## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354059.sorted.bam --OUTPUT SRX7354059.markdup.sorted.bam --METRICS_FILE SRX7354059.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: Fri Oct 27 17:07:25 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 27799 32020437 4495926 1752511 16536 7891735 0 0.24661 53779754 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21577006 21577006 2.0 1.551342 1612366 1612366 3.0 1.855321 360235 360235 4.0 2.022917 162483 162483 5.0 2.115319 94896 94896 6.0 2.166265 61971 61971 7.0 2.194354 43736 43736 8.0 2.20984 32181 32181 9.0 2.218378 25085 25085 10.0 2.223086 19641 19641 11.0 2.225681 15964 15964 12.0 2.227112 13107 13107 13.0 2.227901 10994 10994 14.0 2.228336 9317 9317 15.0 2.228576 7993 7993 16.0 2.228708 6946 6946 17.0 2.228781 5981 5981 18.0 2.228821 5307 5307 19.0 2.228843 4676 4676 20.0 2.228856 4257 4257 21.0 2.228862 3769 3769 22.0 2.228866 3423 3423 23.0 2.228868 3094 3094 24.0 2.228869 2711 2711 25.0 2.22887 2452 2452 26.0 2.22887 2279 2279 27.0 2.22887 2061 2061 28.0 2.22887 1875 1875 29.0 2.228871 1729 1729 30.0 2.228871 1590 1590 31.0 2.228871 1504 1504 32.0 2.228871 1395 1395 33.0 2.228871 1361 1361 34.0 2.228871 1182 1182 35.0 2.228871 1149 1149 36.0 2.228871 991 991 37.0 2.228871 1009 1009 38.0 2.228871 901 901 39.0 2.228871 807 807 40.0 2.228871 843 843 41.0 2.228871 754 754 42.0 2.228871 715 715 43.0 2.228871 661 661 44.0 2.228871 596 596 45.0 2.228871 585 585 46.0 2.228871 577 577 47.0 2.228871 528 528 48.0 2.228871 500 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