## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354148.sorted.bam --OUTPUT SRX7354148.markdup.sorted.bam --METRICS_FILE SRX7354148.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 20:34:08 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 25291 28816820 3707210 3004879 17043 9664848 0 0.335538 32692987 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16933265 16933265 2.0 1.414187 1199812 1199812 3.0 1.585738 336453 336453 4.0 1.656792 167698 167698 5.0 1.686222 103642 103642 6.0 1.698412 70289 70289 7.0 1.70346 51361 51361 8.0 1.705551 38858 38858 9.0 1.706417 30609 30609 10.0 1.706776 24734 24734 11.0 1.706925 20276 20276 12.0 1.706986 17009 17009 13.0 1.707012 14381 14381 14.0 1.707022 12389 12389 15.0 1.707027 10640 10640 16.0 1.707029 9441 9441 17.0 1.707029 8197 8197 18.0 1.70703 7130 7130 19.0 1.70703 6446 6446 20.0 1.70703 5737 5737 21.0 1.70703 5246 5246 22.0 1.70703 4847 4847 23.0 1.70703 4350 4350 24.0 1.70703 3902 3902 25.0 1.70703 3527 3527 26.0 1.70703 3258 3258 27.0 1.70703 3111 3111 28.0 1.70703 2857 2857 29.0 1.70703 2532 2532 30.0 1.70703 2310 2310 31.0 1.70703 2271 2271 32.0 1.70703 2017 2017 33.0 1.70703 1891 1891 34.0 1.70703 1890 1890 35.0 1.70703 1684 1684 36.0 1.70703 1592 1592 37.0 1.70703 1518 1518 38.0 1.70703 1468 1468 39.0 1.70703 1255 1255 40.0 1.70703 1255 1255 41.0 1.70703 1111 1111 42.0 1.70703 1076 1076 43.0 1.70703 1081 1081 44.0 1.70703 1006 1006 45.0 1.70703 954 954 46.0 1.70703 905 905 47.0 1.70703 772 772 48.0 1.70703 800 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