## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354179.sorted.bam --OUTPUT SRX7354179.markdup.sorted.bam --METRICS_FILE SRX7354179.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 15:32:18 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 50442 36725848 4594315 9214754 38066 10960331 0 0.29875 48557827 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21886619 21886619 2.0 1.469385 2549772 2549772 3.0 1.689707 552461 552461 4.0 1.793123 227992 227992 5.0 1.841665 127744 127744 6.0 1.86445 82887 82887 7.0 1.875144 57682 57682 8.0 1.880164 42560 42560 9.0 1.882521 32640 32640 10.0 1.883627 25538 25538 11.0 1.884146 20743 20743 12.0 1.88439 17147 17147 13.0 1.884504 14325 14325 14.0 1.884558 12011 12011 15.0 1.884583 10193 10193 16.0 1.884595 8911 8911 17.0 1.8846 7850 7850 18.0 1.884603 6836 6836 19.0 1.884604 5840 5840 20.0 1.884605 5362 5362 21.0 1.884605 4787 4787 22.0 1.884605 4372 4372 23.0 1.884605 3762 3762 24.0 1.884605 3483 3483 25.0 1.884605 3213 3213 26.0 1.884605 2978 2978 27.0 1.884605 2666 2666 28.0 1.884605 2455 2455 29.0 1.884605 2204 2204 30.0 1.884605 2061 2061 31.0 1.884605 1964 1964 32.0 1.884605 1753 1753 33.0 1.884605 1678 1678 34.0 1.884605 1518 1518 35.0 1.884605 1473 1473 36.0 1.884605 1420 1420 37.0 1.884605 1237 1237 38.0 1.884605 1173 1173 39.0 1.884605 1037 1037 40.0 1.884605 1058 1058 41.0 1.884605 971 971 42.0 1.884605 863 863 43.0 1.884605 868 868 44.0 1.884605 784 784 45.0 1.884605 737 737 46.0 1.884605 749 749 47.0 1.884605 708 708 48.0 1.884605 686 686 49.0 1.884605 653 653 50.0 1.884605 572 572 51.0 1.884605 592 592 52.0 1.884605 515 515 53.0 1.884605 519 519 54.0 1.884605 476 476 55.0 1.884605 467 467 56.0 1.884605 466 466 57.0 1.884605 440 440 58.0 1.884605 403 403 59.0 1.884605 399 399 60.0 1.884605 426 426 61.0 1.884605 327 327 62.0 1.884605 338 338 63.0 1.884605 345 345 64.0 1.884605 315 315 65.0 1.884605 292 292 66.0 1.884605 276 276 67.0 1.884605 276 276 68.0 1.884605 283 283 69.0 1.884605 262 262 70.0 1.884605 241 241 71.0 1.884605 232 232 72.0 1.884605 207 207 73.0 1.884605 216 216 74.0 1.884605 215 215 75.0 1.884605 210 210 76.0 1.884605 210 210 77.0 1.884605 198 198 78.0 1.884605 181 181 79.0 1.884605 173 173 80.0 1.884605 154 154 81.0 1.884605 177 177 82.0 1.884605 167 167 83.0 1.884605 141 141 84.0 1.884605 148 148 85.0 1.884605 155 155 86.0 1.884605 144 144 87.0 1.884605 136 136 88.0 1.884605 131 131 89.0 1.884605 119 119 90.0 1.884605 132 132 91.0 1.884605 127 127 92.0 1.884605 113 113 93.0 1.884605 129 129 94.0 1.884605 116 116 95.0 1.884605 86 86 96.0 1.884605 98 98 97.0 1.884605 108 108 98.0 1.884605 106 106 99.0 1.884605 77 77 100.0 1.884605 95 95 101.0 0 92 92 102.0 0 81 81 103.0 0 87 87 104.0 0 74 74 105.0 0 87 87 106.0 0 73 73 107.0 0 68 68 108.0 0 82 82 109.0 0 66 66 110.0 0 71 71 111.0 0 74 74 112.0 0 59 59 113.0 0 73 73 114.0 0 78 78 115.0 0 66 66 116.0 0 53 53 117.0 0 78 78 118.0 0 48 48 119.0 0 63 63 120.0 0 61 61 121.0 0 63 63 122.0 0 50 50 123.0 0 53 53 124.0 0 52 52 125.0 0 49 49 126.0 0 49 49 127.0 0 51 51 128.0 0 46 46 129.0 0 33 33 130.0 0 35 35 131.0 0 34 34 132.0 0 44 44 133.0 0 40 40 134.0 0 26 26 135.0 0 37 37 136.0 0 39 39 137.0 0 35 35 138.0 0 36 36 139.0 0 40 40 140.0 0 36 36 141.0 0 30 30 142.0 0 27 27 143.0 0 38 38 144.0 0 24 24 145.0 0 29 29 146.0 0 25 25 147.0 0 26 26 148.0 0 30 30 149.0 0 27 27 150.0 0 32 32 151.0 0 25 25 152.0 0 22 22 153.0 0 29 29 154.0 0 29 29 155.0 0 23 23 156.0 0 29 29 157.0 0 15 15 158.0 0 22 22 159.0 0 26 26 160.0 0 32 32 161.0 0 19 19 162.0 0 18 18 163.0 0 25 25 164.0 0 20 20 165.0 0 16 16 166.0 0 22 22 167.0 0 22 22 168.0 0 24 24 169.0 0 24 24 170.0 0 12 12 171.0 0 25 25 172.0 0 18 18 173.0 0 20 20 174.0 0 15 15 175.0 0 15 15 176.0 0 14 14 177.0 0 11 11 178.0 0 19 19 179.0 0 17 17 180.0 0 12 12 181.0 0 22 22 182.0 0 23 23 183.0 0 16 16 184.0 0 22 22 185.0 0 18 18 186.0 0 18 18 187.0 0 16 16 188.0 0 19 19 189.0 0 19 19 190.0 0 9 9 191.0 0 16 16 192.0 0 19 19 193.0 0 12 12 194.0 0 10 10 195.0 0 14 14 196.0 0 20 20 197.0 0 15 15 198.0 0 11 11 199.0 0 14 14 200.0 0 5 5 201.0 0 6 6 202.0 0 4 4 203.0 0 14 14 204.0 0 12 12 205.0 0 9 9 206.0 0 5 5 207.0 0 11 11 208.0 0 9 9 209.0 0 7 7 210.0 0 13 13 211.0 0 10 10 212.0 0 8 8 213.0 0 9 9 214.0 0 8 8 215.0 0 7 7 216.0 0 9 9 217.0 0 13 13 218.0 0 8 8 219.0 0 4 4 220.0 0 9 9 221.0 0 9 9 222.0 0 8 8 223.0 0 14 14 224.0 0 6 6 225.0 0 7 7 226.0 0 11 11 227.0 0 9 9 228.0 0 3 3 229.0 0 7 7 230.0 0 11 11 231.0 0 5 5 232.0 0 12 12 233.0 0 4 4 234.0 0 1 1 235.0 0 5 5 236.0 0 9 9 237.0 0 12 12 238.0 0 6 6 239.0 0 8 8 240.0 0 6 6 241.0 0 4 4 242.0 0 3 3 243.0 0 7 7 244.0 0 3 3 245.0 0 2 2 246.0 0 12 12 247.0 0 5 5 248.0 0 8 8 249.0 0 8 8 250.0 0 10 10 251.0 0 5 5 252.0 0 9 9 253.0 0 5 5 254.0 0 6 6 255.0 0 6 6 256.0 0 3 3 257.0 0 2 2 258.0 0 5 5 259.0 0 7 7 260.0 0 4 4 261.0 0 8 8 262.0 0 1 1 263.0 0 1 1 264.0 0 4 4 265.0 0 3 3 266.0 0 2 2 267.0 0 3 3 268.0 0 4 4 269.0 0 2 2 270.0 0 5 5 271.0 0 6 6 272.0 0 2 2 273.0 0 4 4 274.0 0 4 4 275.0 0 6 6 276.0 0 5 5 277.0 0 6 6 278.0 0 4 4 279.0 0 4 4 280.0 0 5 5 281.0 0 4 4 282.0 0 6 6 283.0 0 3 3 284.0 0 4 4 285.0 0 4 4 286.0 0 1 1 287.0 0 5 5 288.0 0 3 3 290.0 0 5 5 291.0 0 5 5 292.0 0 3 3 293.0 0 4 4 294.0 0 4 4 295.0 0 3 3 296.0 0 3 3 297.0 0 4 4 298.0 0 2 2 299.0 0 2 2 300.0 0 4 4 301.0 0 3 3 303.0 0 4 4 304.0 0 5 5 305.0 0 1 1 306.0 0 1 1 307.0 0 3 3 308.0 0 2 2 309.0 0 1 1 310.0 0 4 4 311.0 0 2 2 312.0 0 3 3 313.0 0 2 2 314.0 0 4 4 315.0 0 2 2 317.0 0 3 3 318.0 0 1 1 319.0 0 1 1 320.0 0 1 1 321.0 0 3 3 322.0 0 2 2 323.0 0 1 1 324.0 0 1 1 326.0 0 4 4 327.0 0 4 4 328.0 0 5 5 329.0 0 2 2 330.0 0 1 1 331.0 0 3 3 332.0 0 5 5 333.0 0 2 2 334.0 0 4 4 336.0 0 1 1 337.0 0 1 1 338.0 0 3 3 339.0 0 1 1 340.0 0 3 3 341.0 0 3 3 342.0 0 1 1 343.0 0 2 2 344.0 0 1 1 346.0 0 1 1 348.0 0 3 3 349.0 0 2 2 350.0 0 2 2 352.0 0 3 3 353.0 0 2 2 354.0 0 3 3 356.0 0 1 1 357.0 0 2 2 358.0 0 3 3 359.0 0 2 2 360.0 0 1 1 362.0 0 2 2 363.0 0 2 2 364.0 0 1 1 365.0 0 3 3 366.0 0 2 2 367.0 0 1 1 370.0 0 1 1 371.0 0 2 2 372.0 0 3 3 373.0 0 1 1 374.0 0 1 1 375.0 0 1 1 379.0 0 1 1 380.0 0 2 2 382.0 0 4 4 383.0 0 2 2 386.0 0 3 3 389.0 0 4 4 393.0 0 2 2 396.0 0 1 1 399.0 0 1 1 402.0 0 1 1 405.0 0 1 1 406.0 0 1 1 408.0 0 2 2 410.0 0 1 1 411.0 0 1 1 412.0 0 1 1 413.0 0 2 2 415.0 0 1 1 416.0 0 2 2 417.0 0 2 2 421.0 0 1 1 422.0 0 4 4 423.0 0 2 2 424.0 0 1 1 425.0 0 2 2 426.0 0 1 1 427.0 0 1 1 431.0 0 1 1 434.0 0 1 1 436.0 0 1 1 441.0 0 1 1 443.0 0 2 2 444.0 0 2 2 446.0 0 2 2 447.0 0 1 1 449.0 0 1 1 450.0 0 1 1 452.0 0 1 1 453.0 0 1 1 454.0 0 1 1 455.0 0 1 1 458.0 0 2 2 460.0 0 2 2 461.0 0 1 1 466.0 0 1 1 470.0 0 1 1 473.0 0 1 1 475.0 0 1 1 476.0 0 2 2 481.0 0 1 1 487.0 0 1 1 488.0 0 1 1 494.0 0 1 1 505.0 0 1 1 509.0 0 1 1 512.0 0 1 1 514.0 0 1 1 524.0 0 3 3 526.0 0 1 1 528.0 0 1 1 537.0 0 1 1 539.0 0 2 2 541.0 0 1 1 544.0 0 1 1 547.0 0 1 1 551.0 0 1 1 555.0 0 1 1 560.0 0 1 1 563.0 0 1 1 566.0 0 1 1 570.0 0 2 2 576.0 0 1 1 578.0 0 1 1 583.0 0 1 1 597.0 0 1 1 609.0 0 1 1 618.0 0 1 1 639.0 0 1 1 644.0 0 1 1 645.0 0 1 1 653.0 0 1 1 664.0 0 1 1 728.0 0 1 1 739.0 0 1 1 748.0 0 1 1 790.0 0 1 1 828.0 0 1 1 917.0 0 1 1 923.0 0 1 1 924.0 0 1 1 1036.0 0 1 1 1110.0 0 1 1 1710.0 0 1 1