## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-H3K36me3_R1.target.filtered.sorted.bam --OUTPUT DE-H3K36me3_R1.target.markdup.bam --METRICS_FILE DE-H3K36me3_R1.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORT_ORDER coordinate --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --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 --ASSUME_SORTED 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 --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Jun 15 14:54:37 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 0 9777473 0 0 0 192195 1347 0.019657 247119995 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000135 9396780 0 9398048 2.0 1.961472 185175 1345 183983 3.0 2.885515 3127 1 3054 4.0 3.773712 132 0 129 5.0 4.627453 33 0 33 6.0 5.448074 9 0 9 7.0 6.236861 9 0 9 8.0 6.995048 6 0 6 9.0 7.723823 4 0 4 10.0 8.424326 0 0 0 11.0 9.097655 0 0 0 12.0 9.744863 1 0 1 13.0 10.366964 0 0 0 14.0 10.964931 0 0 0 15.0 11.539702 0 0 0 16.0 12.092175 0 0 0 17.0 12.623216 0 0 0 18.0 13.133656 0 0 0 19.0 13.624295 0 0 0 20.0 14.0959 0 0 0 21.0 14.54921 0 0 0 22.0 14.984935 0 0 0 23.0 15.403757 0 0 0 24.0 15.806331 1 0 1 25.0 16.193288 0 0 0 26.0 16.565234 0 0 0 27.0 16.922751 0 0 0 28.0 17.266398 0 0 0 29.0 17.596715 0 0 0 30.0 17.914217 0 0 0 31.0 18.219403 0 0 0 32.0 18.512749 1 0 1 33.0 18.794715 0 0 0 34.0 19.065744 0 0 0 35.0 19.326258 0 0 0 36.0 19.576666 0 0 0 37.0 19.817359 0 0 0 38.0 20.048716 0 0 0 39.0 20.271097 0 0 0 40.0 20.484852 0 0 0 41.0 20.690314 0 0 0 42.0 20.887806 0 0 0 43.0 21.077636 0 0 0 44.0 21.260103 0 0 0 45.0 21.435491 0 0 0 46.0 21.604075 0 0 0 47.0 21.766119 0 0 0 48.0 21.921877 0 0 0 49.0 22.071592 0 0 0 50.0 22.2155 0 0 0 51.0 22.353825 0 0 0 52.0 22.486784 0 0 0 53.0 22.614585 0 0 0 54.0 22.737428 0 0 0 55.0 22.855506 0 0 0 56.0 22.969003 0 0 0 57.0 23.078097 0 0 0 58.0 23.182959 0 0 0 59.0 23.283753 0 0 0 60.0 23.380637 0 0 0 61.0 23.473763 0 0 0 62.0 23.563276 0 0 0 63.0 23.649316 0 0 0 64.0 23.732019 0 0 0 65.0 23.811513 0 0 0 66.0 23.887924 0 0 0 67.0 23.96137 0 0 0 68.0 24.031967 0 0 0 69.0 24.099826 0 0 0 70.0 24.165052 0 0 0 71.0 24.227747 0 0 0 72.0 24.288011 0 0 0 73.0 24.345937 0 0 0 74.0 24.401615 0 0 0 75.0 24.455134 0 0 0 76.0 24.506576 0 0 0 77.0 24.556023 0 0 0 78.0 24.603552 0 0 0 79.0 24.649236 0 0 0 80.0 24.693149 0 0 0 81.0 24.735358 0 0 0 82.0 24.77593 0 0 0 83.0 24.814927 0 0 0 84.0 24.852412 0 0 0 85.0 24.888443 0 0 0 86.0 24.923076 0 0 0 87.0 24.956366 0 0 0 88.0 24.988364 0 0 0 89.0 25.01912 0 0 0 90.0 25.048684 0 0 0 91.0 25.077101 0 0 0 92.0 25.104415 0 0 0 93.0 25.13067 0 0 0 94.0 25.155906 0 0 0 95.0 25.180163 0 0 0 96.0 25.20348 0 0 0 97.0 25.225891 0 0 0 98.0 25.247434 0 0 0 99.0 25.26814 0 0 0 100.0 25.288044 0 0 0