## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354180.sorted.bam --OUTPUT SRX7354180.markdup.sorted.bam --METRICS_FILE SRX7354180.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Homo_sapiens_assembly38_noALT_noHLA_noDecoy_patched_ERCC92.fasta --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 --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: Mon Oct 30 09:01:46 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 23858 31535627 3980178 2198286 17209 10681183 0 0.338847 35308704 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17597917 17597917 2.0 1.409368 2084541 2084541 3.0 1.57695 455381 455381 4.0 1.645553 192516 192516 5.0 1.673637 111729 111729 6.0 1.685134 74031 74031 7.0 1.68984 52901 52901 8.0 1.691767 39723 39723 9.0 1.692556 31231 31231 10.0 1.692878 24898 24898 11.0 1.693011 20126 20126 12.0 1.693065 16838 16838 13.0 1.693087 14127 14127 14.0 1.693096 12315 12315 15.0 1.6931 10527 10527 16.0 1.693101 9094 9094 17.0 1.693102 7911 7911 18.0 1.693102 7070 7070 19.0 1.693102 6371 6371 20.0 1.693102 5699 5699 21.0 1.693102 5077 5077 22.0 1.693102 4616 4616 23.0 1.693102 4185 4185 24.0 1.693102 3751 3751 25.0 1.693102 3415 3415 26.0 1.693102 3077 3077 27.0 1.693102 2828 2828 28.0 1.693102 2686 2686 29.0 1.693102 2439 2439 30.0 1.693102 2302 2302 31.0 1.693102 2141 2141 32.0 1.693102 1941 1941 33.0 1.693102 1845 1845 34.0 1.693102 1721 1721 35.0 1.693102 1563 1563 36.0 1.693102 1531 1531 37.0 1.693102 1401 1401 38.0 1.693102 1295 1295 39.0 1.693102 1231 1231 40.0 1.693102 1148 1148 41.0 1.693102 1128 1128 42.0 1.693102 1122 1122 43.0 1.693102 980 980 44.0 1.693102 897 897 45.0 1.693102 881 881 46.0 1.693102 845 845 47.0 1.693102 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