## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT ACR-173-TP3.bam --OUTPUT ACR-173-TP3.md.bam --METRICS_FILE ACR-173-TP3.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 632 15635658 3279330 0 549 10027963 2983855 0.641357 6562044 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.062181 1816120 0 2226234 2.0 1.160217 1409068 881563 1611953 3.0 1.169266 953484 320334 923150 4.0 1.170101 583303 151338 450290 5.0 1.170178 340951 79976 201475 6.0 1.170185 195270 44515 89135 7.0 1.170186 113704 25577 41187 8.0 1.170186 67682 14609 21262 9.0 1.170186 41661 8552 11819 10.0 1.170186 25954 5202 7329 11.0 1.170186 16704 3063 4847 12.0 1.170186 11237 1841 3458 13.0 1.170186 7602 1101 2527 14.0 1.170186 5379 716 1971 15.0 1.170186 3743 423 1492 16.0 1.170186 2753 259 1259 17.0 1.170186 2134 178 1005 18.0 1.170186 1569 118 840 19.0 1.170186 1233 62 700 20.0 1.170186 1015 40 577 21.0 1.170186 796 38 479 22.0 1.170186 630 28 426 23.0 1.170186 572 17 369 24.0 1.170186 517 8 329 25.0 1.170186 377 16 277 26.0 1.170186 366 11 287 27.0 1.170186 342 5 250 28.0 1.170186 270 7 172 29.0 1.170186 228 4 183 30.0 1.170186 226 2 175 31.0 1.170186 199 0 150 32.0 1.170186 168 3 116 33.0 1.170186 141 2 119 34.0 1.170186 142 0 126 35.0 1.170186 129 1 104 36.0 1.170186 117 2 88 37.0 1.170186 110 3 99 38.0 1.170186 102 3 76 39.0 1.170186 100 2 64 40.0 1.170186 88 0 79 41.0 1.170186 75 4 62 42.0 1.170186 68 1 65 43.0 1.170186 68 0 43 44.0 1.170186 61 1 42 45.0 1.170186 67 0 55 46.0 1.170186 57 0 49 47.0 1.170186 58 0 49 48.0 1.170186 46 0 37 49.0 1.170186 46 0 36 50.0 1.170186 48 0 41 51.0 1.170186 45 1 32 52.0 1.170186 40 0 30 53.0 1.170186 35 1 17 54.0 1.170186 21 0 24 55.0 1.170186 37 1 24 56.0 1.170186 23 0 21 57.0 1.170186 31 0 21 58.0 1.170186 21 0 17 59.0 1.170186 31 0 17 60.0 1.170186 19 0 23 61.0 1.170186 20 0 18 62.0 1.170186 21 2 22 63.0 1.170186 26 0 21 64.0 1.170186 17 0 14 65.0 1.170186 23 0 16 66.0 1.170186 10 0 14 67.0 1.170186 17 0 14 68.0 1.170186 16 0 10 69.0 1.170186 13 0 16 70.0 1.170186 15 0 9 71.0 1.170186 12 0 11 72.0 1.170186 17 0 8 73.0 1.170186 10 0 4 74.0 1.170186 7 0 10 75.0 1.170186 10 0 8 76.0 1.170186 7 0 6 77.0 1.170186 10 0 15 78.0 1.170186 11 0 9 79.0 1.170186 10 0 8 80.0 1.170186 9 0 11 81.0 1.170186 11 0 10 82.0 1.170186 7 0 7 83.0 1.170186 9 0 5 84.0 1.170186 7 0 7 85.0 1.170186 11 0 3 86.0 1.170186 7 0 6 87.0 1.170186 4 0 5 88.0 1.170186 6 0 4 89.0 1.170186 6 0 10 90.0 1.170186 7 0 5 91.0 1.170186 4 0 2 92.0 1.170186 4 0 6 93.0 1.170186 6 0 3 94.0 1.170186 4 0 6 95.0 1.170186 3 0 2 96.0 1.170186 9 0 4 97.0 1.170186 6 0 4 98.0 1.170186 6 0 3 99.0 1.170186 8 0 3 100.0 1.170186 5 0 3 101.0 0 6 0 2 102.0 0 4 0 1 103.0 0 3 1 2 104.0 0 6 0 5 105.0 0 4 0 2 106.0 0 3 0 4 107.0 0 3 0 2 108.0 0 5 0 2 109.0 0 1 0 3 110.0 0 2 0 4 111.0 0 1 0 4 112.0 0 1 0 4 113.0 0 4 0 3 114.0 0 3 0 3 115.0 0 4 0 2 116.0 0 2 0 2 117.0 0 3 0 0 118.0 0 4 0 2 119.0 0 2 0 1 120.0 0 5 0 4 121.0 0 3 0 4 122.0 0 2 0 2 123.0 0 2 0 2 124.0 0 2 0 4 125.0 0 4 0 3 126.0 0 2 0 1 127.0 0 2 0 5 128.0 0 2 0 0 129.0 0 3 0 0 130.0 0 4 0 2 131.0 0 4 0 3 132.0 0 2 0 1 133.0 0 3 0 3 134.0 0 2 0 1 135.0 0 1 0 2 136.0 0 1 0 2 138.0 0 3 0 0 139.0 0 1 0 1 140.0 0 4 0 2 141.0 0 0 0 2 142.0 0 1 0 0 143.0 0 1 0 1 145.0 0 1 0 2 146.0 0 1 0 2 147.0 0 1 0 3 148.0 0 2 0 1 149.0 0 2 0 3 150.0 0 0 0 2 152.0 0 1 0 1 153.0 0 0 0 2 154.0 0 5 0 1 155.0 0 0 0 1 156.0 0 3 0 1 157.0 0 1 0 1 158.0 0 4 0 0 159.0 0 2 0 2 160.0 0 1 0 0 162.0 0 1 0 1 164.0 0 0 0 2 165.0 0 2 0 0 168.0 0 1 0 1 169.0 0 1 0 1 170.0 0 1 0 0 171.0 0 0 0 1 172.0 0 1 0 1 174.0 0 1 0 1 175.0 0 1 0 1 177.0 0 2 0 1 178.0 0 2 0 0 179.0 0 1 0 0 180.0 0 0 0 2 181.0 0 1 0 1 183.0 0 0 0 2 184.0 0 1 0 0 186.0 0 1 0 0 187.0 0 1 0 1 188.0 0 1 0 0 189.0 0 1 0 0 190.0 0 0 0 2 191.0 0 1 0 1 192.0 0 0 0 1 197.0 0 1 0 0 198.0 0 0 0 1 200.0 0 0 0 1 201.0 0 0 0 2 202.0 0 1 0 0 204.0 0 2 0 1 205.0 0 0 0 2 206.0 0 1 0 1 207.0 0 1 0 2 208.0 0 1 0 1 210.0 0 1 0 0 212.0 0 0 0 1 214.0 0 2 0 0 216.0 0 0 0 1 218.0 0 2 0 2 219.0 0 2 0 0 221.0 0 0 0 1 225.0 0 3 0 0 227.0 0 0 0 1 228.0 0 1 0 0 229.0 0 1 0 0 233.0 0 0 0 1 235.0 0 1 0 0 236.0 0 0 0 1 238.0 0 1 0 0 240.0 0 1 0 0 242.0 0 1 0 0 246.0 0 0 0 2 248.0 0 1 0 0 249.0 0 1 0 0 254.0 0 1 0 0 268.0 0 0 0 1 287.0 0 0 0 1 291.0 0 0 0 1 294.0 0 1 0 0 300.0 0 0 0 1 305.0 0 1 0 0 308.0 0 0 0 1 315.0 0 0 0 1 318.0 0 1 0 0 324.0 0 1 0 0 326.0 0 1 0 0 334.0 0 1 0 0 341.0 0 1 0 0 392.0 0 0 0 1 413.0 0 0 0 1 429.0 0 1 0 0 435.0 0 1 0 0 499.0 0 0 0 1 502.0 0 0 0 1 512.0 0 0 0 1 515.0 0 1 0 0 524.0 0 1 0 0 536.0 0 1 0 0 567.0 0 0 0 1 588.0 0 1 0 0 645.0 0 0 0 1 688.0 0 1 0 0 771.0 0 0 0 1 786.0 0 1 0 0