## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354334.sorted.bam --OUTPUT SRX7354334.markdup.sorted.bam --METRICS_FILE SRX7354334.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 21:42:29 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 64655 34122885 14295749 8477015 52011 16051061 0 0.470706 23672101 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 11027954 11027954 2.0 1.236577 4308556 4308556 3.0 1.292546 1487177 1487177 4.0 1.305787 525666 525666 5.0 1.308919 223465 223465 6.0 1.30966 118331 118331 7.0 1.309836 74473 74473 8.0 1.309877 51999 51999 9.0 1.309887 39072 39072 10.0 1.309889 29627 29627 11.0 1.30989 23619 23619 12.0 1.30989 18951 18951 13.0 1.30989 15510 15510 14.0 1.30989 13176 13176 15.0 1.30989 11161 11161 16.0 1.30989 9521 9521 17.0 1.30989 8305 8305 18.0 1.30989 7023 7023 19.0 1.30989 6299 6299 20.0 1.30989 5518 5518 21.0 1.30989 4914 4914 22.0 1.30989 4503 4503 23.0 1.30989 3875 3875 24.0 1.30989 3471 3471 25.0 1.30989 3098 3098 26.0 1.30989 2881 2881 27.0 1.30989 2688 2688 28.0 1.30989 2475 2475 29.0 1.30989 2154 2154 30.0 1.30989 2062 2062 31.0 1.30989 1931 1931 32.0 1.30989 1677 1677 33.0 1.30989 1606 1606 34.0 1.30989 1509 1509 35.0 1.30989 1339 1339 36.0 1.30989 1273 1273 37.0 1.30989 1169 1169 38.0 1.30989 1090 1090 39.0 1.30989 988 988 40.0 1.30989 948 948 41.0 1.30989 861 861 42.0 1.30989 824 824 43.0 1.30989 797 797 44.0 1.30989 769 769 45.0 1.30989 720 720 46.0 1.30989 658 658 47.0 1.30989 613 613 48.0 1.30989 578 578 49.0 1.30989 537 537 50.0 1.30989 542 542 51.0 1.30989 533 533 52.0 1.30989 502 502 53.0 1.30989 472 472 54.0 1.30989 440 440 55.0 1.30989 416 416 56.0 1.30989 366 366 57.0 1.30989 395 395 58.0 1.30989 360 360 59.0 1.30989 358 358 60.0 1.30989 334 334 61.0 1.30989 310 310 62.0 1.30989 304 304 63.0 1.30989 296 296 64.0 1.30989 296 296 65.0 1.30989 302 302 66.0 1.30989 236 236 67.0 1.30989 231 231 68.0 1.30989 230 230 69.0 1.30989 228 228 70.0 1.30989 212 212 71.0 1.30989 171 171 72.0 1.30989 225 225 73.0 1.30989 168 168 74.0 1.30989 166 166 75.0 1.30989 179 179 76.0 1.30989 170 170 77.0 1.30989 149 149 78.0 1.30989 133 133 79.0 1.30989 172 172 80.0 1.30989 143 143 81.0 1.30989 136 136 82.0 1.30989 129 129 83.0 1.30989 129 129 84.0 1.30989 169 169 85.0 1.30989 132 132 86.0 1.30989 121 121 87.0 1.30989 107 107 88.0 1.30989 108 108 89.0 1.30989 100 100 90.0 1.30989 93 93 91.0 1.30989 109 109 92.0 1.30989 95 95 93.0 1.30989 103 103 94.0 1.30989 114 114 95.0 1.30989 101 101 96.0 1.30989 88 88 97.0 1.30989 101 101 98.0 1.30989 83 83 99.0 1.30989 75 75 100.0 1.30989 73 73 101.0 0 83 83 102.0 0 71 71 103.0 0 64 64 104.0 0 57 57 105.0 0 62 62 106.0 0 47 47 107.0 0 78 78 108.0 0 53 53 109.0 0 63 63 110.0 0 62 62 111.0 0 49 49 112.0 0 61 61 113.0 0 49 49 114.0 0 48 48 115.0 0 47 47 116.0 0 43 43 117.0 0 50 50 118.0 0 48 48 119.0 0 51 51 120.0 0 42 42 121.0 0 45 45 122.0 0 51 51 123.0 0 44 44 124.0 0 35 35 125.0 0 31 31 126.0 0 33 33 127.0 0 45 45 128.0 0 26 26 129.0 0 26 26 130.0 0 28 28 131.0 0 23 23 132.0 0 41 41 133.0 0 33 33 134.0 0 38 38 135.0 0 40 40 136.0 0 34 34 137.0 0 33 33 138.0 0 26 26 139.0 0 27 27 140.0 0 26 26 141.0 0 18 18 142.0 0 26 26 143.0 0 25 25 144.0 0 24 24 145.0 0 22 22 146.0 0 27 27 147.0 0 14 14 148.0 0 29 29 149.0 0 21 21 150.0 0 27 27 151.0 0 18 18 152.0 0 17 17 153.0 0 10 10 154.0 0 15 15 155.0 0 16 16 156.0 0 19 19 157.0 0 16 16 158.0 0 18 18 159.0 0 19 19 160.0 0 18 18 161.0 0 14 14 162.0 0 15 15 163.0 0 17 17 164.0 0 15 15 165.0 0 19 19 166.0 0 15 15 167.0 0 7 7 168.0 0 14 14 169.0 0 15 15 170.0 0 13 13 171.0 0 19 19 172.0 0 10 10 173.0 0 5 5 174.0 0 9 9 175.0 0 12 12 176.0 0 6 6 177.0 0 12 12 178.0 0 12 12 179.0 0 10 10 180.0 0 13 13 181.0 0 10 10 182.0 0 10 10 183.0 0 15 15 184.0 0 9 9 185.0 0 9 9 186.0 0 9 9 187.0 0 12 12 188.0 0 12 12 189.0 0 9 9 190.0 0 6 6 191.0 0 13 13 192.0 0 12 12 193.0 0 10 10 194.0 0 13 13 195.0 0 7 7 196.0 0 13 13 197.0 0 8 8 198.0 0 7 7 199.0 0 2 2 200.0 0 7 7 201.0 0 6 6 202.0 0 9 9 203.0 0 1 1 204.0 0 7 7 205.0 0 8 8 206.0 0 5 5 207.0 0 3 3 208.0 0 6 6 209.0 0 6 6 210.0 0 8 8 211.0 0 9 9 212.0 0 7 7 213.0 0 7 7 214.0 0 8 8 215.0 0 8 8 216.0 0 2 2 217.0 0 6 6 218.0 0 8 8 219.0 0 11 11 220.0 0 4 4 221.0 0 8 8 222.0 0 9 9 223.0 0 4 4 224.0 0 6 6 225.0 0 7 7 226.0 0 5 5 227.0 0 8 8 228.0 0 7 7 229.0 0 2 2 230.0 0 1 1 231.0 0 8 8 232.0 0 3 3 233.0 0 4 4 234.0 0 4 4 235.0 0 1 1 236.0 0 5 5 237.0 0 7 7 238.0 0 4 4 239.0 0 5 5 240.0 0 5 5 241.0 0 7 7 242.0 0 3 3 243.0 0 1 1 244.0 0 3 3 245.0 0 4 4 246.0 0 2 2 247.0 0 5 5 248.0 0 3 3 249.0 0 4 4 250.0 0 3 3 251.0 0 4 4 252.0 0 3 3 253.0 0 3 3 254.0 0 3 3 255.0 0 3 3 256.0 0 3 3 257.0 0 1 1 258.0 0 8 8 259.0 0 2 2 260.0 0 1 1 261.0 0 3 3 262.0 0 6 6 263.0 0 4 4 264.0 0 2 2 265.0 0 4 4 266.0 0 3 3 267.0 0 3 3 268.0 0 3 3 269.0 0 1 1 270.0 0 2 2 271.0 0 3 3 272.0 0 4 4 273.0 0 4 4 274.0 0 2 2 275.0 0 2 2 276.0 0 1 1 277.0 0 1 1 278.0 0 2 2 279.0 0 3 3 280.0 0 2 2 281.0 0 2 2 282.0 0 1 1 283.0 0 2 2 284.0 0 1 1 285.0 0 2 2 286.0 0 1 1 287.0 0 2 2 288.0 0 4 4 289.0 0 3 3 290.0 0 6 6 293.0 0 1 1 294.0 0 1 1 295.0 0 2 2 296.0 0 2 2 297.0 0 4 4 298.0 0 3 3 299.0 0 2 2 300.0 0 2 2 303.0 0 3 3 305.0 0 1 1 306.0 0 3 3 307.0 0 2 2 308.0 0 1 1 309.0 0 2 2 310.0 0 2 2 311.0 0 3 3 312.0 0 2 2 313.0 0 1 1 314.0 0 1 1 316.0 0 2 2 317.0 0 3 3 318.0 0 1 1 319.0 0 2 2 320.0 0 1 1 321.0 0 1 1 322.0 0 3 3 325.0 0 1 1 327.0 0 2 2 328.0 0 1 1 330.0 0 1 1 331.0 0 1 1 332.0 0 2 2 333.0 0 1 1 334.0 0 1 1 337.0 0 1 1 339.0 0 2 2 340.0 0 1 1 341.0 0 1 1 344.0 0 1 1 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