## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354381.sorted.bam --OUTPUT SRX7354381.markdup.sorted.bam --METRICS_FILE SRX7354381.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 22:52:08 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 37168 28982148 4472961 3511822 26076 8920997 0 0.308062 36818578 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17714376 17714376 2.0 1.455135 1354874 1354874 3.0 1.662283 348930 348930 4.0 1.756563 168249 168249 5.0 1.799474 100326 100326 6.0 1.819004 67206 67206 7.0 1.827892 47986 47986 8.0 1.831938 36346 36346 9.0 1.833779 28528 28528 10.0 1.834617 22522 22522 11.0 1.834999 18497 18497 12.0 1.835172 15312 15312 13.0 1.835251 12768 12768 14.0 1.835287 11013 11013 15.0 1.835304 9485 9485 16.0 1.835311 8136 8136 17.0 1.835314 7480 7480 18.0 1.835316 6432 6432 19.0 1.835317 5842 5842 20.0 1.835317 5111 5111 21.0 1.835317 4591 4591 22.0 1.835317 4091 4091 23.0 1.835317 3746 3746 24.0 1.835317 3510 3510 25.0 1.835317 3087 3087 26.0 1.835317 2969 2969 27.0 1.835317 2560 2560 28.0 1.835317 2514 2514 29.0 1.835317 2207 2207 30.0 1.835317 2103 2103 31.0 1.835317 1915 1915 32.0 1.835317 1751 1751 33.0 1.835317 1719 1719 34.0 1.835317 1589 1589 35.0 1.835317 1438 1438 36.0 1.835317 1322 1322 37.0 1.835317 1239 1239 38.0 1.835317 1200 1200 39.0 1.835317 1143 1143 40.0 1.835317 1051 1051 41.0 1.835317 1002 1002 42.0 1.835317 956 956 43.0 1.835317 864 864 44.0 1.835317 845 845 45.0 1.835317 730 730 46.0 1.835317 847 847 47.0 1.835317 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