 1.593465 184 184 91.0 1.593465 176 176 92.0 1.593465 184 184 93.0 1.593465 167 167 94.0 1.593465 189 189 95.0 1.593465 186 186 96.0 1.593465 176 176 97.0 1.593465 159 159 98.0 1.593465 143 143 99.0 1.593465 149 149 100.0 1.593465 134 134 101.0 0 151 151 102.0 0 149 149 103.0 0 122 122 104.0 0 143 143 105.0 0 129 129 106.0 0 125 125 107.0 0 121 121 108.0 0 114 114 109.0 0 109 109 110.0 0 127 127 111.0 0 118 118 112.0 0 103 103 113.0 0 104 104 114.0 0 93 93 115.0 0 81 81 116.0 0 97 97 117.0 0 101 101 118.0 0 105 105 119.0 0 76 76 120.0 0 83 83 121.0 0 81 81 122.0 0 69 69 123.0 0 86 86 124.0 0 94 94 125.0 0 82 82 126.0 0 82 82 127.0 0 78 78 128.0 0 85 85 129.0 0 60 60 130.0 0 74 74 131.0 0 65 65 132.0 0 65 65 133.0 0 81 81 134.0 0 68 68 135.0 0 62 62 136.0 0 72 72 137.0 0 57 57 138.0 0 76 76 139.0 0 43 43 140.0 0 73 73 141.0 0 59 59 142.0 0 57 57 143.0 0 49 49 144.0 0 44 44 145.0 0 51 51 146.0 0 45 45 147.0 0 45 45 148.0 0 52 52 149.0 0 47 47 150.0 0 40 40 151.0 0 60 60 152.0 0 44 44 153.0 0 42 42 154.0 0 38 38 155.0 0 40 40 156.0 0 36 36 157.0 0 46 46 158.0 0 39 39 159.0 0 36 36 160.0 0 42 42 161.0 0 40 40 162.0 0 47 47 163.0 0 34 34 164.0 0 38 38 165.0 0 38 38 166.0 0 45 45 167.0 0 45 45 168.0 0 41 41 169.0 0 29 29 170.0 0 35 35 171.0 0 30 30 172.0 0 32 32 173.0 0 36 36 174.0 0 30 30 175.0 0 34 34 176.0 0 26 26 177.0 0 30 30 178.0 0 33 33 179.0 0 26 26 180.0 0 37 37 181.0 0 26 26 182.0 0 27 27 183.0 0 26 26 184.0 0 26 26 185.0 0 31 31 186.0 0 23 23 187.0 0 29 29 188.0 0 29 29 189.0 0 26 26 190.0 0 28 28 191.0 0 32 32 192.0 0 19 19 193.0 0 20 20 194.0 0 17 17 195.0 0 20 20 196.0 0 15 15 197.0 0 26 26 198.0 0 15 15 199.0 0 30 30 200.0 0 21 21 201.0 0 20 20 202.0 0 26 26 203.0 0 27 27 204.0 0 15 15 205.0 0 28 28 206.0 0 22 22 207.0 0 16 16 208.0 0 18 18 209.0 0 22 22 210.0 0 14 14 211.0 0 23 23 212.0 0 15 15 213.0 0 12 12 214.0 0 15 15 215.0 0 16 16 216.0 0 17 17 217.0 0 19 19 218.0 0 12 12 219.0 0 15 15 220.0 0 23 23 221.0 0 16 16 222.0 0 18 18 223.0 0 17 17 224.0 0 17 17 225.0 0 15 15 226.0 0 16 16 227.0 0 12 12 228.0 0 11 11 229.0 0 17 17 230.0 0 15 15 231.0 0 15 15 232.0 0 12 12 233.0 0 12 12 234.0 0 12 12 235.0 0 12 12 236.0 0 5 5 237.0 0 19 19 238.0 0 15 15 239.0 0 11 11 240.0 0 12 12 241.0 0 8 8 242.0 0 11 11 243.0 0 15 15 244.0 0 11 11 245.0 0 12 12 246.0 0 10 10 247.0 0 13 13 248.0 0 11 11 249.0 0 11 11 250.0 0 8 8 251.0 0 9 9 252.0 0 15 15 253.0 0 13 13 254.0 0 8 8 255.0 0 11 11 256.0 0 11 11 257.0 0 12 12 258.0 0 10 10 259.0 0 11 11 260.0 0 8 8 261.0 0 7 7 262.0 0 12 12 263.0 0 11 11 264.0 0 18 18 265.0 0 15 15 266.0 0 9 9 267.0 0 10 10 268.0 0 9 9 269.0 0 7 7 270.0 0 6 6 271.0 0 6 6 272.0 0 3 3 273.0 0 10 10 274.0 0 6 6 275.0 0 11 11 276.0 0 5 5 277.0 0 9 9 278.0 0 10 10 279.0 0 8 8 280.0 0 5 5 281.0 0 10 10 282.0 0 7 7 283.0 0 5 5 284.0 0 7 7 285.0 0 12 12 286.0 0 5 5 287.0 0 6 6 288.0 0 8 8 289.0 0 13 13 290.0 0 9 9 291.0 0 8 8 292.0 0 5 5 293.0 0 9 9 294.0 0 8 8 295.0 0 12 12 296.0 0 7 7 297.0 0 5 5 298.0 0 3 3 299.0 0 4 4 300.0 0 3 3 301.0 0 3 3 302.0 0 4 4 303.0 0 3 3 304.0 0 13 13 305.0 0 8 8 306.0 0 6 6 307.0 0 7 7 308.0 0 9 9 309.0 0 3 3 310.0 0 7 7 311.0 0 3 3 312.0 0 4 4 313.0 0 4 4 314.0 0 1 1 315.0 0 5 5 316.0 0 5 5 317.0 0 1 1 318.0 0 5 5 319.0 0 6 6 320.0 0 3 3 321.0 0 7 7 322.0 0 6 6 323.0 0 7 7 324.0 0 4 4 325.0 0 5 5 326.0 0 6 6 327.0 0 5 5 328.0 0 5 5 329.0 0 6 6 330.0 0 3 3 331.0 0 3 3 332.0 0 2 2 333.0 0 4 4 334.0 0 4 4 335.0 0 4 4 336.0 0 5 5 337.0 0 6 6 338.0 0 5 5 339.0 0 5 5 340.0 0 5 5 341.0 0 7 7 342.0 0 3 3 343.0 0 4 4 344.0 0 5 5 345.0 0 3 3 346.0 0 2 2 347.0 0 3 3 348.0 0 4 4 349.0 0 4 4 351.0 0 4 4 352.0 0 4 4 353.0 0 5 5 354.0 0 2 2 355.0 0 6 6 356.0 0 5 5 357.0 0 5 5 358.0 0 8 8 360.0 0 1 1 361.0 0 1 1 362.0 0 2 2 363.0 0 4 4 364.0 0 4 4 365.0 0 2 2 366.0 0 5 5 367.0 0 2 2 368.0 0 1 1 369.0 0 4 4 370.0 0 1 1 371.0 0 4 4 372.0 0 1 1 373.0 0 7 7 374.0 0 1 1 375.0 0 2 2 376.0 0 2 2 377.0 0 2 2 378.0 0 3 3 379.0 0 3 3 380.0 0 1 1 381.0 0 5 5 382.0 0 4 4 383.0 0 4 4 384.0 0 3 3 385.0 0 4 4 386.0 0 4 4 387.0 0 2 2 388.0 0 4 4 389.0 0 1 1 390.0 0 1 1 391.0 0 4 4 392.0 0 4 4 393.0 0 5 5 394.0 0 6 6 395.0 0 6 6 396.0 0 4 4 397.0 0 1 1 398.0 0 4 4 401.0 0 3 3 402.0 0 4 4 403.0 0 2 2 404.0 0 1 1 405.0 0 3 3 406.0 0 1 1 408.0 0 3 3 410.0 0 3 3 412.0 0 4 4 414.0 0 6 6 416.0 0 1 1 417.0 0 3 3 418.0 0 3 3 419.0 0 5 5 420.0 0 1 1 421.0 0 1 1 423.0 0 5 5 424.0 0 3 3 425.0 0 1 1 426.0 0 2 2 427.0 0 2 2 428.0 0 3 3 429.0 0 4 4 430.0 0 3 3 431.0 0 3 3 433.0 0 3 3 434.0 0 2 2 435.0 0 3 3 436.0 0 3 3 438.0 0 2 2 439.0 0 1 1 440.0 0 2 2 441.0 0 2 2 442.0 0 2 2 443.0 0 3 3 444.0 0 1 1 445.0 0 1 1 447.0 0 2 2 449.0 0 1 1 450.0 0 5 5 451.0 0 2 2 453.0 0 1 1 455.0 0 1 1 456.0 0 1 1 457.0 0 2 2 458.0 0 3 3 459.0 0 3 3 460.0 0 1 1 461.0 0 2 2 462.0 0 1 1 464.0 0 3 3 465.0 0 1 1 466.0 0 1 1 467.0 0 1 1 468.0 0 1 1 469.0 0 1 1 470.0 0 2 2 471.0 0 3 3 472.0 0 1 1 473.0 0 2 2 475.0 0 1 1 477.0 0 2 2 478.0 0 2 2 479.0 0 3 3 480.0 0 1 1 481.0 0 1 1 482.0 0 1 1 484.0 0 1 1 485.0 0 1 1 486.0 0 2 2 487.0 0 2 2 488.0 0 2 2 489.0 0 4 4 490.0 0 1 1 492.0 0 1 1 494.0 0 3 3 495.0 0 2 2 497.0 0 1 1 500.0 0 3 3 501.0 0 2 2 503.0 0 1 1 504.0 0 1 1 505.0 0 1 1 506.0 0 1 1 507.0 0 1 1 510.0 0 1 1 512.0 0 2 2 513.0 0 1 1 516.0 0 2 2 518.0 0 3 3 520.0 0 1 1 521.0 0 1 1 522.0 0 1 1 523.0 0 1 1 524.0 0 2 2 526.0 0 1 1 528.0 0 1 1 529.0 0 3 3 530.0 0 2 2 531.0 0 1 1 533.0 0 1 1 534.0 0 2 2 537.0 0 2 2 538.0 0 1 1 541.0 0 1 1 543.0 0 1 1 545.0 0 1 1 548.0 0 2 2 549.0 0 1 1 554.0 0 1 1 555.0 0 1 1 556.0 0 1 1 557.0 0 2 2 564.0 0 1 1 565.0 0 3 3 566.0 0 1 1 568.0 0 2 2 569.0 0 1 1 570.0 0 1 1 571.0 0 1 1 574.0 0 1 1 575.0 0 1 1 578.0 0 1 1 580.0 0 1 1 581.0 0 2 2 583.0 0 3 3 584.0 0 1 1 585.0 0 1 1 588.0 0 2 2 594.0 0 2 2 597.0 0 1 1 602.0 0 1 1 605.0 0 1 1 606.0 0 1 1 607.0 0 1 1 608.0 0 1 1 610.0 0 1 1 611.0 0 2 2 612.0 0 4 4 613.0 0 2 2 615.0 0 1 1 617.0 0 1 1 619.0 0 2 2 621.0 0 1 1 625.0 0 1 1 629.0 0 2 2 631.0 0 1 1 635.0 0 1 1 636.0 0 1 1 637.0 0 1 1 638.0 0 1 1 640.0 0 1 1 644.0 0 2 2 645.0 0 1 1 649.0 0 2 2 650.0 0 1 1 652.0 0 1 1 654.0 0 1 1 655.0 0 2 2 656.0 0 1 1 657.0 0 1 1 662.0 0 1 1 664.0 0 1 1 667.0 0 1 1 675.0 0 1 1 682.0 0 2 2 684.0 0 3 3 687.0 0 1 1 688.0 0 1 1 691.0 0 1 1 703.0 0 2 2 704.0 0 1 1 710.0 0 1 1 714.0 0 1 1 722.0 0 1 1 725.0 0 1 1 726.0 0 1 1 747.0 0 1 1 749.0 0 1 1 751.0 0 1 1 752.0 0 1 1 755.0 0 1 1 757.0 0 1 1 769.0 0 1 1 774.0 0 1 1 775.0 0 1 1 782.0 0 1 1 785.0 0 1 1 792.0 0 1 1 800.0 0 1 1 804.0 0 1 1 811.0 0 1 1 814.0 0 1 1 816.0 0 1 1 822.0 0 1 1 829.0 0 1 1 846.0 0 2 2 858.0 0 1 1 864.0 0 1 1 872.0 0 1 1 876.0 0 1 1 879.0 0 1 1 882.0 0 1 1 885.0 0 1 1 907.0 0 2 2 912.0 0 1 1 913.0 0 1 1 931.0 0 1 1 932.0 0 1 1 947.0 0 1 1 960.0 0 1 1 962.0 0 1 1 965.0 0 1 1 967.0 0 1 1 988.0 0 1 1 994.0 0 2 2 1017.0 0 1 1 1083.0 0 1 1 1167.0 0 1 1 1171.0 0 1 1 1177.0 0 1 1 1215.0 0 1 1 1249.0 0 1 1 1250.0 0 1 1 1297.0 0 1 1 1318.0 0 1 1 1363.0 0 1 1 1369.0 0 1 1 1411.0 0 1 1 1428.0 0 1 1 1490.0 0 1 1 1524.0 0 1 1 1558.0 0 1 1 1615.0 0 1 1 1660.0 0 1 1 1771.0 0 1 1 1853.0 0 1 1 3994.0 0 1 1