## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354204.sorted.bam --OUTPUT SRX7354204.markdup.sorted.bam --METRICS_FILE SRX7354204.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 10:42:04 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 57003 46958020 5528742 11403601 44166 17560145 0 0.374197 45895487 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23141561 23141561 2.0 1.35946 4170990 4170990 3.0 1.488672 951413 951413 4.0 1.535119 341235 341235 5.0 1.551814 178221 178221 6.0 1.557816 113457 113457 7.0 1.559973 79531 79531 8.0 1.560749 59132 59132 9.0 1.561027 45722 45722 10.0 1.561128 36745 36745 11.0 1.561164 29483 29483 12.0 1.561177 24668 24668 13.0 1.561181 21031 21031 14.0 1.561183 17714 17714 15.0 1.561183 15645 15645 16.0 1.561184 13474 13474 17.0 1.561184 11947 11947 18.0 1.561184 10625 10625 19.0 1.561184 9210 9210 20.0 1.561184 8324 8324 21.0 1.561184 7416 7416 22.0 1.561184 6648 6648 23.0 1.561184 6166 6166 24.0 1.561184 5480 5480 25.0 1.561184 5250 5250 26.0 1.561184 4748 4748 27.0 1.561184 4327 4327 28.0 1.561184 3924 3924 29.0 1.561184 3689 3689 30.0 1.561184 3422 3422 31.0 1.561184 3115 3115 32.0 1.561184 3024 3024 33.0 1.561184 2783 2783 34.0 1.561184 2574 2574 35.0 1.561184 2514 2514 36.0 1.561184 2194 2194 37.0 1.561184 2082 2082 38.0 1.561184 2017 2017 39.0 1.561184 1883 1883 40.0 1.561184 1645 1645 41.0 1.561184 1654 1654 42.0 1.561184 1540 1540 43.0 1.561184 1464 1464 44.0 1.561184 1413 1413 45.0 1.561184 1393 1393 46.0 1.561184 1326 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