## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354339.sorted.bam --OUTPUT SRX7354339.markdup.sorted.bam --METRICS_FILE SRX7354339.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 23:57:33 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 28295 32025030 4810047 7175313 21650 13465607 0 0.420624 26422536 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 13701634 13701634 2.0 1.297591 3156246 3156246 3.0 1.386152 814912 814912 4.0 1.412506 287336 287336 5.0 1.420349 142190 142190 6.0 1.422683 87775 87775 7.0 1.423378 61036 61036 8.0 1.423585 44575 44575 9.0 1.423646 34334 34334 10.0 1.423665 27434 27434 11.0 1.42367 21981 21981 12.0 1.423672 18211 18211 13.0 1.423672 15349 15349 14.0 1.423672 12807 12807 15.0 1.423672 11183 11183 16.0 1.423672 9579 9579 17.0 1.423672 8713 8713 18.0 1.423672 7544 7544 19.0 1.423672 6638 6638 20.0 1.423672 5851 5851 21.0 1.423672 5334 5334 22.0 1.423672 4869 4869 23.0 1.423672 4358 4358 24.0 1.423672 3937 3937 25.0 1.423672 3656 3656 26.0 1.423672 3357 3357 27.0 1.423672 3021 3021 28.0 1.423672 2904 2904 29.0 1.423672 2609 2609 30.0 1.423672 2365 2365 31.0 1.423672 2250 2250 32.0 1.423672 2123 2123 33.0 1.423672 1955 1955 34.0 1.423672 1798 1798 35.0 1.423672 1659 1659 36.0 1.423672 1546 1546 37.0 1.423672 1440 1440 38.0 1.423672 1409 1409 39.0 1.423672 1324 1324 40.0 1.423672 1255 1255 41.0 1.423672 1152 1152 42.0 1.423672 1141 1141 43.0 1.423672 1009 1009 44.0 1.423672 1004 1004 45.0 1.423672 938 938 46.0 1.423672 853 853 47.0 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