## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354084.sorted.bam --OUTPUT SRX7354084.markdup.sorted.bam --METRICS_FILE SRX7354084.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 17:02:40 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 52660 34570775 4505076 6384848 42701 14207731 0 0.41128 29504812 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 13942283 13942283 2.0 1.30984 4193333 4193333 3.0 1.405841 1208107 1208107 4.0 1.435586 399568 399568 5.0 1.444802 174409 174409 6.0 1.447657 98833 98833 7.0 1.448542 65454 65454 8.0 1.448816 46203 46203 9.0 1.448901 35121 35121 10.0 1.448927 27170 27170 11.0 1.448936 21792 21792 12.0 1.448938 17688 17688 13.0 1.448939 14283 14283 14.0 1.448939 12168 12168 15.0 1.448939 10322 10322 16.0 1.448939 9027 9027 17.0 1.448939 7746 7746 18.0 1.448939 6654 6654 19.0 1.448939 5910 5910 20.0 1.448939 5335 5335 21.0 1.448939 4684 4684 22.0 1.448939 4129 4129 23.0 1.448939 3695 3695 24.0 1.448939 3241 3241 25.0 1.448939 3027 3027 26.0 1.448939 2691 2691 27.0 1.448939 2466 2466 28.0 1.448939 2309 2309 29.0 1.448939 2064 2064 30.0 1.448939 1898 1898 31.0 1.448939 1705 1705 32.0 1.448939 1693 1693 33.0 1.448939 1402 1402 34.0 1.448939 1381 1381 35.0 1.448939 1280 1280 36.0 1.448939 1165 1165 37.0 1.448939 1088 1088 38.0 1.448939 1014 1014 39.0 1.448939 969 969 40.0 1.448939 932 932 41.0 1.448939 884 884 42.0 1.448939 809 809 43.0 1.448939 778 778 44.0 1.448939 664 664 45.0 1.448939 720 720 46.0 1.448939 620 620 47.0 1.448939 600 600 48.0 1.448939 552 552 49.0 1.448939 506 506 50.0 1.448939 540 540 51.0 1.448939 465 465 52.0 1.448939 430 430 53.0 1.448939 383 383 54.0 1.448939 389 389 55.0 1.448939 368 368 56.0 1.448939 334 334 57.0 1.448939 330 330 58.0 1.448939 314 314 59.0 1.448939 322 322 60.0 1.448939 291 291 61.0 1.448939 276 276 62.0 1.448939 249 249 63.0 1.448939 253 253 64.0 1.448939 220 220 65.0 1.448939 251 251 66.0 1.448939 242 242 67.0 1.448939 197 197 68.0 1.448939 223 223 69.0 1.448939 200 200 70.0 1.448939 202 202 71.0 1.448939 180 180 72.0 1.448939 188 188 73.0 1.448939 174 174 74.0 1.448939 162 162 75.0 1.448939 159 159 76.0 1.448939 126 126 77.0 1.448939 150 150 78.0 1.448939 149 149 79.0 1.448939 139 139 80.0 1.448939 133 133 81.0 1.448939 142 142 82.0 1.448939 118 118 83.0 1.448939 94 94 84.0 1.448939 117 117 85.0 1.448939 108 108 86.0 1.448939 100 100 87.0 1.448939 117 117 88.0 1.448939 104 104 89.0 1.448939 87 87 90.0 1.448939 87 87 91.0 1.448939 81 81 92.0 1.448939 75 75 93.0 1.448939 90 90 94.0 1.448939 71 71 95.0 1.448939 73 73 96.0 1.448939 73 73 97.0 1.448939 84 84 98.0 1.448939 70 70 99.0 1.448939 80 80 100.0 1.448939 57 57 101.0 0 68 68 102.0 0 67 67 103.0 0 49 49 104.0 0 42 42 105.0 0 54 54 106.0 0 44 44 107.0 0 58 58 108.0 0 55 55 109.0 0 41 41 110.0 0 55 55 111.0 0 50 50 112.0 0 55 55 113.0 0 48 48 114.0 0 45 45 115.0 0 44 44 116.0 0 48 48 117.0 0 45 45 118.0 0 49 49 119.0 0 40 40 120.0 0 39 39 121.0 0 30 30 122.0 0 28 28 123.0 0 52 52 124.0 0 35 35 125.0 0 32 32 126.0 0 33 33 127.0 0 39 39 128.0 0 33 33 129.0 0 24 24 130.0 0 26 26 131.0 0 23 23 132.0 0 24 24 133.0 0 31 31 134.0 0 25 25 135.0 0 33 33 136.0 0 26 26 137.0 0 30 30 138.0 0 25 25 139.0 0 18 18 140.0 0 21 21 141.0 0 17 17 142.0 0 21 21 143.0 0 27 27 144.0 0 24 24 145.0 0 25 25 146.0 0 17 17 147.0 0 20 20 148.0 0 13 13 149.0 0 19 19 150.0 0 15 15 151.0 0 19 19 152.0 0 11 11 153.0 0 13 13 154.0 0 13 13 155.0 0 9 9 156.0 0 15 15 157.0 0 16 16 158.0 0 8 8 159.0 0 13 13 160.0 0 15 15 161.0 0 16 16 162.0 0 19 19 163.0 0 16 16 164.0 0 11 11 165.0 0 18 18 166.0 0 12 12 167.0 0 18 18 168.0 0 15 15 169.0 0 13 13 170.0 0 7 7 171.0 0 16 16 172.0 0 12 12 173.0 0 14 14 174.0 0 11 11 175.0 0 14 14 176.0 0 10 10 177.0 0 7 7 178.0 0 10 10 179.0 0 21 21 180.0 0 10 10 181.0 0 5 5 182.0 0 15 15 183.0 0 8 8 184.0 0 5 5 185.0 0 9 9 186.0 0 8 8 187.0 0 3 3 188.0 0 8 8 189.0 0 10 10 190.0 0 7 7 191.0 0 9 9 192.0 0 12 12 193.0 0 9 9 194.0 0 7 7 195.0 0 4 4 196.0 0 6 6 197.0 0 3 3 198.0 0 10 10 199.0 0 6 6 200.0 0 7 7 201.0 0 2 2 202.0 0 10 10 203.0 0 9 9 204.0 0 9 9 205.0 0 3 3 206.0 0 5 5 207.0 0 10 10 208.0 0 4 4 209.0 0 10 10 210.0 0 12 12 211.0 0 13 13 212.0 0 3 3 213.0 0 7 7 214.0 0 2 2 215.0 0 3 3 216.0 0 7 7 217.0 0 3 3 218.0 0 7 7 219.0 0 6 6 220.0 0 5 5 221.0 0 3 3 222.0 0 2 2 223.0 0 7 7 224.0 0 4 4 225.0 0 5 5 226.0 0 7 7 227.0 0 4 4 228.0 0 3 3 229.0 0 7 7 230.0 0 5 5 231.0 0 4 4 232.0 0 1 1 233.0 0 5 5 234.0 0 4 4 235.0 0 1 1 236.0 0 5 5 237.0 0 4 4 238.0 0 7 7 239.0 0 4 4 240.0 0 3 3 241.0 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1 353.0 0 1 1 355.0 0 1 1 356.0 0 2 2 360.0 0 1 1 367.0 0 1 1 369.0 0 1 1 375.0 0 1 1 378.0 0 1 1 379.0 0 1 1 385.0 0 1 1 389.0 0 3 3 393.0 0 1 1 394.0 0 1 1 397.0 0 1 1 398.0 0 1 1 401.0 0 1 1 402.0 0 1 1 407.0 0 3 3 408.0 0 1 1 409.0 0 2 2 413.0 0 1 1 415.0 0 1 1 416.0 0 1 1 417.0 0 1 1 419.0 0 1 1 420.0 0 1 1 422.0 0 1 1 423.0 0 1 1 436.0 0 1 1 441.0 0 2 2 444.0 0 1 1 448.0 0 1 1 449.0 0 1 1 453.0 0 1 1 457.0 0 1 1 463.0 0 1 1 478.0 0 1 1 488.0 0 1 1 489.0 0 1 1 513.0 0 1 1 535.0 0 1 1 537.0 0 1 1 542.0 0 1 1 545.0 0 1 1 556.0 0 1 1 581.0 0 2 2 589.0 0 1 1 591.0 0 1 1 597.0 0 1 1 599.0 0 1 1 627.0 0 1 1 698.0 0 1 1 699.0 0 1 1 718.0 0 1 1 742.0 0 1 1 743.0 0 1 1 751.0 0 1 1 803.0 0 1 1 890.0 0 1 1 973.0 0 1 1 1099.0 0 1 1