## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-H3K9me3_R1.target.filtered.sorted.bam --OUTPUT DE-H3K9me3_R1.target.markdup.bam --METRICS_FILE DE-H3K9me3_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 15:10:37 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 9433736 0 0 0 243663 1827 0.025829 180770581 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000189 8953702 0 8955393 2.0 1.94952 230502 1827 228940 3.0 2.85058 5364 0 5242 4.0 3.705822 287 0 280 5.0 4.517578 73 0 73 6.0 5.288057 37 0 37 7.0 6.019359 24 0 24 8.0 6.713476 19 0 19 9.0 7.372298 11 0 11 10.0 7.997621 14 0 14 11.0 8.591147 8 0 8 12.0 9.154494 6 0 6 13.0 9.689196 7 0 7 14.0 10.196709 1 0 1 15.0 10.678416 0 0 0 16.0 11.13563 4 0 4 17.0 11.569595 3 0 3 18.0 11.981494 1 0 1 19.0 12.372449 0 0 0 20.0 12.743524 3 0 3 21.0 13.095731 0 0 0 22.0 13.430029 2 0 2 23.0 13.747329 0 0 0 24.0 14.048495 2 0 2 25.0 14.334347 0 0 0 26.0 14.605664 0 0 0 27.0 14.863185 1 0 1 28.0 15.107612 1 0 1 29.0 15.33961 0 0 0 30.0 15.559811 0 0 0 31.0 15.768816 0 0 0 32.0 15.967193 0 0 0 33.0 16.155483 0 0 0 34.0 16.3342 0 0 0 35.0 16.503828 0 0 0 36.0 16.664832 0 0 0 37.0 16.817648 0 0 0 38.0 16.962695 0 0 0 39.0 17.100366 1 0 1 40.0 17.231037 0 0 0 41.0 17.355063 0 0 0 42.0 17.472783 0 0 0 43.0 17.584517 0 0 0 44.0 17.69057 0 0 0 45.0 17.79123 0 0 0 46.0 17.886772 0 0 0 47.0 17.977455 0 0 0 48.0 18.063528 0 0 0 49.0 18.145224 0 0 0 50.0 18.222766 0 0 0 51.0 18.296365 0 0 0 52.0 18.366221 0 0 0 53.0 18.432526 0 0 0 54.0 18.495459 0 0 0 55.0 18.555192 0 0 0 56.0 18.611888 0 0 0 57.0 18.665701 0 0 0 58.0 18.716778 0 0 0 59.0 18.765257 0 0 0 60.0 18.811272 0 0 0 61.0 18.854947 0 0 0 62.0 18.896401 0 0 0 63.0 18.935747 0 0 0 64.0 18.973092 0 0 0 65.0 19.008539 0 0 0 66.0 19.042183 0 0 0 67.0 19.074116 0 0 0 68.0 19.104426 0 0 0 69.0 19.133194 0 0 0 70.0 19.1605 0 0 0 71.0 19.186417 0 0 0 72.0 19.211017 0 0 0 73.0 19.234365 0 0 0 74.0 19.256527 0 0 0 75.0 19.277561 0 0 0 76.0 19.297526 0 0 0 77.0 19.316476 0 0 0 78.0 19.334462 0 0 0 79.0 19.351533 0 0 0 80.0 19.367737 0 0 0 81.0 19.383117 0 0 0 82.0 19.397714 0 0 0 83.0 19.41157 0 0 0 84.0 19.424721 0 0 0 85.0 19.437203 0 0 0 86.0 19.44905 0 0 0 87.0 19.460295 0 0 0 88.0 19.470968 0 0 0 89.0 19.481099 0 0 0 90.0 19.490714 0 0 0 91.0 19.499841 0 0 0 92.0 19.508503 0 0 0 93.0 19.516725 0 0 0 94.0 19.524529 0 0 0 95.0 19.531936 0 0 0 96.0 19.538967 0 0 0 97.0 19.54564 0 0 0 98.0 19.551973 0 0 0 99.0 19.557985 0 0 0 100.0 19.563691 0 0 0