## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354070.sorted.bam --OUTPUT SRX7354070.markdup.sorted.bam --METRICS_FILE SRX7354070.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 17:40:57 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 25666 39395911 5193425 3207988 18632 14037627 0 0.356442 41173211 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21415093 21415093 2.0 1.384107 2426813 2426813 3.0 1.531646 575101 575101 4.0 1.588316 255073 255073 5.0 1.610084 148025 148025 6.0 1.618445 97069 97069 7.0 1.621656 69397 69397 8.0 1.62289 51407 51407 9.0 1.623364 40202 40202 10.0 1.623546 32103 32103 11.0 1.623616 25817 25817 12.0 1.623642 21812 21812 13.0 1.623653 18024 18024 14.0 1.623657 15767 15767 15.0 1.623658 13578 13578 16.0 1.623659 11644 11644 17.0 1.623659 10095 10095 18.0 1.623659 9126 9126 19.0 1.623659 7999 7999 20.0 1.623659 7304 7304 21.0 1.623659 6626 6626 22.0 1.623659 5888 5888 23.0 1.623659 5358 5358 24.0 1.623659 4825 4825 25.0 1.623659 4428 4428 26.0 1.623659 4126 4126 27.0 1.623659 3810 3810 28.0 1.623659 3505 3505 29.0 1.623659 3228 3228 30.0 1.623659 2913 2913 31.0 1.623659 2773 2773 32.0 1.623659 2616 2616 33.0 1.623659 2328 2328 34.0 1.623659 2272 2272 35.0 1.623659 2158 2158 36.0 1.623659 1969 1969 37.0 1.623659 1919 1919 38.0 1.623659 1738 1738 39.0 1.623659 1715 1715 40.0 1.623659 1615 1615 41.0 1.623659 1495 1495 42.0 1.623659 1428 1428 43.0 1.623659 1368 1368 44.0 1.623659 1210 1210 45.0 1.623659 1200 1200 46.0 1.623659 1137 1137 47.0 1.623659 1088 1088 48.0 1.623659 978 978 49.0 1.623659 950 950 50.0 1.623659 944 944 51.0 1.623659 903 903 52.0 1.623659 804 804 53.0 1.623659 771 771 54.0 1.623659 800 800 55.0 1.623659 802 802 56.0 1.623659 702 702 57.0 1.623659 693 693 58.0 1.623659 693 693 59.0 1.623659 637 637 60.0 1.623659 549 549 61.0 1.623659 564 564 62.0 1.623659 522 522 63.0 1.623659 520 520 64.0 1.623659 527 527 65.0 1.623659 497 497 66.0 1.623659 484 484 67.0 1.623659 459 459 68.0 1.623659 445 445 69.0 1.623659 428 428 70.0 1.623659 433 433 71.0 1.623659 384 384 72.0 1.623659 360 360 73.0 1.623659 372 372 74.0 1.623659 369 369 75.0 1.623659 338 338 76.0 1.623659 353 353 77.0 1.623659 316 316 78.0 1.623659 298 298 79.0 1.623659 300 300 80.0 1.623659 298 298 81.0 1.623659 283 283 82.0 1.623659 264 264 83.0 1.623659 279 279 84.0 1.623659 268 268 85.0 1.623659 238 238 86.0 1.623659 239 239 87.0 1.623659 257 257 88.0 1.623659 242 242 89.0 1.623659 216 216 90.0 1.623659 228 228 91.0 1.623659 208 208 92.0 1.623659 199 199 93.0 1.623659 204 204 94.0 1.623659 169 169 95.0 1.623659 179 179 96.0 1.623659 230 230 97.0 1.623659 158 158 98.0 1.623659 198 198 99.0 1.623659 179 179 100.0 1.623659 139 139 101.0 0 164 164 102.0 0 158 158 103.0 0 159 159 104.0 0 151 151 105.0 0 163 163 106.0 0 156 156 107.0 0 140 140 108.0 0 148 148 109.0 0 152 152 110.0 0 137 137 111.0 0 117 117 112.0 0 100 100 113.0 0 105 105 114.0 0 143 143 115.0 0 125 125 116.0 0 109 109 117.0 0 111 111 118.0 0 122 122 119.0 0 117 117 120.0 0 75 75 121.0 0 83 83 122.0 0 107 107 123.0 0 106 106 124.0 0 100 100 125.0 0 97 97 126.0 0 88 88 127.0 0 75 75 128.0 0 81 81 129.0 0 82 82 130.0 0 85 85 131.0 0 83 83 132.0 0 68 68 133.0 0 85 85 134.0 0 79 79 135.0 0 81 81 136.0 0 69 69 137.0 0 82 82 138.0 0 72 72 139.0 0 74 74 140.0 0 68 68 141.0 0 58 58 142.0 0 66 66 143.0 0 66 66 144.0 0 64 64 145.0 0 46 46 146.0 0 61 61 147.0 0 69 69 148.0 0 51 51 149.0 0 76 76 150.0 0 69 69 151.0 0 57 57 152.0 0 47 47 153.0 0 56 56 154.0 0 59 59 155.0 0 53 53 156.0 0 50 50 157.0 0 54 54 158.0 0 42 42 159.0 0 56 56 160.0 0 42 42 161.0 0 42 42 162.0 0 64 64 163.0 0 46 46 164.0 0 44 44 165.0 0 38 38 166.0 0 46 46 167.0 0 47 47 168.0 0 42 42 169.0 0 37 37 170.0 0 46 46 171.0 0 44 44 172.0 0 43 43 173.0 0 40 40 174.0 0 33 33 175.0 0 29 29 176.0 0 29 29 177.0 0 25 25 178.0 0 25 25 179.0 0 33 33 180.0 0 29 29 181.0 0 34 34 182.0 0 29 29 183.0 0 31 31 184.0 0 26 26 185.0 0 25 25 186.0 0 22 22 187.0 0 42 42 188.0 0 37 37 189.0 0 29 29 190.0 0 37 37 191.0 0 33 33 192.0 0 24 24 193.0 0 30 30 194.0 0 26 26 195.0 0 24 24 196.0 0 35 35 197.0 0 28 28 198.0 0 16 16 199.0 0 20 20 200.0 0 29 29 201.0 0 31 31 202.0 0 24 24 203.0 0 30 30 204.0 0 28 28 205.0 0 30 30 206.0 0 31 31 207.0 0 22 22 208.0 0 23 23 209.0 0 21 21 210.0 0 25 25 211.0 0 26 26 212.0 0 21 21 213.0 0 26 26 214.0 0 25 25 215.0 0 27 27 216.0 0 23 23 217.0 0 16 16 218.0 0 18 18 219.0 0 21 21 220.0 0 23 23 221.0 0 15 15 222.0 0 10 10 223.0 0 19 19 224.0 0 24 24 225.0 0 27 27 226.0 0 20 20 227.0 0 23 23 228.0 0 19 19 229.0 0 14 14 230.0 0 18 18 231.0 0 13 13 232.0 0 13 13 233.0 0 19 19 234.0 0 13 13 235.0 0 26 26 236.0 0 20 20 237.0 0 16 16 238.0 0 15 15 239.0 0 21 21 240.0 0 11 11 241.0 0 13 13 242.0 0 16 16 243.0 0 9 9 244.0 0 13 13 245.0 0 18 18 246.0 0 12 12 247.0 0 13 13 248.0 0 11 11 249.0 0 15 15 250.0 0 15 15 251.0 0 8 8 252.0 0 14 14 253.0 0 13 13 254.0 0 15 15 255.0 0 10 10 256.0 0 16 16 257.0 0 9 9 258.0 0 15 15 259.0 0 9 9 260.0 0 15 15 261.0 0 11 11 262.0 0 8 8 263.0 0 8 8 264.0 0 17 17 265.0 0 18 18 266.0 0 12 12 267.0 0 10 10 268.0 0 12 12 269.0 0 14 14 270.0 0 10 10 271.0 0 14 14 272.0 0 16 16 273.0 0 9 9 274.0 0 7 7 275.0 0 6 6 276.0 0 12 12 277.0 0 16 16 278.0 0 10 10 279.0 0 8 8 280.0 0 11 11 281.0 0 7 7 282.0 0 12 12 283.0 0 7 7 284.0 0 8 8 285.0 0 7 7 286.0 0 7 7 287.0 0 9 9 288.0 0 9 9 289.0 0 8 8 290.0 0 8 8 291.0 0 10 10 292.0 0 5 5 293.0 0 9 9 294.0 0 8 8 295.0 0 11 11 296.0 0 5 5 297.0 0 7 7 298.0 0 10 10 299.0 0 5 5 300.0 0 10 10 301.0 0 5 5 302.0 0 6 6 303.0 0 2 2 304.0 0 8 8 305.0 0 8 8 306.0 0 5 5 307.0 0 12 12 308.0 0 4 4 309.0 0 14 14 310.0 0 5 5 311.0 0 5 5 312.0 0 7 7 313.0 0 4 4 314.0 0 7 7 315.0 0 8 8 316.0 0 3 3 317.0 0 9 9 318.0 0 7 7 319.0 0 5 5 320.0 0 12 12 321.0 0 6 6 322.0 0 6 6 323.0 0 4 4 324.0 0 11 11 325.0 0 3 3 326.0 0 5 5 327.0 0 5 5 328.0 0 7 7 329.0 0 1 1 330.0 0 10 10 331.0 0 6 6 332.0 0 2 2 333.0 0 4 4 334.0 0 6 6 335.0 0 8 8 336.0 0 6 6 337.0 0 7 7 338.0 0 6 6 339.0 0 2 2 340.0 0 3 3 341.0 0 4 4 342.0 0 8 8 343.0 0 5 5 344.0 0 4 4 345.0 0 5 5 346.0 0 3 3 347.0 0 2 2 348.0 0 4 4 349.0 0 6 6 350.0 0 4 4 351.0 0 5 5 352.0 0 5 5 353.0 0 5 5 354.0 0 8 8 355.0 0 5 5 356.0 0 2 2 357.0 0 2 2 358.0 0 3 3 359.0 0 3 3 360.0 0 5 5 361.0 0 2 2 362.0 0 4 4 363.0 0 1 1 364.0 0 2 2 365.0 0 3 3 366.0 0 6 6 367.0 0 2 2 368.0 0 3 3 369.0 0 5 5 370.0 0 6 6 371.0 0 2 2 372.0 0 6 6 373.0 0 2 2 374.0 0 3 3 375.0 0 5 5 376.0 0 2 2 377.0 0 4 4 378.0 0 7 7 379.0 0 1 1 380.0 0 2 2 381.0 0 3 3 382.0 0 4 4 383.0 0 2 2 384.0 0 8 8 385.0 0 3 3 387.0 0 5 5 388.0 0 3 3 389.0 0 5 5 390.0 0 4 4 391.0 0 2 2 393.0 0 4 4 394.0 0 2 2 395.0 0 3 3 396.0 0 2 2 398.0 0 5 5 399.0 0 1 1 400.0 0 5 5 401.0 0 4 4 403.0 0 1 1 404.0 0 5 5 405.0 0 3 3 406.0 0 2 2 407.0 0 6 6 408.0 0 7 7 409.0 0 3 3 410.0 0 4 4 411.0 0 2 2 412.0 0 2 2 413.0 0 1 1 414.0 0 2 2 415.0 0 3 3 416.0 0 2 2 417.0 0 1 1 418.0 0 3 3 419.0 0 3 3 420.0 0 5 5 421.0 0 3 3 422.0 0 1 1 424.0 0 3 3 425.0 0 3 3 426.0 0 1 1 427.0 0 4 4 429.0 0 2 2 430.0 0 3 3 431.0 0 3 3 432.0 0 4 4 433.0 0 1 1 434.0 0 6 6 435.0 0 3 3 436.0 0 3 3 437.0 0 1 1 438.0 0 2 2 439.0 0 2 2 440.0 0 1 1 441.0 0 4 4 442.0 0 2 2 443.0 0 3 3 444.0 0 4 4 445.0 0 2 2 447.0 0 2 2 448.0 0 1 1 450.0 0 2 2 452.0 0 4 4 453.0 0 1 1 454.0 0 1 1 455.0 0 1 1 456.0 0 1 1 457.0 0 4 4 458.0 0 2 2 459.0 0 1 1 461.0 0 2 2 463.0 0 1 1 464.0 0 2 2 465.0 0 4 4 466.0 0 1 1 467.0 0 2 2 468.0 0 1 1 469.0 0 1 1 471.0 0 1 1 472.0 0 1 1 475.0 0 2 2 476.0 0 1 1 478.0 0 2 2 479.0 0 1 1 481.0 0 1 1 483.0 0 2 2 484.0 0 1 1 485.0 0 1 1 486.0 0 4 4 487.0 0 3 3 488.0 0 1 1 490.0 0 1 1 491.0 0 2 2 493.0 0 1 1 494.0 0 3 3 495.0 0 5 5 496.0 0 3 3 497.0 0 2 2 498.0 0 3 3 499.0 0 2 2 500.0 0 5 5 502.0 0 3 3 504.0 0 4 4 505.0 0 1 1 506.0 0 2 2 507.0 0 1 1 508.0 0 3 3 509.0 0 1 1 510.0 0 1 1 511.0 0 1 1 512.0 0 1 1 513.0 0 2 2 514.0 0 1 1 515.0 0 2 2 516.0 0 1 1 517.0 0 1 1 518.0 0 2 2 522.0 0 2 2 523.0 0 2 2 524.0 0 1 1 525.0 0 1 1 526.0 0 3 3 527.0 0 1 1 528.0 0 1 1 532.0 0 2 2 535.0 0 3 3 538.0 0 2 2 539.0 0 2 2 540.0 0 1 1 542.0 0 2 2 544.0 0 2 2 545.0 0 1 1 546.0 0 1 1 547.0 0 1 1 548.0 0 1 1 549.0 0 1 1 550.0 0 2 2 551.0 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 1 1 558.0 0 3 3 559.0 0 1 1 560.0 0 1 1 561.0 0 1 1 564.0 0 1 1 566.0 0 2 2 568.0 0 2 2 569.0 0 2 2 570.0 0 1 1 571.0 0 1 1 573.0 0 2 2 574.0 0 1 1 575.0 0 1 1 576.0 0 1 1 577.0 0 1 1 578.0 0 2 2 579.0 0 1 1 581.0 0 2 2 583.0 0 1 1 585.0 0 2 2 587.0 0 1 1 588.0 0 2 2 589.0 0 1 1 590.0 0 1 1 592.0 0 1 1 593.0 0 1 1 598.0 0 1 1 603.0 0 1 1 605.0 0 1 1 606.0 0 2 2 608.0 0 1 1 609.0 0 1 1 610.0 0 1 1 618.0 0 1 1 622.0 0 2 2 623.0 0 1 1 626.0 0 1 1 630.0 0 2 2 633.0 0 2 2 635.0 0 1 1 636.0 0 2 2 637.0 0 1 1 639.0 0 3 3 641.0 0 3 3 643.0 0 2 2 653.0 0 1 1 656.0 0 1 1 658.0 0 1 1 661.0 0 1 1 663.0 0 2 2 665.0 0 2 2 673.0 0 2 2 674.0 0 1 1 675.0 0 2 2 678.0 0 1 1 683.0 0 1 1 684.0 0 1 1 685.0 0 1 1 688.0 0 1 1 689.0 0 1 1 692.0 0 2 2 693.0 0 2 2 698.0 0 1 1 699.0 0 1 1 701.0 0 1 1 708.0 0 3 3 710.0 0 1 1 712.0 0 1 1 719.0 0 2 2 720.0 0 1 1 722.0 0 1 1 726.0 0 1 1 727.0 0 1 1 728.0 0 1 1 729.0 0 1 1 732.0 0 1 1 734.0 0 1 1 738.0 0 1 1 746.0 0 1 1 747.0 0 1 1 748.0 0 1 1 750.0 0 1 1 751.0 0 1 1 755.0 0 2 2 758.0 0 1 1 767.0 0 1 1 771.0 0 1 1 779.0 0 1 1 783.0 0 1 1 792.0 0 1 1 794.0 0 1 1 797.0 0 1 1 807.0 0 1 1 812.0 0 1 1 813.0 0 1 1 824.0 0 1 1 826.0 0 1 1 831.0 0 3 3 838.0 0 2 2 846.0 0 1 1 855.0 0 1 1 858.0 0 1 1 871.0 0 3 3 877.0 0 1 1 879.0 0 1 1 886.0 0 1 1 887.0 0 1 1 890.0 0 1 1 897.0 0 1 1 899.0 0 1 1 904.0 0 1 1 909.0 0 2 2 922.0 0 2 2 923.0 0 1 1 947.0 0 1 1 955.0 0 1 1 956.0 0 1 1 959.0 0 1 1 961.0 0 1 1 967.0 0 1 1 972.0 0 1 1 976.0 0 1 1 978.0 0 1 1 980.0 0 1 1 998.0 0 1 1 1011.0 0 1 1 1014.0 0 1 1 1017.0 0 1 1 1040.0 0 1 1 1061.0 0 1 1 1063.0 0 1 1 1078.0 0 1 1 1092.0 0 1 1 1102.0 0 1 1 1104.0 0 1 1 1110.0 0 1 1 1119.0 0 1 1 1196.0 0 1 1 1227.0 0 2 2 1288.0 0 1 1 1410.0 0 1 1 1446.0 0 1 1 1465.0 0 1 1 1478.0 0 1 1 1737.0 0 1 1 1780.0 0 1 1 1931.0 0 1 1