## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354403.sorted.bam --OUTPUT SRX7354403.markdup.sorted.bam --METRICS_FILE SRX7354403.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: Tue Oct 31 15:10:14 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 61654 53521751 6600015 9399940 48052 22370342 0 0.418175 44553033 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 25162835 25162835 2.0 1.300802 3715051 3715051 3.0 1.391283 871994 871994 4.0 1.4185 362854 362854 5.0 1.426687 208889 208889 6.0 1.42915 139736 139736 7.0 1.429891 101082 101082 8.0 1.430113 76116 76116 9.0 1.43018 60177 60177 10.0 1.430201 48049 48049 11.0 1.430207 40234 40234 12.0 1.430208 33698 33698 13.0 1.430209 28210 28210 14.0 1.430209 24252 24252 15.0 1.430209 21366 21366 16.0 1.430209 18492 18492 17.0 1.430209 16120 16120 18.0 1.430209 14557 14557 19.0 1.430209 13030 13030 20.0 1.430209 11808 11808 21.0 1.430209 10544 10544 22.0 1.430209 9676 9676 23.0 1.430209 8778 8778 24.0 1.430209 8138 8138 25.0 1.430209 7395 7395 26.0 1.430209 6774 6774 27.0 1.430209 6242 6242 28.0 1.430209 5822 5822 29.0 1.430209 5423 5423 30.0 1.430209 5103 5103 31.0 1.430209 4742 4742 32.0 1.430209 4385 4385 33.0 1.430209 4177 4177 34.0 1.430209 3796 3796 35.0 1.430209 3660 3660 36.0 1.430209 3329 3329 37.0 1.430209 3251 3251 38.0 1.430209 3005 3005 39.0 1.430209 2823 2823 40.0 1.430209 2745 2745 41.0 1.430209 2652 2652 42.0 1.430209 2413 2413 43.0 1.430209 2368 2368 44.0 1.430209 2109 2109 45.0 1.430209 2071 2071 46.0 1.430209 1996 1996 47.0 1.430209 1877 1877 48.0 1.430209 1772 1772 49.0 1.430209 1711 1711 50.0 1.430209 1629 1629 51.0 1.430209 1589 1589 52.0 1.430209 1440 1440 53.0 1.430209 1491 1491 54.0 1.430209 1300 1300 55.0 1.430209 1288 1288 56.0 1.430209 1257 1257 57.0 1.430209 1230 1230 58.0 1.430209 1136 1136 59.0 1.430209 1111 1111 60.0 1.430209 1040 1040 61.0 1.430209 1058 1058 62.0 1.430209 1049 1049 63.0 1.430209 971 971 64.0 1.430209 913 913 65.0 1.430209 868 868 66.0 1.430209 823 823 67.0 1.430209 820 820 68.0 1.430209 773 773 69.0 1.430209 757 757 70.0 1.430209 695 695 71.0 1.430209 709 709 72.0 1.430209 709 709 73.0 1.430209 705 705 74.0 1.430209 623 623 75.0 1.430209 612 612 76.0 1.430209 605 605 77.0 1.430209 581 581 78.0 1.430209 611 611 79.0 1.430209 527 527 80.0 1.430209 519 519 81.0 1.430209 520 520 82.0 1.430209 467 467 83.0 1.430209 490 490 84.0 1.430209 452 452 85.0 1.430209 504 504 86.0 1.430209 509 509 87.0 1.430209 447 447 88.0 1.430209 431 431 89.0 1.430209 408 408 90.0 1.430209 396 396 91.0 1.430209 409 409 92.0 1.430209 379 379 93.0 1.430209 351 351 94.0 1.430209 362 362 95.0 1.430209 374 374 96.0 1.430209 378 378 97.0 1.430209 362 362 98.0 1.430209 320 320 99.0 1.430209 325 325 100.0 1.430209 320 320 101.0 0 296 296 102.0 0 296 296 103.0 0 292 292 104.0 0 271 271 105.0 0 279 279 106.0 0 269 269 107.0 0 295 295 108.0 0 223 223 109.0 0 243 243 110.0 0 226 226 111.0 0 216 216 112.0 0 246 246 113.0 0 212 212 114.0 0 205 205 115.0 0 232 232 116.0 0 233 233 117.0 0 210 210 118.0 0 183 183 119.0 0 201 201 120.0 0 204 204 121.0 0 179 179 122.0 0 172 172 123.0 0 198 198 124.0 0 181 181 125.0 0 187 187 126.0 0 172 172 127.0 0 158 158 128.0 0 149 149 129.0 0 162 162 130.0 0 153 153 131.0 0 130 130 132.0 0 139 139 133.0 0 137 137 134.0 0 162 162 135.0 0 147 147 136.0 0 120 120 137.0 0 109 109 138.0 0 136 136 139.0 0 134 134 140.0 0 121 121 141.0 0 123 123 142.0 0 103 103 143.0 0 120 120 144.0 0 131 131 145.0 0 94 94 146.0 0 112 112 147.0 0 100 100 148.0 0 106 106 149.0 0 109 109 150.0 0 104 104 151.0 0 99 99 152.0 0 109 109 153.0 0 91 91 154.0 0 93 93 155.0 0 100 100 156.0 0 99 99 157.0 0 85 85 158.0 0 93 93 159.0 0 76 76 160.0 0 80 80 161.0 0 84 84 162.0 0 92 92 163.0 0 79 79 164.0 0 66 66 165.0 0 73 73 166.0 0 77 77 167.0 0 63 63 168.0 0 66 66 169.0 0 80 80 170.0 0 69 69 171.0 0 57 57 172.0 0 65 65 173.0 0 61 61 174.0 0 74 74 175.0 0 63 63 176.0 0 70 70 177.0 0 78 78 178.0 0 67 67 179.0 0 63 63 180.0 0 58 58 181.0 0 57 57 182.0 0 73 73 183.0 0 77 77 184.0 0 42 42 185.0 0 53 53 186.0 0 48 48 187.0 0 64 64 188.0 0 52 52 189.0 0 48 48 190.0 0 49 49 191.0 0 44 44 192.0 0 53 53 193.0 0 52 52 194.0 0 58 58 195.0 0 54 54 196.0 0 38 38 197.0 0 48 48 198.0 0 62 62 199.0 0 33 33 200.0 0 44 44 201.0 0 50 50 202.0 0 43 43 203.0 0 44 44 204.0 0 39 39 205.0 0 38 38 206.0 0 40 40 207.0 0 48 48 208.0 0 55 55 209.0 0 41 41 210.0 0 43 43 211.0 0 35 35 212.0 0 38 38 213.0 0 44 44 214.0 0 38 38 215.0 0 33 33 216.0 0 37 37 217.0 0 38 38 218.0 0 34 34 219.0 0 37 37 220.0 0 41 41 221.0 0 37 37 222.0 0 35 35 223.0 0 42 42 224.0 0 32 32 225.0 0 31 31 226.0 0 25 25 227.0 0 43 43 228.0 0 30 30 229.0 0 33 33 230.0 0 43 43 231.0 0 21 21 232.0 0 26 26 233.0 0 22 22 234.0 0 28 28 235.0 0 31 31 236.0 0 27 27 237.0 0 31 31 238.0 0 28 28 239.0 0 35 35 240.0 0 22 22 241.0 0 13 13 242.0 0 21 21 243.0 0 34 34 244.0 0 33 33 245.0 0 22 22 246.0 0 31 31 247.0 0 21 21 248.0 0 21 21 249.0 0 23 23 250.0 0 27 27 251.0 0 15 15 252.0 0 29 29 253.0 0 24 24 254.0 0 18 18 255.0 0 14 14 256.0 0 22 22 257.0 0 19 19 258.0 0 21 21 259.0 0 16 16 260.0 0 13 13 261.0 0 27 27 262.0 0 24 24 263.0 0 19 19 264.0 0 16 16 265.0 0 24 24 266.0 0 29 29 267.0 0 13 13 268.0 0 15 15 269.0 0 21 21 270.0 0 12 12 271.0 0 17 17 272.0 0 10 10 273.0 0 14 14 274.0 0 17 17 275.0 0 15 15 276.0 0 12 12 277.0 0 25 25 278.0 0 19 19 279.0 0 11 11 280.0 0 17 17 281.0 0 12 12 282.0 0 16 16 283.0 0 9 9 284.0 0 19 19 285.0 0 13 13 286.0 0 18 18 287.0 0 15 15 288.0 0 17 17 289.0 0 24 24 290.0 0 16 16 291.0 0 21 21 292.0 0 15 15 293.0 0 17 17 294.0 0 20 20 295.0 0 14 14 296.0 0 15 15 297.0 0 12 12 298.0 0 13 13 299.0 0 15 15 300.0 0 18 18 301.0 0 18 18 302.0 0 17 17 303.0 0 11 11 304.0 0 13 13 305.0 0 17 17 306.0 0 11 11 307.0 0 14 14 308.0 0 8 8 309.0 0 9 9 310.0 0 13 13 311.0 0 9 9 312.0 0 13 13 313.0 0 10 10 314.0 0 13 13 315.0 0 8 8 316.0 0 10 10 317.0 0 12 12 318.0 0 8 8 319.0 0 10 10 320.0 0 14 14 321.0 0 10 10 322.0 0 6 6 323.0 0 7 7 324.0 0 10 10 325.0 0 10 10 326.0 0 9 9 327.0 0 7 7 328.0 0 16 16 329.0 0 11 11 330.0 0 6 6 331.0 0 17 17 332.0 0 9 9 333.0 0 13 13 334.0 0 12 12 335.0 0 10 10 336.0 0 17 17 337.0 0 9 9 338.0 0 13 13 339.0 0 6 6 340.0 0 7 7 341.0 0 13 13 342.0 0 12 12 343.0 0 9 9 344.0 0 7 7 345.0 0 11 11 346.0 0 8 8 347.0 0 8 8 348.0 0 5 5 349.0 0 10 10 350.0 0 8 8 351.0 0 5 5 352.0 0 8 8 353.0 0 9 9 354.0 0 9 9 355.0 0 8 8 356.0 0 9 9 357.0 0 10 10 358.0 0 8 8 359.0 0 6 6 360.0 0 6 6 361.0 0 6 6 362.0 0 7 7 363.0 0 7 7 364.0 0 6 6 365.0 0 6 6 366.0 0 9 9 367.0 0 3 3 368.0 0 4 4 369.0 0 8 8 370.0 0 5 5 371.0 0 8 8 372.0 0 3 3 373.0 0 3 3 374.0 0 6 6 375.0 0 7 7 376.0 0 8 8 377.0 0 7 7 378.0 0 1 1 379.0 0 7 7 380.0 0 8 8 381.0 0 8 8 382.0 0 11 11 383.0 0 8 8 384.0 0 6 6 385.0 0 10 10 386.0 0 3 3 387.0 0 8 8 388.0 0 6 6 389.0 0 11 11 390.0 0 3 3 391.0 0 5 5 392.0 0 7 7 393.0 0 3 3 394.0 0 5 5 395.0 0 1 1 396.0 0 6 6 397.0 0 6 6 398.0 0 6 6 399.0 0 3 3 400.0 0 4 4 401.0 0 2 2 402.0 0 4 4 403.0 0 5 5 404.0 0 4 4 405.0 0 5 5 406.0 0 6 6 407.0 0 2 2 408.0 0 1 1 409.0 0 8 8 410.0 0 3 3 411.0 0 5 5 412.0 0 7 7 413.0 0 3 3 414.0 0 5 5 415.0 0 1 1 416.0 0 2 2 417.0 0 2 2 418.0 0 7 7 419.0 0 2 2 420.0 0 9 9 421.0 0 5 5 422.0 0 4 4 423.0 0 3 3 424.0 0 2 2 425.0 0 4 4 426.0 0 7 7 427.0 0 5 5 428.0 0 3 3 429.0 0 5 5 430.0 0 1 1 431.0 0 2 2 432.0 0 3 3 433.0 0 5 5 434.0 0 4 4 435.0 0 3 3 436.0 0 3 3 437.0 0 7 7 438.0 0 6 6 439.0 0 5 5 440.0 0 4 4 441.0 0 3 3 442.0 0 3 3 443.0 0 3 3 444.0 0 7 7 445.0 0 1 1 446.0 0 5 5 447.0 0 5 5 448.0 0 3 3 449.0 0 6 6 450.0 0 4 4 451.0 0 3 3 452.0 0 1 1 453.0 0 3 3 454.0 0 2 2 455.0 0 4 4 456.0 0 2 2 458.0 0 2 2 460.0 0 2 2 461.0 0 1 1 462.0 0 2 2 463.0 0 5 5 464.0 0 3 3 465.0 0 3 3 466.0 0 5 5 467.0 0 4 4 468.0 0 2 2 469.0 0 4 4 470.0 0 1 1 471.0 0 4 4 472.0 0 2 2 473.0 0 4 4 474.0 0 3 3 475.0 0 4 4 478.0 0 2 2 479.0 0 2 2 480.0 0 2 2 481.0 0 6 6 482.0 0 3 3 483.0 0 7 7 484.0 0 5 5 485.0 0 4 4 486.0 0 1 1 487.0 0 3 3 488.0 0 4 4 489.0 0 6 6 490.0 0 4 4 491.0 0 2 2 492.0 0 6 6 493.0 0 1 1 494.0 0 4 4 495.0 0 3 3 496.0 0 4 4 497.0 0 5 5 499.0 0 4 4 500.0 0 1 1 501.0 0 3 3 502.0 0 1 1 503.0 0 3 3 504.0 0 4 4 505.0 0 2 2 506.0 0 7 7 509.0 0 1 1 510.0 0 1 1 511.0 0 1 1 513.0 0 3 3 514.0 0 2 2 515.0 0 2 2 517.0 0 1 1 518.0 0 4 4 519.0 0 2 2 520.0 0 2 2 521.0 0 3 3 522.0 0 1 1 523.0 0 1 1 524.0 0 3 3 525.0 0 3 3 526.0 0 2 2 527.0 0 1 1 528.0 0 5 5 529.0 0 3 3 531.0 0 2 2 532.0 0 4 4 533.0 0 2 2 534.0 0 2 2 535.0 0 1 1 536.0 0 2 2 537.0 0 1 1 538.0 0 2 2 539.0 0 1 1 540.0 0 3 3 541.0 0 2 2 542.0 0 1 1 543.0 0 3 3 544.0 0 2 2 545.0 0 3 3 548.0 0 2 2 549.0 0 2 2 551.0 0 2 2 552.0 0 5 5 553.0 0 1 1 554.0 0 2 2 555.0 0 1 1 556.0 0 1 1 557.0 0 1 1 560.0 0 4 4 562.0 0 1 1 563.0 0 1 1 565.0 0 1 1 566.0 0 2 2 567.0 0 3 3 568.0 0 1 1 570.0 0 1 1 572.0 0 3 3 573.0 0 1 1 576.0 0 1 1 577.0 0 1 1 578.0 0 1 1 581.0 0 3 3 582.0 0 1 1 585.0 0 1 1 587.0 0 2 2 588.0 0 2 2 589.0 0 4 4 591.0 0 3 3 594.0 0 2 2 595.0 0 1 1 596.0 0 1 1 597.0 0 1 1 598.0 0 1 1 600.0 0 1 1 601.0 0 1 1 602.0 0 1 1 603.0 0 1 1 604.0 0 2 2 605.0 0 4 4 607.0 0 2 2 608.0 0 1 1 609.0 0 1 1 610.0 0 1 1 611.0 0 2 2 612.0 0 2 2 613.0 0 1 1 615.0 0 2 2 616.0 0 3 3 617.0 0 2 2 618.0 0 2 2 620.0 0 2 2 621.0 0 1 1 622.0 0 1 1 624.0 0 2 2 625.0 0 2 2 628.0 0 1 1 629.0 0 1 1 630.0 0 2 2 631.0 0 2 2 632.0 0 1 1 634.0 0 2 2 635.0 0 1 1 636.0 0 1 1 640.0 0 1 1 641.0 0 2 2 642.0 0 1 1 643.0 0 1 1 646.0 0 1 1 648.0 0 1 1 650.0 0 1 1 652.0 0 1 1 653.0 0 1 1 655.0 0 2 2 656.0 0 1 1 659.0 0 1 1 660.0 0 2 2 661.0 0 1 1 662.0 0 3 3 665.0 0 1 1 666.0 0 2 2 667.0 0 2 2 668.0 0 1 1 670.0 0 1 1 672.0 0 1 1 674.0 0 1 1 677.0 0 1 1 682.0 0 1 1 684.0 0 1 1 685.0 0 1 1 687.0 0 1 1 689.0 0 3 3 692.0 0 1 1 693.0 0 1 1 694.0 0 2 2 696.0 0 1 1 701.0 0 1 1 703.0 0 1 1 708.0 0 1 1 714.0 0 1 1 721.0 0 2 2 724.0 0 1 1 725.0 0 1 1 729.0 0 2 2 730.0 0 1 1 731.0 0 2 2 732.0 0 1 1 734.0 0 1 1 737.0 0 1 1 738.0 0 1 1 741.0 0 3 3 746.0 0 1 1 750.0 0 1 1 751.0 0 2 2 758.0 0 1 1 764.0 0 2 2 766.0 0 1 1 774.0 0 1 1 776.0 0 1 1 779.0 0 1 1 785.0 0 1 1 796.0 0 1 1 805.0 0 1 1 808.0 0 1 1 815.0 0 1 1 819.0 0 1 1 822.0 0 1 1 826.0 0 1 1 828.0 0 1 1 830.0 0 1 1 833.0 0 1 1 856.0 0 1 1 861.0 0 1 1 875.0 0 2 2 887.0 0 1 1 889.0 0 1 1 892.0 0 1 1 902.0 0 1 1 904.0 0 1 1 912.0 0 1 1 920.0 0 2 2 947.0 0 1 1 949.0 0 1 1 951.0 0 1 1 953.0 0 1 1 966.0 0 1 1 976.0 0 1 1 980.0 0 1 1 985.0 0 1 1 993.0 0 1 1 1024.0 0 1 1 1029.0 0 1 1 1030.0 0 1 1 1043.0 0 1 1 1070.0 0 1 1 1076.0 0 1 1 1082.0 0 1 1 1083.0 0 1 1 1102.0 0 1 1 1137.0 0 1 1 1145.0 0 1 1 1147.0 0 1 1 1163.0 0 1 1 1176.0 0 1 1 1177.0 0 2 2 1217.0 0 1 1 1236.0 0 1 1 1285.0 0 1 1 1550.0 0 1 1 1801.0 0 1 1 2287.0 0 1 1 2289.0 0 1 1 2518.0 0 1 1