## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354120.sorted.bam --OUTPUT SRX7354120.markdup.sorted.bam --METRICS_FILE SRX7354120.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: Sat Oct 28 15:20:40 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 46505 34119872 4390582 6625723 35746 12864125 0 0.377294 32966425 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18227387 18227387 2.0 1.35523 1760397 1760397 3.0 1.481419 421584 421584 4.0 1.526245 201059 201059 5.0 1.542169 123515 123515 6.0 1.547825 84786 84786 7.0 1.549835 62448 62448 8.0 1.550548 47659 47659 9.0 1.550802 37935 37935 10.0 1.550892 30629 30629 11.0 1.550924 25319 25319 12.0 1.550935 21531 21531 13.0 1.55094 18443 18443 14.0 1.550941 15684 15684 15.0 1.550941 13774 13774 16.0 1.550942 12069 12069 17.0 1.550942 10886 10886 18.0 1.550942 9513 9513 19.0 1.550942 8455 8455 20.0 1.550942 7575 7575 21.0 1.550942 6815 6815 22.0 1.550942 6307 6307 23.0 1.550942 5717 5717 24.0 1.550942 5265 5265 25.0 1.550942 4894 4894 26.0 1.550942 4460 4460 27.0 1.550942 4056 4056 28.0 1.550942 3799 3799 29.0 1.550942 3594 3594 30.0 1.550942 3350 3350 31.0 1.550942 3094 3094 32.0 1.550942 2841 2841 33.0 1.550942 2602 2602 34.0 1.550942 2462 2462 35.0 1.550942 2287 2287 36.0 1.550942 2149 2149 37.0 1.550942 2055 2055 38.0 1.550942 1858 1858 39.0 1.550942 1817 1817 40.0 1.550942 1732 1732 41.0 1.550942 1556 1556 42.0 1.550942 1500 1500 43.0 1.550942 1524 1524 44.0 1.550942 1368 1368 45.0 1.550942 1357 1357 46.0 1.550942 1263 1263 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