## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354372.sorted.bam --OUTPUT SRX7354372.markdup.sorted.bam --METRICS_FILE SRX7354372.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 22:36:26 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 24658 27348120 3576599 1856902 16844 9830078 0 0.359588 28241178 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14889969 14889969 2.0 1.379699 1567120 1567120 3.0 1.52387 378598 378598 4.0 1.578611 174882 174882 5.0 1.599396 105218 105218 6.0 1.607289 71226 71226 7.0 1.610285 50933 50933 8.0 1.611423 38260 38260 9.0 1.611855 30232 30232 10.0 1.612019 24242 24242 11.0 1.612081 19628 19628 12.0 1.612105 16540 16540 13.0 1.612114 13902 13902 14.0 1.612117 11954 11954 15.0 1.612119 10388 10388 16.0 1.612119 9094 9094 17.0 1.612119 7908 7908 18.0 1.61212 7006 7006 19.0 1.61212 6309 6309 20.0 1.61212 5615 5615 21.0 1.61212 4900 4900 22.0 1.61212 4573 4573 23.0 1.61212 4041 4041 24.0 1.61212 3718 3718 25.0 1.61212 3381 3381 26.0 1.61212 3164 3164 27.0 1.61212 2815 2815 28.0 1.61212 2627 2627 29.0 1.61212 2474 2474 30.0 1.61212 2256 2256 31.0 1.61212 2176 2176 32.0 1.61212 1939 1939 33.0 1.61212 1880 1880 34.0 1.61212 1760 1760 35.0 1.61212 1626 1626 36.0 1.61212 1501 1501 37.0 1.61212 1383 1383 38.0 1.61212 1316 1316 39.0 1.61212 1209 1209 40.0 1.61212 1172 1172 41.0 1.61212 1089 1089 42.0 1.61212 1072 1072 43.0 1.61212 1025 1025 44.0 1.61212 954 954 45.0 1.61212 910 910 46.0 1.61212 782 782 47.0 1.61212 792 792 48.0 1.61212 784 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