## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354375.sorted.bam --OUTPUT SRX7354375.markdup.sorted.bam --METRICS_FILE SRX7354375.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: Mon Oct 30 22:21:26 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 63243 32952477 4375797 4806065 50466 12863600 0 0.390759 30304465 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14496272 14496272 2.0 1.337098 3729697 3729697 3.0 1.450734 969500 969500 4.0 1.48904 322086 322086 5.0 1.501953 150377 150377 6.0 1.506306 89034 89034 7.0 1.507773 60261 60261 8.0 1.508268 43239 43239 9.0 1.508435 33090 33090 10.0 1.508491 25571 25571 11.0 1.50851 20636 20636 12.0 1.508516 17004 17004 13.0 1.508519 13985 13985 14.0 1.508519 11823 11823 15.0 1.508519 9885 9885 16.0 1.50852 8593 8593 17.0 1.50852 7508 7508 18.0 1.50852 6644 6644 19.0 1.50852 5733 5733 20.0 1.50852 5092 5092 21.0 1.50852 4710 4710 22.0 1.50852 4038 4038 23.0 1.50852 3699 3699 24.0 1.50852 3313 3313 25.0 1.50852 2916 2916 26.0 1.50852 2720 2720 27.0 1.50852 2500 2500 28.0 1.50852 2300 2300 29.0 1.50852 2044 2044 30.0 1.50852 1910 1910 31.0 1.50852 1793 1793 32.0 1.50852 1604 1604 33.0 1.50852 1465 1465 34.0 1.50852 1316 1316 35.0 1.50852 1311 1311 36.0 1.50852 1187 1187 37.0 1.50852 1104 1104 38.0 1.50852 1071 1071 39.0 1.50852 984 984 40.0 1.50852 894 894 41.0 1.50852 859 859 42.0 1.50852 756 756 43.0 1.50852 782 782 44.0 1.50852 676 676 45.0 1.50852 707 707 46.0 1.50852 640 640 47.0 1.50852 604 604 48.0 1.50852 535 535 49.0 1.50852 524 524 50.0 1.50852 528 528 51.0 1.50852 489 489 52.0 1.50852 460 460 53.0 1.50852 429 429 54.0 1.50852 437 437 55.0 1.50852 398 398 56.0 1.50852 418 418 57.0 1.50852 370 370 58.0 1.50852 354 354 59.0 1.50852 320 320 60.0 1.50852 328 328 61.0 1.50852 303 303 62.0 1.50852 293 293 63.0 1.50852 284 284 64.0 1.50852 302 302 65.0 1.50852 265 265 66.0 1.50852 241 241 67.0 1.50852 247 247 68.0 1.50852 241 241 69.0 1.50852 194 194 70.0 1.50852 206 206 71.0 1.50852 212 212 72.0 1.50852 182 182 73.0 1.50852 206 206 74.0 1.50852 153 153 75.0 1.50852 168 168 76.0 1.50852 178 178 77.0 1.50852 154 154 78.0 1.50852 149 149 79.0 1.50852 163 163 80.0 1.50852 144 144 81.0 1.50852 143 143 82.0 1.50852 138 138 83.0 1.50852 117 117 84.0 1.50852 115 115 85.0 1.50852 125 125 86.0 1.50852 111 111 87.0 1.50852 108 108 88.0 1.50852 105 105 89.0 1.50852 111 111 90.0 1.50852 106 106 91.0 1.50852 99 99 92.0 1.50852 89 89 93.0 1.50852 84 84 94.0 1.50852 89 89 95.0 1.50852 80 80 96.0 1.50852 74 74 97.0 1.50852 64 64 98.0 1.50852 77 77 99.0 1.50852 73 73 100.0 1.50852 71 71 101.0 0 70 70 102.0 0 72 72 103.0 0 59 59 104.0 0 68 68 105.0 0 53 53 106.0 0 59 59 107.0 0 73 73 108.0 0 51 51 109.0 0 51 51 110.0 0 52 52 111.0 0 49 49 112.0 0 57 57 113.0 0 39 39 114.0 0 44 44 115.0 0 51 51 116.0 0 50 50 117.0 0 47 47 118.0 0 36 36 119.0 0 49 49 120.0 0 39 39 121.0 0 47 47 122.0 0 47 47 123.0 0 41 41 124.0 0 33 33 125.0 0 38 38 126.0 0 33 33 127.0 0 22 22 128.0 0 39 39 129.0 0 35 35 130.0 0 35 35 131.0 0 34 34 132.0 0 25 25 133.0 0 24 24 134.0 0 32 32 135.0 0 25 25 136.0 0 27 27 137.0 0 22 22 138.0 0 30 30 139.0 0 21 21 140.0 0 29 29 141.0 0 27 27 142.0 0 25 25 143.0 0 23 23 144.0 0 24 24 145.0 0 20 20 146.0 0 25 25 147.0 0 18 18 148.0 0 21 21 149.0 0 23 23 150.0 0 17 17 151.0 0 19 19 152.0 0 20 20 153.0 0 20 20 154.0 0 15 15 155.0 0 13 13 156.0 0 16 16 157.0 0 15 15 158.0 0 15 15 159.0 0 17 17 160.0 0 22 22 161.0 0 24 24 162.0 0 24 24 163.0 0 16 16 164.0 0 14 14 165.0 0 13 13 166.0 0 11 11 167.0 0 17 17 168.0 0 14 14 169.0 0 8 8 170.0 0 10 10 171.0 0 14 14 172.0 0 17 17 173.0 0 12 12 174.0 0 16 16 175.0 0 14 14 176.0 0 9 9 177.0 0 13 13 178.0 0 17 17 179.0 0 11 11 180.0 0 9 9 181.0 0 7 7 182.0 0 7 7 183.0 0 8 8 184.0 0 12 12 185.0 0 17 17 186.0 0 9 9 187.0 0 5 5 188.0 0 11 11 189.0 0 16 16 190.0 0 7 7 191.0 0 9 9 192.0 0 11 11 193.0 0 5 5 194.0 0 3 3 195.0 0 10 10 196.0 0 9 9 197.0 0 12 12 198.0 0 9 9 199.0 0 8 8 200.0 0 11 11 201.0 0 6 6 202.0 0 4 4 203.0 0 5 5 204.0 0 10 10 205.0 0 6 6 206.0 0 10 10 207.0 0 9 9 208.0 0 4 4 209.0 0 4 4 210.0 0 11 11 211.0 0 8 8 212.0 0 11 11 213.0 0 5 5 214.0 0 7 7 215.0 0 7 7 216.0 0 7 7 217.0 0 6 6 218.0 0 5 5 219.0 0 6 6 220.0 0 5 5 221.0 0 3 3 222.0 0 8 8 223.0 0 8 8 224.0 0 2 2 225.0 0 7 7 226.0 0 3 3 227.0 0 7 7 228.0 0 5 5 229.0 0 8 8 230.0 0 6 6 231.0 0 4 4 232.0 0 1 1 233.0 0 4 4 234.0 0 5 5 235.0 0 5 5 236.0 0 5 5 237.0 0 4 4 238.0 0 7 7 239.0 0 4 4 240.0 0 4 4 241.0 0 4 4 242.0 0 4 4 243.0 0 5 5 244.0 0 7 7 245.0 0 4 4 246.0 0 4 4 247.0 0 3 3 249.0 0 4 4 250.0 0 3 3 251.0 0 4 4 252.0 0 6 6 253.0 0 2 2 254.0 0 4 4 255.0 0 2 2 256.0 0 2 2 257.0 0 1 1 258.0 0 3 3 259.0 0 3 3 260.0 0 2 2 261.0 0 3 3 262.0 0 4 4 263.0 0 2 2 265.0 0 6 6 266.0 0 3 3 267.0 0 5 5 268.0 0 1 1 269.0 0 1 1 270.0 0 3 3 271.0 0 3 3 272.0 0 3 3 273.0 0 2 2 274.0 0 3 3 276.0 0 2 2 277.0 0 2 2 278.0 0 1 1 279.0 0 2 2 280.0 0 1 1 281.0 0 1 1 282.0 0 4 4 283.0 0 1 1 284.0 0 1 1 285.0 0 4 4 288.0 0 2 2 290.0 0 3 3 291.0 0 2 2 293.0 0 3 3 294.0 0 2 2 295.0 0 1 1 296.0 0 2 2 297.0 0 2 2 298.0 0 1 1 300.0 0 2 2 301.0 0 3 3 303.0 0 2 2 304.0 0 1 1 305.0 0 3 3 306.0 0 1 1 308.0 0 2 2 310.0 0 2 2 311.0 0 3 3 312.0 0 1 1 313.0 0 2 2 314.0 0 1 1 316.0 0 2 2 318.0 0 1 1 319.0 0 2 2 320.0 0 1 1 321.0 0 4 4 322.0 0 1 1 323.0 0 1 1 324.0 0 1 1 327.0 0 2 2 328.0 0 2 2 329.0 0 1 1 330.0 0 1 1 331.0 0 1 1 332.0 0 1 1 333.0 0 1 1 336.0 0 3 3 337.0 0 1 1 341.0 0 3 3 342.0 0 1 1 344.0 0 2 2 347.0 0 1 1 348.0 0 1 1 351.0 0 3 3 352.0 0 1 1 354.0 0 1 1 359.0 0 1 1 360.0 0 1 1 363.0 0 1 1 364.0 0 1 1 366.0 0 1 1 367.0 0 4 4 369.0 0 1 1 373.0 0 1 1 374.0 0 1 1 376.0 0 1 1 378.0 0 1 1 379.0 0 1 1 382.0 0 1 1 384.0 0 1 1 385.0 0 1 1 390.0 0 2 2 393.0 0 3 3 396.0 0 1 1 398.0 0 1 1 402.0 0 1 1 403.0 0 1 1 406.0 0 1 1 409.0 0 1 1 414.0 0 1 1 415.0 0 2 2 419.0 0 1 1 422.0 0 2 2 425.0 0 1 1 427.0 0 1 1 429.0 0 1 1 431.0 0 1 1 434.0 0 1 1 445.0 0 1 1 450.0 0 2 2 452.0 0 1 1 453.0 0 1 1 454.0 0 1 1 456.0 0 1 1 458.0 0 1 1 459.0 0 1 1 460.0 0 1 1 477.0 0 2 2 483.0 0 1 1 494.0 0 1 1 502.0 0 1 1 504.0 0 1 1 510.0 0 1 1 517.0 0 1 1 527.0 0 1 1 542.0 0 1 1 549.0 0 1 1 568.0 0 1 1 569.0 0 1 1 570.0 0 1 1 590.0 0 1 1 592.0 0 1 1 605.0 0 1 1 621.0 0 1 1 628.0 0 1 1 666.0 0 1 1 788.0 0 1 1 884.0 0 1 1 897.0 0 1 1 993.0 0 1 1 1206.0 0 1 1 1249.0 0 1 1 1382.0 0 1 1