## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT ACR-150-TP4.bam --OUTPUT ACR-150-TP4.md.bam --METRICS_FILE ACR-150-TP4.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 18:14:17 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 226 17261809 3365361 0 155 10066696 4625681 0.583178 10059694 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.146752 3062967 0 4014174 2.0 1.352932 1807126 1140637 1945815 3.0 1.390003 1002132 470291 769000 4.0 1.396668 546680 242303 274702 5.0 1.397866 302180 134525 98848 6.0 1.398081 174952 77944 38745 7.0 1.39812 104294 45918 18066 8.0 1.398127 64419 27616 9822 9.0 1.398128 41065 16425 6156 10.0 1.398129 26831 9937 4117 11.0 1.398129 17522 6219 2937 12.0 1.398129 11987 3798 2193 13.0 1.398129 8245 2384 1670 14.0 1.398129 5656 1517 1254 15.0 1.398129 4023 933 1049 16.0 1.398129 2953 613 866 17.0 1.398129 2183 422 687 18.0 1.398129 1538 246 564 19.0 1.398129 1275 184 456 20.0 1.398129 957 126 422 21.0 1.398129 768 72 362 22.0 1.398129 676 59 316 23.0 1.398129 482 41 254 24.0 1.398129 406 28 236 25.0 1.398129 365 17 210 26.0 1.398129 314 19 165 27.0 1.398129 276 23 160 28.0 1.398129 224 9 122 29.0 1.398129 192 13 122 30.0 1.398129 192 12 120 31.0 1.398129 163 9 110 32.0 1.398129 135 9 95 33.0 1.398129 145 6 89 34.0 1.398129 123 1 85 35.0 1.398129 104 3 73 36.0 1.398129 120 3 73 37.0 1.398129 94 2 63 38.0 1.398129 87 4 51 39.0 1.398129 75 0 55 40.0 1.398129 68 4 54 41.0 1.398129 65 1 45 42.0 1.398129 65 0 35 43.0 1.398129 60 1 47 44.0 1.398129 43 0 28 45.0 1.398129 61 0 26 46.0 1.398129 44 1 22 47.0 1.398129 28 0 25 48.0 1.398129 37 0 29 49.0 1.398129 25 1 26 50.0 1.398129 47 0 28 51.0 1.398129 30 1 29 52.0 1.398129 30 1 13 53.0 1.398129 26 0 19 54.0 1.398129 33 0 12 55.0 1.398129 23 0 16 56.0 1.398129 19 1 14 57.0 1.398129 16 0 9 58.0 1.398129 24 0 12 59.0 1.398129 20 0 8 60.0 1.398129 11 1 6 61.0 1.398129 21 0 6 62.0 1.398129 24 1 13 63.0 1.398129 9 0 8 64.0 1.398129 7 0 10 65.0 1.398129 13 1 16 66.0 1.398129 15 1 7 67.0 1.398129 14 1 15 68.0 1.398129 9 0 5 69.0 1.398129 11 0 5 70.0 1.398129 13 0 8 71.0 1.398129 7 0 10 72.0 1.398129 7 0 7 73.0 1.398129 7 1 8 74.0 1.398129 8 0 10 75.0 1.398129 5 1 4 76.0 1.398129 8 0 8 77.0 1.398129 8 1 6 78.0 1.398129 6 0 6 79.0 1.398129 8 0 3 80.0 1.398129 11 0 2 81.0 1.398129 1 0 5 82.0 1.398129 9 0 6 83.0 1.398129 6 0 6 84.0 1.398129 4 0 3 85.0 1.398129 3 0 1 86.0 1.398129 9 0 2 87.0 1.398129 5 0 3 88.0 1.398129 7 0 4 89.0 1.398129 5 0 4 90.0 1.398129 3 0 2 91.0 1.398129 5 0 4 92.0 1.398129 1 0 2 93.0 1.398129 3 0 0 94.0 1.398129 5 0 2 95.0 1.398129 0 0 0 96.0 1.398129 5 0 2 97.0 1.398129 2 0 2 98.0 1.398129 1 0 1 99.0 1.398129 4 0 2 100.0 1.398129 6 0 1 101.0 0 2 0 2 102.0 0 3 0 2 103.0 0 0 0 5 104.0 0 1 0 0 105.0 0 2 0 0 106.0 0 1 0 1 107.0 0 2 0 2 108.0 0 3 0 2 109.0 0 1 0 2 110.0 0 3 0 2 111.0 0 1 0 1 112.0 0 3 0 2 113.0 0 4 0 1 114.0 0 1 0 1 115.0 0 2 0 3 117.0 0 0 0 1 118.0 0 1 0 5 119.0 0 2 0 1 120.0 0 4 0 2 121.0 0 2 0 3 122.0 0 3 0 5 123.0 0 2 0 1 124.0 0 3 0 0 125.0 0 1 0 1 126.0 0 3 0 0 127.0 0 1 0 0 128.0 0 2 0 1 129.0 0 0 0 1 130.0 0 2 0 0 131.0 0 1 0 0 132.0 0 2 0 0 134.0 0 1 0 0 135.0 0 0 0 1 136.0 0 2 0 1 137.0 0 0 0 1 139.0 0 0 0 1 140.0 0 2 0 0 143.0 0 0 0 2 144.0 0 2 0 1 145.0 0 0 0 1 146.0 0 1 0 1 147.0 0 1 0 0 148.0 0 1 0 2 149.0 0 0 0 1 150.0 0 4 0 0 152.0 0 0 0 1 153.0 0 1 0 2 156.0 0 1 0 0 158.0 0 2 0 0 159.0 0 0 0 1 160.0 0 1 0 1 161.0 0 1 0 1 163.0 0 0 0 2 164.0 0 1 0 1 165.0 0 0 0 3 168.0 0 1 0 0 170.0 0 1 0 0 171.0 0 1 0 1 173.0 0 1 0 0 176.0 0 0 0 1 177.0 0 2 0 0 178.0 0 1 0 1 180.0 0 1 0 0 181.0 0 1 0 0 186.0 0 2 0 0 187.0 0 1 0 0 190.0 0 2 0 0 191.0 0 0 0 1 193.0 0 1 0 1 196.0 0 0 0 1 198.0 0 1 0 1 203.0 0 1 0 0 206.0 0 1 0 0 208.0 0 1 0 1 211.0 0 0 0 1 214.0 0 0 0 1 220.0 0 1 0 0 232.0 0 1 0 0 236.0 0 0 0 1 247.0 0 0 0 1 250.0 0 0 0 1 252.0 0 0 0 1 256.0 0 1 0 0 262.0 0 2 0 0 263.0 0 0 0 1 264.0 0 0 0 1 269.0 0 1 0 0 270.0 0 1 0 0 273.0 0 0 0 1 280.0 0 1 0 0 283.0 0 0 0 1 284.0 0 0 0 1 290.0 0 1 0 0 297.0 0 1 0 0 304.0 0 1 0 0 319.0 0 1 0 0 326.0 0 0 0 1 329.0 0 1 0 0 333.0 0 0 0 1 354.0 0 1 0 0 376.0 0 0 0 1 381.0 0 0 0 1 384.0 0 1 0 0 400.0 0 1 0 0 431.0 0 0 0 1 459.0 0 1 0 0 530.0 0 0 0 1 551.0 0 1 0 0 706.0 0 0 0 1 754.0 0 1 0 0