## htsjdk.samtools.metrics.StringHeader # MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[three.sorted.bam] OUTPUT=three.markdup.bam METRICS_FILE=three.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.KC4GAAfXa2] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false 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 ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Jun 08 19:34:27 UTC 2026 ## 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 three 6 870998 0 1606 6 692528 4598 0.795098 179928 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000204 48739 0 48971 2.0 1.008107 45752 4142 45988 3.0 1.008169 23198 201 23104 4.0 1.008169 14311 18 14210 5.0 1.008169 9540 0 9535 6.0 1.008169 6694 0 6612 7.0 1.008169 4630 0 4600 8.0 1.008169 3629 0 3630 9.0 1.008169 2801 0 2757 10.0 1.008169 2349 0 2370 11.0 1.008169 1808 0 1791 12.0 1.008169 1633 0 1611 13.0 1.008169 1347 0 1350 14.0 1.008169 1179 0 1178 15.0 1.008169 927 0 894 16.0 1.008169 814 0 819 17.0 1.008169 715 0 714 18.0 1.008169 614 0 606 19.0 1.008169 567 0 554 20.0 1.008169 471 0 480 21.0 1.008169 463 0 451 22.0 1.008169 411 0 415 23.0 1.008169 330 0 325 24.0 1.008169 343 0 336 25.0 1.008169 321 0 320 26.0 1.008169 285 0 290 27.0 1.008169 268 0 269 28.0 1.008169 237 0 229 29.0 1.008169 248 0 252 30.0 1.008169 197 0 192 31.0 1.008169 175 0 174 32.0 1.008169 209 0 211 33.0 1.008169 165 0 159 34.0 1.008169 166 0 186 35.0 1.008169 136 0 108 36.0 1.008169 129 0 141 37.0 1.008169 142 0 136 38.0 1.008169 117 0 122 39.0 1.008169 101 0 100 40.0 1.008169 130 0 123 41.0 1.008169 77 0 72 42.0 1.008169 91 0 90 43.0 1.008169 81 0 90 44.0 1.008169 74 0 66 45.0 1.008169 69 0 70 46.0 1.008169 65 0 64 47.0 1.008169 61 0 59 48.0 1.008169 60 0 61 49.0 1.008169 72 0 73 50.0 1.008169 44 0 43 51.0 1.008169 63 0 66 52.0 1.008169 51 0 45 53.0 1.008169 60 0 63 54.0 1.008169 38 0 46 55.0 1.008169 59 0 46 56.0 1.008169 65 0 69 57.0 1.008169 29 0 30 58.0 1.008169 47 0 42 59.0 1.008169 40 0 44 60.0 1.008169 56 0 66 61.0 1.008169 53 0 46 62.0 1.008169 48 0 45 63.0 1.008169 35 0 32 64.0 1.008169 34 0 33 65.0 1.008169 33 0 37 66.0 1.008169 62 0 66 67.0 1.008169 37 0 29 68.0 1.008169 25 0 27 69.0 1.008169 27 0 30 70.0 1.008169 38 0 30 71.0 1.008169 27 0 26 72.0 1.008169 13 0 15 73.0 1.008169 22 0 34 74.0 1.008169 34 0 27 75.0 1.008169 31 0 33 76.0 1.008169 26 0 26 77.0 1.008169 21 0 15 78.0 1.008169 32 0 40 79.0 1.008169 38 0 31 80.0 1.008169 23 0 29 81.0 1.008169 27 0 14 82.0 1.008169 14 0 14 83.0 1.008169 11 0 14 84.0 1.008169 23 0 39 85.0 1.008169 25 0 12 86.0 1.008169 16 0 15 87.0 1.008169 15 0 9 88.0 1.008169 17 0 26 89.0 1.008169 20 0 21 90.0 1.008169 13 0 10 91.0 1.008169 17 0 16 92.0 1.008169 12 0 11 93.0 1.008169 16 0 25 94.0 1.008169 23 0 18 95.0 1.008169 14 0 9 96.0 1.008169 13 0 12 97.0 1.008169 10 0 8 98.0 1.008169 10 0 6 99.0 1.008169 7 0 10 100.0 1.008169 5 0 4 101.0 0 3 0 1 102.0 0 1 0 2 103.0 0 1 0 0 104.0 0 0 0 1 106.0 0 1 0 1 107.0 0 2 0 1 114.0 0 1 0 1 116.0 0 1 0 1