## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-H3K27me3_R1.target.filtered.sorted.bam --OUTPUT DE-H3K27me3_R1.target.markdup.bam --METRICS_FILE DE-H3K27me3_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 15:10:13 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 12627796 0 0 0 393894 1996 0.031193 199152315 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000153 11853829 0 11855671 2.0 1.938858 367271 1994 365577 3.0 2.819889 11979 1 11837 4.0 3.64679 696 0 690 5.0 4.422887 100 0 100 6.0 5.151301 18 0 18 7.0 5.834962 6 0 6 8.0 6.476619 1 0 1 9.0 7.078853 0 0 0 10.0 7.644087 0 0 0 11.0 8.174593 0 0 0 12.0 8.672505 0 0 0 13.0 9.139825 0 0 0 14.0 9.578434 0 0 0 15.0 9.990095 0 0 0 16.0 10.376464 1 0 1 17.0 10.739095 0 0 0 18.0 11.079446 0 0 0 19.0 11.398886 0 0 0 20.0 11.698699 0 0 0 21.0 11.980093 0 0 0 22.0 12.244198 0 0 0 23.0 12.492076 0 0 0 24.0 12.724725 0 0 0 25.0 12.94308 0 0 0 26.0 13.14802 0 0 0 27.0 13.340368 0 0 0 28.0 13.520898 0 0 0 29.0 13.690337 0 0 0 30.0 13.849366 1 0 1 31.0 13.998624 0 0 0 32.0 14.138712 0 0 0 33.0 14.270192 0 0 0 34.0 14.393595 0 0 0 35.0 14.509416 0 0 0 36.0 14.618121 0 0 0 37.0 14.720147 0 0 0 38.0 14.815905 0 0 0 39.0 14.90578 0 0 0 40.0 14.990132 0 0 0 41.0 15.069303 0 0 0 42.0 15.143609 0 0 0 43.0 15.213349 0 0 0 44.0 15.278805 0 0 0 45.0 15.340239 0 0 0 46.0 15.397899 0 0 0 47.0 15.452017 0 0 0 48.0 15.502809 0 0 0 49.0 15.550481 0 0 0 50.0 15.595223 0 0 0 51.0 15.637217 0 0 0 52.0 15.676631 0 0 0 53.0 15.713623 0 0 0 54.0 15.748342 0 0 0 55.0 15.780929 0 0 0 56.0 15.811513 0 0 0 57.0 15.840218 0 0 0 58.0 15.867159 0 0 0 59.0 15.892446 0 0 0 60.0 15.916178 0 0 0 61.0 15.938453 0 0 0 62.0 15.959359 0 0 0 63.0 15.978981 0 0 0 64.0 15.997397 0 0 0 65.0 16.014681 0 0 0 66.0 16.030904 0 0 0 67.0 16.04613 0 0 0 68.0 16.06042 0 0 0 69.0 16.073832 0 0 0 70.0 16.086421 0 0 0 71.0 16.098236 0 0 0 72.0 16.109325 0 0 0 73.0 16.119733 0 0 0 74.0 16.129501 0 0 0 75.0 16.138669 0 0 0 76.0 16.147274 0 0 0 77.0 16.15535 0 0 0 78.0 16.16293 0 0 0 79.0 16.170045 0 0 0 80.0 16.176722 0 0 0 81.0 16.182989 0 0 0 82.0 16.188871 0 0 0 83.0 16.194391 0 0 0 84.0 16.199572 0 0 0 85.0 16.204435 0 0 0 86.0 16.209 0 0 0 87.0 16.213284 0 0 0 88.0 16.217304 0 0 0 89.0 16.221078 0 0 0 90.0 16.22462 0 0 0 91.0 16.227944 0 0 0 92.0 16.231064 0 0 0 93.0 16.233992 0 0 0 94.0 16.23674 0 0 0 95.0 16.23932 0 0 0 96.0 16.241741 0 0 0 97.0 16.244013 0 0 0 98.0 16.246145 0 0 0 99.0 16.248147 0 0 0 100.0 16.250026 0 0 0