## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354083.sorted.bam --OUTPUT SRX7354083.markdup.sorted.bam --METRICS_FILE SRX7354083.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 16:58:08 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 24463 30464423 3683392 2290827 18005 10633585 0 0.349205 32748913 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16745622 16745622 2.0 1.394458 1848047 1848047 3.0 1.550055 459525 459525 4.0 1.611432 210611 210611 5.0 1.635642 124316 124316 6.0 1.645192 82521 82521 7.0 1.64896 58636 58636 8.0 1.650445 44134 44134 9.0 1.651032 33848 33848 10.0 1.651263 26684 26684 11.0 1.651354 22124 22124 12.0 1.65139 18371 18371 13.0 1.651404 15311 15311 14.0 1.65141 12977 12977 15.0 1.651412 11111 11111 16.0 1.651413 9880 9880 17.0 1.651413 8456 8456 18.0 1.651413 7380 7380 19.0 1.651413 6434 6434 20.0 1.651413 6001 6001 21.0 1.651413 5156 5156 22.0 1.651413 4885 4885 23.0 1.651413 4317 4317 24.0 1.651413 3828 3828 25.0 1.651413 3452 3452 26.0 1.651413 3159 3159 27.0 1.651413 2883 2883 28.0 1.651413 2613 2613 29.0 1.651413 2565 2565 30.0 1.651413 2285 2285 31.0 1.651413 2165 2165 32.0 1.651413 1954 1954 33.0 1.651413 1892 1892 34.0 1.651413 1729 1729 35.0 1.651413 1641 1641 36.0 1.651413 1446 1446 37.0 1.651413 1333 1333 38.0 1.651413 1337 1337 39.0 1.651413 1233 1233 40.0 1.651413 1171 1171 41.0 1.651413 1108 1108 42.0 1.651413 1011 1011 43.0 1.651413 973 973 44.0 1.651413 969 969 45.0 1.651413 867 867 46.0 1.651413 846 846 47.0 1.651413 786 786 48.0 1.651413 717 717 49.0 1.651413 709 709 50.0 1.651413 616 616 51.0 1.651413 666 666 52.0 1.651413 643 643 53.0 1.651413 605 605 54.0 1.651413 558 558 55.0 1.651413 498 498 56.0 1.651413 510 510 57.0 1.651413 479 479 58.0 1.651413 496 496 59.0 1.651413 440 440 60.0 1.651413 441 441 61.0 1.651413 406 406 62.0 1.651413 363 363 63.0 1.651413 394 394 64.0 1.651413 344 344 65.0 1.651413 335 335 66.0 1.651413 323 323 67.0 1.651413 323 323 68.0 1.651413 282 282 69.0 1.651413 275 275 70.0 1.651413 303 303 71.0 1.651413 282 282 72.0 1.651413 259 259 73.0 1.651413 277 277 74.0 1.651413 233 233 75.0 1.651413 244 244 76.0 1.651413 221 221 77.0 1.651413 208 208 78.0 1.651413 203 203 79.0 1.651413 179 179 80.0 1.651413 210 210 81.0 1.651413 219 219 82.0 1.651413 180 180 83.0 1.651413 193 193 84.0 1.651413 170 170 85.0 1.651413 150 150 86.0 1.651413 146 146 87.0 1.651413 145 145 88.0 1.651413 174 174 89.0 1.651413 159 159 90.0 1.651413 133 133 91.0 1.651413 127 127 92.0 1.651413 140 140 93.0 1.651413 129 129 94.0 1.651413 133 133 95.0 1.651413 119 119 96.0 1.651413 131 131 97.0 1.651413 141 141 98.0 1.651413 108 108 99.0 1.651413 120 120 100.0 1.651413 110 110 101.0 0 111 111 102.0 0 112 112 103.0 0 91 91 104.0 0 84 84 105.0 0 73 73 106.0 0 98 98 107.0 0 112 112 108.0 0 81 81 109.0 0 73 73 110.0 0 98 98 111.0 0 70 70 112.0 0 80 80 113.0 0 85 85 114.0 0 75 75 115.0 0 85 85 116.0 0 74 74 117.0 0 64 64 118.0 0 57 57 119.0 0 59 59 120.0 0 70 70 121.0 0 55 55 122.0 0 57 57 123.0 0 53 53 124.0 0 59 59 125.0 0 58 58 126.0 0 69 69 127.0 0 67 67 128.0 0 49 49 129.0 0 56 56 130.0 0 51 51 131.0 0 61 61 132.0 0 53 53 133.0 0 49 49 134.0 0 47 47 135.0 0 55 55 136.0 0 47 47 137.0 0 34 34 138.0 0 37 37 139.0 0 30 30 140.0 0 42 42 141.0 0 41 41 142.0 0 41 41 143.0 0 34 34 144.0 0 42 42 145.0 0 39 39 146.0 0 34 34 147.0 0 31 31 148.0 0 31 31 149.0 0 39 39 150.0 0 33 33 151.0 0 31 31 152.0 0 34 34 153.0 0 33 33 154.0 0 33 33 155.0 0 30 30 156.0 0 27 27 157.0 0 37 37 158.0 0 32 32 159.0 0 24 24 160.0 0 35 35 161.0 0 27 27 162.0 0 29 29 163.0 0 30 30 164.0 0 21 21 165.0 0 25 25 166.0 0 29 29 167.0 0 25 25 168.0 0 19 19 169.0 0 23 23 170.0 0 22 22 171.0 0 22 22 172.0 0 18 18 173.0 0 23 23 174.0 0 26 26 175.0 0 20 20 176.0 0 26 26 177.0 0 30 30 178.0 0 23 23 179.0 0 23 23 180.0 0 16 16 181.0 0 14 14 182.0 0 17 17 183.0 0 20 20 184.0 0 18 18 185.0 0 11 11 186.0 0 16 16 187.0 0 18 18 188.0 0 13 13 189.0 0 17 17 190.0 0 13 13 191.0 0 22 22 192.0 0 20 20 193.0 0 17 17 194.0 0 13 13 195.0 0 16 16 196.0 0 13 13 197.0 0 19 19 198.0 0 16 16 199.0 0 22 22 200.0 0 17 17 201.0 0 16 16 202.0 0 11 11 203.0 0 11 11 204.0 0 15 15 205.0 0 8 8 206.0 0 13 13 207.0 0 10 10 208.0 0 12 12 209.0 0 11 11 210.0 0 11 11 211.0 0 14 14 212.0 0 12 12 213.0 0 11 11 214.0 0 11 11 215.0 0 4 4 216.0 0 8 8 217.0 0 10 10 218.0 0 8 8 219.0 0 5 5 220.0 0 6 6 221.0 0 10 10 222.0 0 11 11 223.0 0 11 11 224.0 0 13 13 225.0 0 11 11 226.0 0 5 5 227.0 0 10 10 228.0 0 12 12 229.0 0 8 8 230.0 0 7 7 231.0 0 11 11 232.0 0 10 10 233.0 0 7 7 234.0 0 5 5 235.0 0 10 10 236.0 0 5 5 237.0 0 8 8 238.0 0 9 9 239.0 0 5 5 240.0 0 8 8 241.0 0 8 8 242.0 0 7 7 243.0 0 6 6 244.0 0 8 8 245.0 0 10 10 246.0 0 6 6 247.0 0 4 4 248.0 0 5 5 249.0 0 3 3 250.0 0 5 5 251.0 0 5 5 252.0 0 12 12 253.0 0 8 8 254.0 0 7 7 255.0 0 4 4 256.0 0 5 5 257.0 0 8 8 258.0 0 3 3 259.0 0 7 7 260.0 0 8 8 261.0 0 2 2 262.0 0 9 9 263.0 0 4 4 264.0 0 5 5 265.0 0 8 8 266.0 0 3 3 267.0 0 2 2 268.0 0 5 5 269.0 0 6 6 270.0 0 8 8 271.0 0 6 6 272.0 0 4 4 273.0 0 3 3 274.0 0 3 3 275.0 0 5 5 276.0 0 4 4 277.0 0 8 8 278.0 0 5 5 279.0 0 7 7 280.0 0 8 8 281.0 0 3 3 282.0 0 4 4 283.0 0 6 6 284.0 0 3 3 285.0 0 6 6 286.0 0 3 3 287.0 0 3 3 288.0 0 2 2 289.0 0 3 3 290.0 0 8 8 291.0 0 3 3 292.0 0 4 4 293.0 0 5 5 294.0 0 5 5 295.0 0 6 6 296.0 0 3 3 297.0 0 8 8 298.0 0 4 4 299.0 0 8 8 300.0 0 9 9 301.0 0 4 4 302.0 0 2 2 303.0 0 4 4 304.0 0 3 3 305.0 0 2 2 306.0 0 8 8 307.0 0 4 4 308.0 0 5 5 309.0 0 7 7 310.0 0 3 3 311.0 0 4 4 312.0 0 4 4 313.0 0 4 4 314.0 0 5 5 315.0 0 2 2 316.0 0 1 1 317.0 0 3 3 318.0 0 4 4 320.0 0 4 4 321.0 0 4 4 322.0 0 4 4 323.0 0 2 2 324.0 0 1 1 325.0 0 4 4 326.0 0 4 4 327.0 0 2 2 328.0 0 1 1 330.0 0 4 4 331.0 0 3 3 332.0 0 4 4 333.0 0 5 5 334.0 0 2 2 335.0 0 4 4 336.0 0 2 2 337.0 0 6 6 338.0 0 1 1 340.0 0 1 1 342.0 0 1 1 343.0 0 2 2 345.0 0 2 2 346.0 0 1 1 347.0 0 1 1 348.0 0 3 3 349.0 0 2 2 350.0 0 3 3 351.0 0 1 1 352.0 0 5 5 353.0 0 3 3 354.0 0 2 2 355.0 0 1 1 356.0 0 1 1 357.0 0 3 3 358.0 0 7 7 362.0 0 1 1 363.0 0 6 6 364.0 0 2 2 365.0 0 1 1 366.0 0 5 5 367.0 0 1 1 368.0 0 2 2 369.0 0 3 3 370.0 0 3 3 371.0 0 4 4 372.0 0 2 2 375.0 0 3 3 376.0 0 2 2 377.0 0 2 2 378.0 0 2 2 379.0 0 1 1 380.0 0 4 4 381.0 0 1 1 382.0 0 1 1 383.0 0 4 4 385.0 0 4 4 386.0 0 2 2 388.0 0 1 1 389.0 0 1 1 390.0 0 2 2 392.0 0 1 1 393.0 0 1 1 394.0 0 1 1 395.0 0 1 1 396.0 0 1 1 398.0 0 1 1 399.0 0 3 3 401.0 0 2 2 402.0 0 1 1 403.0 0 1 1 404.0 0 2 2 406.0 0 1 1 407.0 0 1 1 408.0 0 1 1 409.0 0 2 2 410.0 0 1 1 411.0 0 2 2 414.0 0 3 3 415.0 0 2 2 417.0 0 2 2 418.0 0 1 1 419.0 0 1 1 420.0 0 1 1 421.0 0 1 1 423.0 0 1 1 424.0 0 1 1 425.0 0 3 3 426.0 0 1 1 428.0 0 1 1 429.0 0 2 2 431.0 0 2 2 433.0 0 1 1 434.0 0 1 1 436.0 0 1 1 437.0 0 2 2 438.0 0 2 2 439.0 0 1 1 440.0 0 1 1 442.0 0 3 3 444.0 0 1 1 446.0 0 2 2 447.0 0 1 1 449.0 0 1 1 450.0 0 2 2 451.0 0 2 2 457.0 0 1 1 458.0 0 1 1 459.0 0 2 2 460.0 0 2 2 464.0 0 1 1 466.0 0 1 1 467.0 0 1 1 470.0 0 1 1 471.0 0 1 1 476.0 0 1 1 481.0 0 3 3 488.0 0 1 1 490.0 0 1 1 494.0 0 1 1 498.0 0 1 1 501.0 0 1 1 505.0 0 3 3 508.0 0 1 1 512.0 0 1 1 515.0 0 1 1 519.0 0 1 1 520.0 0 2 2 522.0 0 1 1 523.0 0 1 1 524.0 0 1 1 525.0 0 1 1 527.0 0 1 1 528.0 0 1 1 529.0 0 1 1 534.0 0 1 1 538.0 0 1 1 539.0 0 1 1 540.0 0 1 1 544.0 0 2 2 546.0 0 1 1 549.0 0 2 2 551.0 0 1 1 553.0 0 1 1 554.0 0 1 1 558.0 0 1 1 565.0 0 1 1 566.0 0 2 2 567.0 0 1 1 569.0 0 1 1 571.0 0 1 1 574.0 0 1 1 577.0 0 1 1 582.0 0 1 1 588.0 0 1 1 591.0 0 2 2 593.0 0 1 1 599.0 0 1 1 607.0 0 1 1 617.0 0 1 1 623.0 0 1 1 632.0 0 1 1 634.0 0 1 1 637.0 0 1 1 644.0 0 1 1 654.0 0 1 1 655.0 0 1 1 662.0 0 1 1 685.0 0 1 1 694.0 0 1 1 699.0 0 1 1 701.0 0 1 1 730.0 0 1 1 731.0 0 1 1 735.0 0 1 1 739.0 0 1 1 749.0 0 1 1 758.0 0 1 1 760.0 0 1 1 766.0 0 1 1 775.0 0 1 1 778.0 0 1 1 781.0 0 1 1 816.0 0 1 1 827.0 0 1 1 837.0 0 1 1 859.0 0 1 1 880.0 0 1 1 882.0 0 1 1 891.0 0 1 1 1014.0 0 1 1 1030.0 0 1 1 1050.0 0 1 1 1175.0 0 1 1 1351.0 0 1 1 1764.0 0 1 1