## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354266.sorted.bam --OUTPUT SRX7354266.markdup.sorted.bam --METRICS_FILE SRX7354266.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 22:05:14 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 17507 28127383 3693035 1250291 13025 11780265 0 0.41892 23343317 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 12535563 12535563 2.0 1.299709 2486687 2486687 3.0 1.389534 586042 586042 4.0 1.416456 210008 210008 5.0 1.424524 110528 110528 6.0 1.426943 71826 71826 7.0 1.427667 51233 51233 8.0 1.427885 38919 38919 9.0 1.42795 30565 30565 10.0 1.427969 24802 24802 11.0 1.427975 20494 20494 12.0 1.427977 17197 17197 13.0 1.427977 14418 14418 14.0 1.427977 12294 12294 15.0 1.427977 10936 10936 16.0 1.427978 9400 9400 17.0 1.427978 8315 8315 18.0 1.427978 7366 7366 19.0 1.427978 6781 6781 20.0 1.427978 6120 6120 21.0 1.427978 5384 5384 22.0 1.427978 4805 4805 23.0 1.427978 4466 4466 24.0 1.427978 3978 3978 25.0 1.427978 3757 3757 26.0 1.427978 3457 3457 27.0 1.427978 3140 3140 28.0 1.427978 3028 3028 29.0 1.427978 2625 2625 30.0 1.427978 2450 2450 31.0 1.427978 2394 2394 32.0 1.427978 2189 2189 33.0 1.427978 2051 2051 34.0 1.427978 1881 1881 35.0 1.427978 1865 1865 36.0 1.427978 1658 1658 37.0 1.427978 1550 1550 38.0 1.427978 1467 1467 39.0 1.427978 1388 1388 40.0 1.427978 1299 1299 41.0 1.427978 1219 1219 42.0 1.427978 1133 1133 43.0 1.427978 1128 1128 44.0 1.427978 1054 1054 45.0 1.427978 995 995 46.0 1.427978 947 947 47.0 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