## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354323.sorted.bam --OUTPUT SRX7354323.markdup.sorted.bam --METRICS_FILE SRX7354323.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 22:36:38 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 47157 35977352 5026490 7788733 35572 12443138 0 0.346128 39160416 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19209233 19209233 2.0 1.399031 2820777 2820777 3.0 1.558256 628633 628633 4.0 1.621792 249302 249302 5.0 1.647144 140311 140311 6.0 1.657261 91361 91361 7.0 1.661298 65223 65223 8.0 1.662909 48251 48251 9.0 1.663551 37587 37587 10.0 1.663808 29580 29580 11.0 1.66391 24307 24307 12.0 1.663951 19988 19988 13.0 1.663967 16760 16760 14.0 1.663974 14364 14364 15.0 1.663976 12173 12173 16.0 1.663977 10794 10794 17.0 1.663978 9312 9312 18.0 1.663978 8278 8278 19.0 1.663978 7394 7394 20.0 1.663978 6496 6496 21.0 1.663978 5688 5688 22.0 1.663978 5226 5226 23.0 1.663978 4748 4748 24.0 1.663978 4305 4305 25.0 1.663978 3945 3945 26.0 1.663978 3557 3557 27.0 1.663978 3286 3286 28.0 1.663978 3068 3068 29.0 1.663978 2753 2753 30.0 1.663978 2500 2500 31.0 1.663978 2242 2242 32.0 1.663978 2205 2205 33.0 1.663978 1950 1950 34.0 1.663978 1795 1795 35.0 1.663978 1632 1632 36.0 1.663978 1636 1636 37.0 1.663978 1432 1432 38.0 1.663978 1456 1456 39.0 1.663978 1381 1381 40.0 1.663978 1289 1289 41.0 1.663978 1210 1210 42.0 1.663978 1072 1072 43.0 1.663978 1075 1075 44.0 1.663978 972 972 45.0 1.663978 921 921 46.0 1.663978 902 902 47.0 1.663978 818 818 48.0 1.663978 827 827 49.0 1.663978 734 734 50.0 1.663978 749 749 51.0 1.663978 659 659 52.0 1.663978 628 628 53.0 1.663978 587 587 54.0 1.663978 629 629 55.0 1.663978 559 559 56.0 1.663978 490 490 57.0 1.663978 471 471 58.0 1.663978 506 506 59.0 1.663978 490 490 60.0 1.663978 457 457 61.0 1.663978 378 378 62.0 1.663978 416 416 63.0 1.663978 381 381 64.0 1.663978 374 374 65.0 1.663978 335 335 66.0 1.663978 314 314 67.0 1.663978 319 319 68.0 1.663978 308 308 69.0 1.663978 320 320 70.0 1.663978 319 319 71.0 1.663978 300 300 72.0 1.663978 254 254 73.0 1.663978 219 219 74.0 1.663978 267 267 75.0 1.663978 246 246 76.0 1.663978 215 215 77.0 1.663978 244 244 78.0 1.663978 197 197 79.0 1.663978 214 214 80.0 1.663978 214 214 81.0 1.663978 200 200 82.0 1.663978 184 184 83.0 1.663978 184 184 84.0 1.663978 186 186 85.0 1.663978 171 171 86.0 1.663978 164 164 87.0 1.663978 166 166 88.0 1.663978 162 162 89.0 1.663978 149 149 90.0 1.663978 160 160 91.0 1.663978 134 134 92.0 1.663978 128 128 93.0 1.663978 140 140 94.0 1.663978 125 125 95.0 1.663978 110 110 96.0 1.663978 107 107 97.0 1.663978 111 111 98.0 1.663978 105 105 99.0 1.663978 99 99 100.0 1.663978 96 96 101.0 0 91 91 102.0 0 87 87 103.0 0 100 100 104.0 0 109 109 105.0 0 76 76 106.0 0 84 84 107.0 0 87 87 108.0 0 93 93 109.0 0 80 80 110.0 0 67 67 111.0 0 86 86 112.0 0 81 81 113.0 0 81 81 114.0 0 74 74 115.0 0 66 66 116.0 0 59 59 117.0 0 60 60 118.0 0 75 75 119.0 0 70 70 120.0 0 48 48 121.0 0 65 65 122.0 0 39 39 123.0 0 54 54 124.0 0 55 55 125.0 0 49 49 126.0 0 62 62 127.0 0 51 51 128.0 0 43 43 129.0 0 50 50 130.0 0 51 51 131.0 0 44 44 132.0 0 49 49 133.0 0 46 46 134.0 0 45 45 135.0 0 22 22 136.0 0 41 41 137.0 0 43 43 138.0 0 46 46 139.0 0 35 35 140.0 0 41 41 141.0 0 40 40 142.0 0 34 34 143.0 0 32 32 144.0 0 28 28 145.0 0 34 34 146.0 0 29 29 147.0 0 30 30 148.0 0 31 31 149.0 0 31 31 150.0 0 39 39 151.0 0 33 33 152.0 0 21 21 153.0 0 29 29 154.0 0 24 24 155.0 0 32 32 156.0 0 30 30 157.0 0 28 28 158.0 0 28 28 159.0 0 20 20 160.0 0 32 32 161.0 0 22 22 162.0 0 21 21 163.0 0 20 20 164.0 0 22 22 165.0 0 16 16 166.0 0 24 24 167.0 0 21 21 168.0 0 21 21 169.0 0 19 19 170.0 0 23 23 171.0 0 16 16 172.0 0 18 18 173.0 0 14 14 174.0 0 21 21 175.0 0 27 27 176.0 0 15 15 177.0 0 23 23 178.0 0 19 19 179.0 0 23 23 180.0 0 22 22 181.0 0 13 13 182.0 0 19 19 183.0 0 18 18 184.0 0 16 16 185.0 0 13 13 186.0 0 15 15 187.0 0 12 12 188.0 0 11 11 189.0 0 16 16 190.0 0 12 12 191.0 0 18 18 192.0 0 11 11 193.0 0 8 8 194.0 0 8 8 195.0 0 11 11 196.0 0 11 11 197.0 0 10 10 198.0 0 15 15 199.0 0 11 11 200.0 0 7 7 201.0 0 14 14 202.0 0 9 9 203.0 0 10 10 204.0 0 10 10 205.0 0 10 10 206.0 0 13 13 207.0 0 7 7 208.0 0 14 14 209.0 0 10 10 210.0 0 11 11 211.0 0 6 6 212.0 0 9 9 213.0 0 13 13 214.0 0 13 13 215.0 0 4 4 216.0 0 6 6 217.0 0 6 6 218.0 0 7 7 219.0 0 5 5 220.0 0 9 9 221.0 0 10 10 222.0 0 4 4 223.0 0 8 8 224.0 0 7 7 225.0 0 5 5 226.0 0 11 11 227.0 0 3 3 228.0 0 8 8 229.0 0 13 13 230.0 0 4 4 231.0 0 4 4 232.0 0 7 7 233.0 0 9 9 234.0 0 7 7 235.0 0 10 10 236.0 0 7 7 237.0 0 8 8 238.0 0 10 10 239.0 0 9 9 240.0 0 7 7 241.0 0 5 5 242.0 0 5 5 243.0 0 8 8 244.0 0 11 11 245.0 0 6 6 246.0 0 6 6 247.0 0 11 11 248.0 0 4 4 249.0 0 4 4 250.0 0 5 5 251.0 0 6 6 252.0 0 6 6 253.0 0 5 5 254.0 0 5 5 255.0 0 5 5 256.0 0 4 4 257.0 0 2 2 258.0 0 5 5 259.0 0 5 5 260.0 0 2 2 261.0 0 4 4 262.0 0 3 3 263.0 0 3 3 264.0 0 3 3 265.0 0 4 4 266.0 0 4 4 267.0 0 4 4 268.0 0 2 2 269.0 0 3 3 270.0 0 2 2 271.0 0 1 1 272.0 0 2 2 273.0 0 3 3 274.0 0 5 5 275.0 0 2 2 276.0 0 4 4 277.0 0 2 2 278.0 0 2 2 279.0 0 3 3 280.0 0 1 1 281.0 0 5 5 282.0 0 2 2 283.0 0 8 8 284.0 0 3 3 286.0 0 2 2 287.0 0 5 5 289.0 0 1 1 290.0 0 6 6 291.0 0 4 4 292.0 0 6 6 294.0 0 1 1 295.0 0 1 1 296.0 0 3 3 297.0 0 1 1 298.0 0 5 5 300.0 0 2 2 301.0 0 3 3 302.0 0 2 2 303.0 0 2 2 304.0 0 2 2 305.0 0 1 1 306.0 0 1 1 307.0 0 1 1 308.0 0 2 2 309.0 0 1 1 310.0 0 1 1 311.0 0 2 2 312.0 0 2 2 313.0 0 2 2 314.0 0 1 1 315.0 0 1 1 316.0 0 5 5 317.0 0 3 3 318.0 0 2 2 319.0 0 1 1 320.0 0 4 4 322.0 0 3 3 324.0 0 1 1 325.0 0 1 1 326.0 0 3 3 327.0 0 2 2 328.0 0 2 2 329.0 0 2 2 330.0 0 3 3 332.0 0 1 1 333.0 0 1 1 334.0 0 1 1 335.0 0 2 2 336.0 0 3 3 338.0 0 2 2 341.0 0 3 3 342.0 0 2 2 343.0 0 3 3 345.0 0 3 3 348.0 0 1 1 351.0 0 1 1 352.0 0 1 1 354.0 0 1 1 357.0 0 2 2 358.0 0 2 2 359.0 0 2 2 361.0 0 2 2 362.0 0 1 1 363.0 0 1 1 366.0 0 1 1 367.0 0 1 1 368.0 0 1 1 369.0 0 3 3 370.0 0 2 2 371.0 0 1 1 372.0 0 5 5 374.0 0 1 1 375.0 0 3 3 376.0 0 2 2 378.0 0 2 2 379.0 0 1 1 381.0 0 1 1 387.0 0 1 1 388.0 0 4 4 389.0 0 1 1 391.0 0 1 1 393.0 0 1 1 398.0 0 2 2 399.0 0 1 1 400.0 0 1 1 401.0 0 1 1 403.0 0 1 1 404.0 0 2 2 408.0 0 1 1 413.0 0 1 1 414.0 0 2 2 416.0 0 2 2 417.0 0 1 1 418.0 0 1 1 419.0 0 1 1 421.0 0 1 1 423.0 0 1 1 426.0 0 1 1 427.0 0 1 1 430.0 0 1 1 431.0 0 1 1 432.0 0 1 1 437.0 0 1 1 438.0 0 2 2 440.0 0 1 1 449.0 0 1 1 450.0 0 1 1 452.0 0 1 1 455.0 0 4 4 456.0 0 1 1 457.0 0 1 1 459.0 0 2 2 460.0 0 1 1 463.0 0 1 1 477.0 0 2 2 484.0 0 1 1 485.0 0 1 1 501.0 0 1 1 510.0 0 1 1 512.0 0 1 1 515.0 0 1 1 518.0 0 2 2 525.0 0 1 1 534.0 0 1 1 541.0 0 2 2 550.0 0 2 2 559.0 0 1 1 576.0 0 1 1 595.0 0 1 1 606.0 0 1 1 626.0 0 1 1 631.0 0 1 1 644.0 0 1 1 653.0 0 1 1 676.0 0 1 1 957.0 0 1 1 1099.0 0 1 1 1140.0 0 1 1 1181.0 0 1 1 1396.0 0 1 1