## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354055.sorted.bam --OUTPUT SRX7354055.markdup.sorted.bam --METRICS_FILE SRX7354055.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 15:17:57 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 73457 50986108 7885643 2076971 58343 22744997 0 0.446352 38451689 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23578740 23578740 2.0 1.265543 2563761 2563761 3.0 1.336056 697352 697352 4.0 1.35478 337274 337274 5.0 1.359752 206544 206544 6.0 1.361073 139408 139408 7.0 1.361423 102318 102318 8.0 1.361516 77732 77732 9.0 1.361541 61334 61334 10.0 1.361548 49310 49310 11.0 1.36155 40696 40696 12.0 1.36155 34081 34081 13.0 1.36155 29074 29074 14.0 1.36155 25121 25121 15.0 1.36155 22015 22015 16.0 1.36155 19202 19202 17.0 1.36155 16993 16993 18.0 1.36155 15069 15069 19.0 1.36155 13659 13659 20.0 1.36155 12085 12085 21.0 1.36155 10896 10896 22.0 1.36155 10150 10150 23.0 1.36155 9326 9326 24.0 1.36155 8388 8388 25.0 1.36155 7686 7686 26.0 1.36155 7105 7105 27.0 1.36155 6591 6591 28.0 1.36155 6070 6070 29.0 1.36155 5692 5692 30.0 1.36155 5344 5344 31.0 1.36155 4969 4969 32.0 1.36155 4706 4706 33.0 1.36155 4357 4357 34.0 1.36155 4020 4020 35.0 1.36155 3829 3829 36.0 1.36155 3650 3650 37.0 1.36155 3436 3436 38.0 1.36155 3235 3235 39.0 1.36155 3112 3112 40.0 1.36155 2833 2833 41.0 1.36155 2675 2675 42.0 1.36155 2596 2596 43.0 1.36155 2467 2467 44.0 1.36155 2440 2440 45.0 1.36155 2206 2206 46.0 1.36155 2081 2081 47.0 1.36155 2014 2014 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