## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354130.sorted.bam --OUTPUT SRX7354130.markdup.sorted.bam --METRICS_FILE SRX7354130.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 17:40:20 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 23139 31314576 4844355 1353825 15289 11256559 0 0.359578 32334120 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17722362 17722362 2.0 1.379664 1219349 1219349 3.0 1.523809 358017 358017 4.0 1.578535 182375 182375 5.0 1.599313 112379 112379 6.0 1.607202 77077 77077 7.0 1.610197 55812 55812 8.0 1.611334 42785 42785 9.0 1.611766 33752 33752 10.0 1.611929 26959 26959 11.0 1.611992 22693 22693 12.0 1.612015 18584 18584 13.0 1.612024 16131 16131 14.0 1.612028 13740 13740 15.0 1.612029 11897 11897 16.0 1.612029 10549 10549 17.0 1.61203 9272 9272 18.0 1.61203 8291 8291 19.0 1.61203 7427 7427 20.0 1.61203 6576 6576 21.0 1.61203 6040 6040 22.0 1.61203 5479 5479 23.0 1.61203 5055 5055 24.0 1.61203 4458 4458 25.0 1.61203 4195 4195 26.0 1.61203 3875 3875 27.0 1.61203 3601 3601 28.0 1.61203 3393 3393 29.0 1.61203 2967 2967 30.0 1.61203 2935 2935 31.0 1.61203 2692 2692 32.0 1.61203 2509 2509 33.0 1.61203 2288 2288 34.0 1.61203 2088 2088 35.0 1.61203 2033 2033 36.0 1.61203 1911 1911 37.0 1.61203 1784 1784 38.0 1.61203 1678 1678 39.0 1.61203 1571 1571 40.0 1.61203 1427 1427 41.0 1.61203 1344 1344 42.0 1.61203 1369 1369 43.0 1.61203 1378 1378 44.0 1.61203 1260 1260 45.0 1.61203 1224 1224 46.0 1.61203 1063 1063 47.0 1.61203 1035 1035 48.0 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