## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354080.sorted.bam --OUTPUT SRX7354080.markdup.sorted.bam --METRICS_FILE SRX7354080.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: Sat Oct 28 15:17:16 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 40512 33968964 4152809 6031544 30183 11481500 0 0.338242 38139430 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19188456 19188456 2.0 1.410388 1984518 1984518 3.0 1.578806 477435 477435 4.0 1.647923 220128 220128 5.0 1.676288 131611 131611 6.0 1.687929 88059 88059 7.0 1.692706 62971 62971 8.0 1.694666 47403 47403 9.0 1.695471 37084 37084 10.0 1.695801 29782 29782 11.0 1.695936 24183 24183 12.0 1.695992 20048 20048 13.0 1.696015 16944 16944 14.0 1.696024 14390 14390 15.0 1.696028 12527 12527 16.0 1.69603 10809 10809 17.0 1.69603 9626 9626 18.0 1.696031 8533 8533 19.0 1.696031 7430 7430 20.0 1.696031 6698 6698 21.0 1.696031 5898 5898 22.0 1.696031 5361 5361 23.0 1.696031 4850 4850 24.0 1.696031 4483 4483 25.0 1.696031 4042 4042 26.0 1.696031 3632 3632 27.0 1.696031 3358 3358 28.0 1.696031 3019 3019 29.0 1.696031 2913 2913 30.0 1.696031 2608 2608 31.0 1.696031 2505 2505 32.0 1.696031 2270 2270 33.0 1.696031 2082 2082 34.0 1.696031 1904 1904 35.0 1.696031 1855 1855 36.0 1.696031 1757 1757 37.0 1.696031 1661 1661 38.0 1.696031 1474 1474 39.0 1.696031 1398 1398 40.0 1.696031 1324 1324 41.0 1.696031 1234 1234 42.0 1.696031 1188 1188 43.0 1.696031 1167 1167 44.0 1.696031 1016 1016 45.0 1.696031 1006 1006 46.0 1.696031 951 951 47.0 1.696031 871 871 48.0 1.696031 862 862 49.0 1.696031 768 768 50.0 1.696031 723 723 51.0 1.696031 737 737 52.0 1.696031 702 702 53.0 1.696031 662 662 54.0 1.696031 618 618 55.0 1.696031 621 621 56.0 1.696031 579 579 57.0 1.696031 535 535 58.0 1.696031 519 519 59.0 1.696031 533 533 60.0 1.696031 475 475 61.0 1.696031 417 417 62.0 1.696031 439 439 63.0 1.696031 435 435 64.0 1.696031 415 415 65.0 1.696031 379 379 66.0 1.696031 328 328 67.0 1.696031 341 341 68.0 1.696031 302 302 69.0 1.696031 320 320 70.0 1.696031 326 326 71.0 1.696031 314 314 72.0 1.696031 324 324 73.0 1.696031 255 255 74.0 1.696031 252 252 75.0 1.696031 240 240 76.0 1.696031 229 229 77.0 1.696031 260 260 78.0 1.696031 234 234 79.0 1.696031 256 256 80.0 1.696031 214 214 81.0 1.696031 212 212 82.0 1.696031 174 174 83.0 1.696031 222 222 84.0 1.696031 181 181 85.0 1.696031 164 164 86.0 1.696031 171 171 87.0 1.696031 162 162 88.0 1.696031 138 138 89.0 1.696031 168 168 90.0 1.696031 163 163 91.0 1.696031 150 150 92.0 1.696031 147 147 93.0 1.696031 167 167 94.0 1.696031 133 133 95.0 1.696031 129 129 96.0 1.696031 128 128 97.0 1.696031 141 141 98.0 1.696031 116 116 99.0 1.696031 119 119 100.0 1.696031 113 113 101.0 0 108 108 102.0 0 112 112 103.0 0 93 93 104.0 0 96 96 105.0 0 115 115 106.0 0 80 80 107.0 0 122 122 108.0 0 93 93 109.0 0 96 96 110.0 0 101 101 111.0 0 89 89 112.0 0 83 83 113.0 0 76 76 114.0 0 71 71 115.0 0 67 67 116.0 0 80 80 117.0 0 63 63 118.0 0 65 65 119.0 0 47 47 120.0 0 71 71 121.0 0 72 72 122.0 0 65 65 123.0 0 73 73 124.0 0 56 56 125.0 0 61 61 126.0 0 63 63 127.0 0 53 53 128.0 0 58 58 129.0 0 62 62 130.0 0 57 57 131.0 0 60 60 132.0 0 59 59 133.0 0 34 34 134.0 0 50 50 135.0 0 53 53 136.0 0 42 42 137.0 0 43 43 138.0 0 60 60 139.0 0 51 51 140.0 0 44 44 141.0 0 43 43 142.0 0 34 34 143.0 0 36 36 144.0 0 27 27 145.0 0 49 49 146.0 0 38 38 147.0 0 40 40 148.0 0 30 30 149.0 0 41 41 150.0 0 40 40 151.0 0 32 32 152.0 0 32 32 153.0 0 25 25 154.0 0 33 33 155.0 0 27 27 156.0 0 26 26 157.0 0 32 32 158.0 0 29 29 159.0 0 28 28 160.0 0 35 35 161.0 0 11 11 162.0 0 31 31 163.0 0 31 31 164.0 0 24 24 165.0 0 32 32 166.0 0 30 30 167.0 0 19 19 168.0 0 16 16 169.0 0 17 17 170.0 0 15 15 171.0 0 28 28 172.0 0 21 21 173.0 0 15 15 174.0 0 16 16 175.0 0 18 18 176.0 0 14 14 177.0 0 11 11 178.0 0 16 16 179.0 0 24 24 180.0 0 20 20 181.0 0 27 27 182.0 0 21 21 183.0 0 29 29 184.0 0 23 23 185.0 0 20 20 186.0 0 19 19 187.0 0 13 13 188.0 0 15 15 189.0 0 18 18 190.0 0 14 14 191.0 0 12 12 192.0 0 17 17 193.0 0 20 20 194.0 0 13 13 195.0 0 12 12 196.0 0 12 12 197.0 0 10 10 198.0 0 14 14 199.0 0 6 6 200.0 0 18 18 201.0 0 12 12 202.0 0 19 19 203.0 0 12 12 204.0 0 13 13 205.0 0 9 9 206.0 0 10 10 207.0 0 21 21 208.0 0 11 11 209.0 0 8 8 210.0 0 18 18 211.0 0 14 14 212.0 0 15 15 213.0 0 10 10 214.0 0 10 10 215.0 0 16 16 216.0 0 16 16 217.0 0 8 8 218.0 0 13 13 219.0 0 11 11 220.0 0 9 9 221.0 0 9 9 222.0 0 7 7 223.0 0 8 8 224.0 0 7 7 225.0 0 8 8 226.0 0 5 5 227.0 0 7 7 228.0 0 9 9 229.0 0 5 5 230.0 0 10 10 231.0 0 7 7 232.0 0 8 8 233.0 0 6 6 234.0 0 6 6 235.0 0 11 11 236.0 0 9 9 237.0 0 8 8 238.0 0 12 12 239.0 0 6 6 240.0 0 8 8 241.0 0 14 14 242.0 0 4 4 243.0 0 8 8 244.0 0 6 6 245.0 0 10 10 246.0 0 6 6 247.0 0 5 5 248.0 0 5 5 249.0 0 4 4 250.0 0 8 8 251.0 0 12 12 252.0 0 4 4 253.0 0 9 9 254.0 0 5 5 255.0 0 8 8 256.0 0 6 6 257.0 0 4 4 258.0 0 4 4 259.0 0 2 2 260.0 0 5 5 261.0 0 6 6 262.0 0 10 10 263.0 0 4 4 264.0 0 4 4 265.0 0 4 4 266.0 0 6 6 267.0 0 5 5 268.0 0 2 2 269.0 0 3 3 270.0 0 3 3 271.0 0 5 5 272.0 0 3 3 273.0 0 4 4 274.0 0 3 3 275.0 0 6 6 276.0 0 3 3 277.0 0 4 4 278.0 0 6 6 279.0 0 3 3 280.0 0 2 2 281.0 0 3 3 282.0 0 3 3 283.0 0 2 2 284.0 0 5 5 285.0 0 3 3 286.0 0 3 3 287.0 0 5 5 288.0 0 4 4 289.0 0 5 5 290.0 0 6 6 291.0 0 4 4 292.0 0 6 6 293.0 0 4 4 294.0 0 4 4 295.0 0 3 3 296.0 0 5 5 297.0 0 4 4 298.0 0 7 7 299.0 0 4 4 300.0 0 4 4 301.0 0 2 2 302.0 0 6 6 303.0 0 1 1 304.0 0 2 2 305.0 0 1 1 306.0 0 3 3 307.0 0 6 6 308.0 0 3 3 309.0 0 2 2 310.0 0 4 4 311.0 0 4 4 312.0 0 7 7 313.0 0 3 3 314.0 0 1 1 315.0 0 2 2 316.0 0 3 3 317.0 0 4 4 318.0 0 5 5 319.0 0 3 3 320.0 0 3 3 322.0 0 2 2 323.0 0 6 6 324.0 0 2 2 325.0 0 7 7 326.0 0 3 3 327.0 0 1 1 328.0 0 1 1 329.0 0 4 4 330.0 0 1 1 331.0 0 4 4 332.0 0 3 3 333.0 0 2 2 335.0 0 1 1 336.0 0 3 3 338.0 0 2 2 339.0 0 2 2 340.0 0 2 2 341.0 0 3 3 342.0 0 2 2 343.0 0 1 1 344.0 0 1 1 346.0 0 2 2 347.0 0 1 1 348.0 0 3 3 349.0 0 6 6 350.0 0 2 2 351.0 0 1 1 352.0 0 2 2 353.0 0 2 2 354.0 0 1 1 355.0 0 2 2 356.0 0 1 1 357.0 0 1 1 358.0 0 1 1 359.0 0 1 1 361.0 0 2 2 363.0 0 1 1 364.0 0 2 2 365.0 0 1 1 366.0 0 1 1 367.0 0 3 3 369.0 0 1 1 372.0 0 2 2 374.0 0 2 2 375.0 0 1 1 376.0 0 1 1 377.0 0 1 1 378.0 0 2 2 379.0 0 2 2 380.0 0 2 2 381.0 0 2 2 382.0 0 3 3 383.0 0 1 1 384.0 0 3 3 385.0 0 3 3 386.0 0 1 1 387.0 0 1 1 388.0 0 4 4 390.0 0 1 1 392.0 0 2 2 394.0 0 2 2 395.0 0 2 2 396.0 0 3 3 397.0 0 3 3 401.0 0 1 1 402.0 0 2 2 404.0 0 3 3 406.0 0 1 1 408.0 0 2 2 412.0 0 3 3 414.0 0 2 2 415.0 0 1 1 416.0 0 1 1 417.0 0 1 1 418.0 0 4 4 422.0 0 1 1 423.0 0 4 4 425.0 0 1 1 426.0 0 2 2 427.0 0 1 1 428.0 0 2 2 429.0 0 1 1 430.0 0 1 1 431.0 0 1 1 433.0 0 1 1 435.0 0 1 1 436.0 0 2 2 437.0 0 1 1 438.0 0 1 1 440.0 0 1 1 441.0 0 2 2 442.0 0 1 1 443.0 0 1 1 447.0 0 1 1 448.0 0 1 1 450.0 0 1 1 452.0 0 1 1 453.0 0 2 2 455.0 0 1 1 458.0 0 2 2 459.0 0 1 1 460.0 0 2 2 461.0 0 1 1 463.0 0 2 2 465.0 0 1 1 466.0 0 2 2 467.0 0 1 1 469.0 0 1 1 471.0 0 2 2 474.0 0 2 2 477.0 0 1 1 480.0 0 1 1 481.0 0 2 2 485.0 0 1 1 486.0 0 1 1 487.0 0 1 1 488.0 0 1 1 490.0 0 1 1 497.0 0 1 1 499.0 0 1 1 500.0 0 1 1 512.0 0 1 1 525.0 0 1 1 539.0 0 1 1 540.0 0 1 1 541.0 0 1 1 547.0 0 1 1 553.0 0 1 1 554.0 0 1 1 557.0 0 1 1 563.0 0 1 1 568.0 0 1 1 572.0 0 2 2 587.0 0 1 1 589.0 0 1 1 590.0 0 1 1 597.0 0 1 1 616.0 0 1 1 630.0 0 1 1 640.0 0 2 2 647.0 0 1 1 650.0 0 1 1 656.0 0 1 1 662.0 0 1 1 665.0 0 1 1 689.0 0 1 1 716.0 0 1 1 727.0 0 1 1 728.0 0 1 1 751.0 0 1 1 831.0 0 1 1 863.0 0 1 1 962.0 0 1 1 991.0 0 1 1 1235.0 0 1 1