## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354293.sorted.bam --OUTPUT SRX7354293.markdup.sorted.bam --METRICS_FILE SRX7354293.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 22:02:48 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 25093 29172597 3260126 3859059 18797 11741471 0 0.402632 25670320 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 13276254 13276254 2.0 1.320962 2713122 2713122 3.0 1.423978 661616 661616 4.0 1.457043 239134 239134 5.0 1.467655 124927 124927 6.0 1.471061 78370 78370 7.0 1.472155 55366 55366 8.0 1.472506 40756 40756 9.0 1.472618 31515 31515 10.0 1.472654 25118 25118 11.0 1.472666 20487 20487 12.0 1.47267 17065 17065 13.0 1.472671 14223 14223 14.0 1.472671 11911 11911 15.0 1.472671 10302 10302 16.0 1.472671 8851 8851 17.0 1.472671 7935 7935 18.0 1.472671 6897 6897 19.0 1.472671 6261 6261 20.0 1.472671 5385 5385 21.0 1.472671 4905 4905 22.0 1.472671 4327 4327 23.0 1.472671 4131 4131 24.0 1.472671 3639 3639 25.0 1.472671 3386 3386 26.0 1.472671 2970 2970 27.0 1.472671 2839 2839 28.0 1.472671 2579 2579 29.0 1.472671 2388 2388 30.0 1.472671 2181 2181 31.0 1.472671 2018 2018 32.0 1.472671 1838 1838 33.0 1.472671 1817 1817 34.0 1.472671 1629 1629 35.0 1.472671 1557 1557 36.0 1.472671 1393 1393 37.0 1.472671 1347 1347 38.0 1.472671 1263 1263 39.0 1.472671 1159 1159 40.0 1.472671 1083 1083 41.0 1.472671 1024 1024 42.0 1.472671 974 974 43.0 1.472671 909 909 44.0 1.472671 871 871 45.0 1.472671 861 861 46.0 1.472671 737 737 47.0 1.472671 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