## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354244.sorted.bam --OUTPUT SRX7354244.markdup.sorted.bam --METRICS_FILE SRX7354244.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 19:41:31 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 13490 18280040 2369659 1687854 9193 5812334 0 0.318095 22259499 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 10596116 10596116 2.0 1.439893 1184123 1184123 3.0 1.633398 265374 265374 4.0 1.71852 115582 115582 5.0 1.755965 67991 67991 6.0 1.772436 45108 45108 7.0 1.779682 32066 32066 8.0 1.782869 23945 23945 9.0 1.784271 18558 18558 10.0 1.784888 14589 14589 11.0 1.785159 11852 11852 12.0 1.785279 9861 9861 13.0 1.785331 8189 8189 14.0 1.785354 7027 7027 15.0 1.785364 6086 6086 16.0 1.785369 5254 5254 17.0 1.785371 4534 4534 18.0 1.785372 3937 3937 19.0 1.785372 3545 3545 20.0 1.785372 3069 3069 21.0 1.785372 2860 2860 22.0 1.785372 2506 2506 23.0 1.785372 2221 2221 24.0 1.785372 2118 2118 25.0 1.785372 1950 1950 26.0 1.785372 1640 1640 27.0 1.785372 1606 1606 28.0 1.785372 1475 1475 29.0 1.785372 1320 1320 30.0 1.785372 1229 1229 31.0 1.785372 1081 1081 32.0 1.785372 1083 1083 33.0 1.785372 982 982 34.0 1.785372 918 918 35.0 1.785372 838 838 36.0 1.785372 845 845 37.0 1.785372 689 689 38.0 1.785372 703 703 39.0 1.785372 671 671 40.0 1.785372 599 599 41.0 1.785372 533 533 42.0 1.785372 558 558 43.0 1.785372 489 489 44.0 1.785372 502 502 45.0 1.785372 411 411 46.0 1.785372 407 407 47.0 1.785372 429 429 48.0 1.785372 347 347 49.0 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