## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354112.sorted.bam --OUTPUT SRX7354112.markdup.sorted.bam --METRICS_FILE SRX7354112.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: Sat Oct 28 15:18:37 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 43883 37331193 4297185 7406477 34065 14357255 0 0.384821 35069561 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18518037 18518037 2.0 1.344904 2885948 2885948 3.0 1.463862 645326 645326 4.0 1.504892 252932 252932 5.0 1.519043 141385 141385 6.0 1.523924 93219 93219 7.0 1.525607 66528 66528 8.0 1.526188 50264 50264 9.0 1.526388 39096 39096 10.0 1.526457 31293 31293 11.0 1.526481 26130 26130 12.0 1.526489 21790 21790 13.0 1.526492 18425 18425 14.0 1.526493 15690 15690 15.0 1.526493 13512 13512 16.0 1.526493 11666 11666 17.0 1.526493 10597 10597 18.0 1.526493 9246 9246 19.0 1.526493 8218 8218 20.0 1.526493 7182 7182 21.0 1.526493 6746 6746 22.0 1.526493 5928 5928 23.0 1.526493 5412 5412 24.0 1.526493 4986 4986 25.0 1.526493 4675 4675 26.0 1.526493 4172 4172 27.0 1.526493 3777 3777 28.0 1.526493 3515 3515 29.0 1.526493 3332 3332 30.0 1.526493 3168 3168 31.0 1.526493 2882 2882 32.0 1.526493 2703 2703 33.0 1.526493 2396 2396 34.0 1.526493 2211 2211 35.0 1.526493 2179 2179 36.0 1.526493 2017 2017 37.0 1.526493 1887 1887 38.0 1.526493 1738 1738 39.0 1.526493 1711 1711 40.0 1.526493 1632 1632 41.0 1.526493 1510 1510 42.0 1.526493 1366 1366 43.0 1.526493 1344 1344 44.0 1.526493 1302 1302 45.0 1.526493 1203 1203 46.0 1.526493 1143 1143 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