## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354330.sorted.bam --OUTPUT SRX7354330.markdup.sorted.bam --METRICS_FILE SRX7354330.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 23:47:00 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 86845 44797715 6205154 14309273 72103 21527032 0 0.480877 30022459 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 15015055 15015055 2.0 1.224891 5123842 5123842 3.0 1.275467 1648049 1648049 4.0 1.286841 570494 570494 5.0 1.289399 246496 246496 6.0 1.289974 135836 135836 7.0 1.290103 89161 89161 8.0 1.290132 64569 64569 9.0 1.290139 48860 48860 10.0 1.29014 38327 38327 11.0 1.290141 31555 31555 12.0 1.290141 25890 25890 13.0 1.290141 21980 21980 14.0 1.290141 18502 18502 15.0 1.290141 15905 15905 16.0 1.290141 13757 13757 17.0 1.290141 12162 12162 18.0 1.290141 10755 10755 19.0 1.290141 9551 9551 20.0 1.290141 8462 8462 21.0 1.290141 7682 7682 22.0 1.290141 6899 6899 23.0 1.290141 6157 6157 24.0 1.290141 5775 5775 25.0 1.290141 5269 5269 26.0 1.290141 4866 4866 27.0 1.290141 4409 4409 28.0 1.290141 3933 3933 29.0 1.290141 3713 3713 30.0 1.290141 3455 3455 31.0 1.290141 3309 3309 32.0 1.290141 2968 2968 33.0 1.290141 2792 2792 34.0 1.290141 2622 2622 35.0 1.290141 2441 2441 36.0 1.290141 2227 2227 37.0 1.290141 2119 2119 38.0 1.290141 1982 1982 39.0 1.290141 1935 1935 40.0 1.290141 1793 1793 41.0 1.290141 1670 1670 42.0 1.290141 1574 1574 43.0 1.290141 1556 1556 44.0 1.290141 1394 1394 45.0 1.290141 1369 1369 46.0 1.290141 1306 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