## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT ACR-186-TP2.bam --OUTPUT ACR-186-TP2.md.bam --METRICS_FILE ACR-186-TP2.md.MarkDuplicates.metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Apulcra-genome.fa --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_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_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 --REMOVE_DUPLICATES false --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: Tue Jul 22 18:14:57 GMT 2025 ## 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 130 13337420 2787698 0 76 7235151 3844738 0.54247 9888947 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.19989 2997273 0 4017418 2.0 1.511348 1482245 977904 1424377 3.0 1.592194 731429 400759 431606 4.0 1.613179 373849 204285 128633 5.0 1.618626 202639 111408 43875 6.0 1.62004 115678 63185 18726 7.0 1.620407 68439 36580 9905 8.0 1.620503 42340 20917 6247 9.0 1.620527 26849 12512 4134 10.0 1.620534 17388 7566 3053 11.0 1.620535 11401 4346 2250 12.0 1.620536 7697 2622 1765 13.0 1.620536 5302 1711 1389 14.0 1.620536 3779 1073 1138 15.0 1.620536 2694 677 891 16.0 1.620536 2052 442 782 17.0 1.620536 1565 326 636 18.0 1.620536 1197 207 566 19.0 1.620536 1023 155 472 20.0 1.620536 819 131 404 21.0 1.620536 681 98 341 22.0 1.620536 538 66 325 23.0 1.620536 468 61 269 24.0 1.620536 398 45 225 25.0 1.620536 345 31 232 26.0 1.620536 340 31 184 27.0 1.620536 292 30 167 28.0 1.620536 254 29 148 29.0 1.620536 254 24 155 30.0 1.620536 225 29 119 31.0 1.620536 181 18 113 32.0 1.620536 159 20 114 33.0 1.620536 127 8 96 34.0 1.620536 131 17 115 35.0 1.620536 127 15 71 36.0 1.620536 97 13 68 37.0 1.620536 115 10 81 38.0 1.620536 108 7 65 39.0 1.620536 116 2 64 40.0 1.620536 83 5 55 41.0 1.620536 78 9 48 42.0 1.620536 78 4 50 43.0 1.620536 64 1 44 44.0 1.620536 66 5 42 45.0 1.620536 66 6 52 46.0 1.620536 55 7 34 47.0 1.620536 54 4 18 48.0 1.620536 44 2 39 49.0 1.620536 33 4 29 50.0 1.620536 46 4 29 51.0 1.620536 39 8 16 52.0 1.620536 45 5 22 53.0 1.620536 36 1 21 54.0 1.620536 36 2 24 55.0 1.620536 28 3 12 56.0 1.620536 39 1 19 57.0 1.620536 28 1 18 58.0 1.620536 27 3 22 59.0 1.620536 28 2 10 60.0 1.620536 20 2 13 61.0 1.620536 26 0 15 62.0 1.620536 22 3 11 63.0 1.620536 32 2 11 64.0 1.620536 24 1 18 65.0 1.620536 12 0 7 66.0 1.620536 13 3 16 67.0 1.620536 13 0 12 68.0 1.620536 22 0 11 69.0 1.620536 20 1 15 70.0 1.620536 13 1 8 71.0 1.620536 14 1 10 72.0 1.620536 9 2 6 73.0 1.620536 8 0 10 74.0 1.620536 6 0 10 75.0 1.620536 14 0 5 76.0 1.620536 13 0 5 77.0 1.620536 9 0 4 78.0 1.620536 13 2 7 79.0 1.620536 8 0 10 80.0 1.620536 14 0 6 81.0 1.620536 6 0 9 82.0 1.620536 6 1 6 83.0 1.620536 15 0 6 84.0 1.620536 12 0 10 85.0 1.620536 5 0 8 86.0 1.620536 8 0 6 87.0 1.620536 4 0 7 88.0 1.620536 7 0 6 89.0 1.620536 10 1 6 90.0 1.620536 7 0 4 91.0 1.620536 9 1 5 92.0 1.620536 7 0 5 93.0 1.620536 8 0 4 94.0 1.620536 7 0 1 95.0 1.620536 9 0 2 96.0 1.620536 4 1 3 97.0 1.620536 3 0 3 98.0 1.620536 3 0 1 99.0 1.620536 5 0 2 100.0 1.620536 5 0 4 101.0 0 3 2 1 102.0 0 6 0 4 103.0 0 6 0 2 104.0 0 5 0 2 105.0 0 6 0 2 106.0 0 5 0 3 107.0 0 2 0 4 108.0 0 4 0 3 109.0 0 4 0 1 110.0 0 7 0 5 111.0 0 6 0 1 112.0 0 2 0 1 113.0 0 3 0 5 114.0 0 4 1 3 115.0 0 2 0 0 116.0 0 2 1 1 117.0 0 3 0 1 118.0 0 4 1 5 119.0 0 5 0 4 120.0 0 5 0 1 121.0 0 5 0 4 122.0 0 4 0 2 123.0 0 3 0 4 124.0 0 5 0 1 125.0 0 3 0 1 126.0 0 1 0 2 127.0 0 4 1 0 128.0 0 2 0 1 129.0 0 3 0 2 130.0 0 1 0 2 131.0 0 1 0 1 132.0 0 2 0 1 133.0 0 0 0 1 134.0 0 1 0 1 135.0 0 2 0 4 136.0 0 0 0 1 137.0 0 2 0 0 138.0 0 3 0 1 139.0 0 0 0 1 140.0 0 2 0 2 141.0 0 2 0 2 142.0 0 2 0 0 143.0 0 2 0 0 144.0 0 2 0 1 145.0 0 2 0 0 146.0 0 0 0 1 147.0 0 0 0 2 148.0 0 2 0 1 151.0 0 2 1 2 152.0 0 1 0 0 153.0 0 1 0 1 154.0 0 0 0 1 155.0 0 4 0 1 156.0 0 1 0 0 157.0 0 2 0 0 158.0 0 0 0 1 160.0 0 0 0 2 161.0 0 2 0 0 162.0 0 1 0 2 163.0 0 0 0 1 164.0 0 1 0 0 165.0 0 1 0 1 166.0 0 1 0 0 167.0 0 1 0 1 168.0 0 4 0 0 169.0 0 1 0 1 170.0 0 1 0 0 171.0 0 0 0 2 173.0 0 0 0 2 174.0 0 3 0 0 175.0 0 1 0 0 176.0 0 0 0 1 178.0 0 1 0 0 179.0 0 1 0 0 180.0 0 3 0 1 181.0 0 0 0 1 182.0 0 0 0 1 184.0 0 2 0 0 185.0 0 1 0 0 187.0 0 2 0 0 188.0 0 1 0 0 189.0 0 0 0 1 191.0 0 1 0 0 193.0 0 0 0 1 194.0 0 2 0 0 197.0 0 1 0 0 199.0 0 0 0 1 203.0 0 1 0 0 204.0 0 1 0 0 205.0 0 0 0 1 208.0 0 1 0 0 209.0 0 2 0 0 212.0 0 0 0 1 213.0 0 1 0 0 214.0 0 0 0 2 217.0 0 0 0 1 219.0 0 2 0 0 221.0 0 0 0 1 226.0 0 2 0 0 227.0 0 1 0 0 230.0 0 1 0 0 235.0 0 1 0 0 236.0 0 0 0 1 237.0 0 0 0 1 241.0 0 0 0 2 245.0 0 2 0 0 246.0 0 2 0 0 250.0 0 1 0 0 258.0 0 1 0 0 265.0 0 0 0 1 275.0 0 0 0 1 282.0 0 0 0 1 304.0 0 0 0 1 318.0 0 1 0 0 319.0 0 1 0 0 332.0 0 0 0 1 333.0 0 1 0 0 349.0 0 1 0 0 351.0 0 0 0 1 355.0 0 0 0 1 365.0 0 1 0 0 382.0 0 1 0 0 386.0 0 0 0 1 397.0 0 0 0 1 407.0 0 0 0 1 410.0 0 1 0 0 415.0 0 0 0 1 418.0 0 0 0 1 420.0 0 1 0 0 430.0 0 1 0 0 435.0 0 1 0 0 438.0 0 1 0 0 439.0 0 0 0 1 440.0 0 1 0 0 448.0 0 0 0 1 455.0 0 1 0 0 475.0 0 1 0 0 639.0 0 0 0 1 661.0 0 1 0 0