## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354146.sorted.bam --OUTPUT SRX7354146.markdup.sorted.bam --METRICS_FILE SRX7354146.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: Fri Oct 27 18:24:31 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 95419 41758058 6378173 1498271 82393 26319500 0 0.630552 16853023 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 6744865 6744865 2.0 1.083929 3342763 3342763 3.0 1.090974 2002046 2002046 4.0 1.091565 1237397 1237397 5.0 1.091614 758097 758097 6.0 1.091619 459512 459512 7.0 1.091619 278107 278107 8.0 1.091619 170553 170553 9.0 1.091619 106205 106205 10.0 1.091619 68204 68204 11.0 1.091619 46624 46624 12.0 1.091619 33687 33687 13.0 1.091619 25225 25225 14.0 1.091619 19903 19903 15.0 1.091619 16008 16008 16.0 1.091619 13387 13387 17.0 1.091619 11331 11331 18.0 1.091619 9732 9732 19.0 1.091619 8263 8263 20.0 1.091619 7407 7407 21.0 1.091619 6412 6412 22.0 1.091619 5530 5530 23.0 1.091619 4922 4922 24.0 1.091619 4378 4378 25.0 1.091619 3929 3929 26.0 1.091619 3657 3657 27.0 1.091619 3257 3257 28.0 1.091619 2967 2967 29.0 1.091619 2682 2682 30.0 1.091619 2441 2441 31.0 1.091619 2287 2287 32.0 1.091619 2116 2116 33.0 1.091619 1929 1929 34.0 1.091619 1840 1840 35.0 1.091619 1708 1708 36.0 1.091619 1538 1538 37.0 1.091619 1373 1373 38.0 1.091619 1293 1293 39.0 1.091619 1206 1206 40.0 1.091619 1145 1145 41.0 1.091619 1037 1037 42.0 1.091619 992 992 43.0 1.091619 889 889 44.0 1.091619 875 875 45.0 1.091619 806 806 46.0 1.091619 712 712 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