## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354264.sorted.bam --OUTPUT SRX7354264.markdup.sorted.bam --METRICS_FILE SRX7354264.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 20:10:42 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 24899 30273897 3721128 1267935 17808 9096905 0 0.300657 39676146 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17679852 17679852 2.0 1.466254 2363103 2363103 3.0 1.683646 494733 494733 4.0 1.785007 193491 193491 5.0 1.832266 106254 106254 6.0 1.854301 68499 68499 7.0 1.864575 47670 47670 8.0 1.869365 34925 34925 9.0 1.871599 26973 26973 10.0 1.87264 20914 20914 11.0 1.873126 16788 16788 12.0 1.873352 13778 13778 13.0 1.873457 11637 11637 14.0 1.873507 9481 9481 15.0 1.87353 8244 8244 16.0 1.87354 7152 7152 17.0 1.873545 6214 6214 18.0 1.873548 5430 5430 19.0 1.873549 4944 4944 20.0 1.873549 4251 4251 21.0 1.873549 3722 3722 22.0 1.87355 3310 3310 23.0 1.87355 3074 3074 24.0 1.87355 2817 2817 25.0 1.87355 2528 2528 26.0 1.87355 2270 2270 27.0 1.87355 2060 2060 28.0 1.87355 1826 1826 29.0 1.87355 1738 1738 30.0 1.87355 1588 1588 31.0 1.87355 1447 1447 32.0 1.87355 1345 1345 33.0 1.87355 1190 1190 34.0 1.87355 1163 1163 35.0 1.87355 1087 1087 36.0 1.87355 1013 1013 37.0 1.87355 936 936 38.0 1.87355 869 869 39.0 1.87355 819 819 40.0 1.87355 713 713 41.0 1.87355 709 709 42.0 1.87355 684 684 43.0 1.87355 595 595 44.0 1.87355 622 622 45.0 1.87355 569 569 46.0 1.87355 542 542 47.0 1.87355 469 469 48.0 1.87355 464 464 49.0 1.87355 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