## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354392.sorted.bam --OUTPUT SRX7354392.markdup.sorted.bam --METRICS_FILE SRX7354392.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 23:56:51 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 37739 44696610 5710486 2412497 27414 13674051 0 0.306108 57235004 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 26545953 26545953 2.0 1.457979 2883232 2883232 3.0 1.667724 646044 646044 4.0 1.763783 274088 274088 5.0 1.807776 153857 153857 6.0 1.827924 99396 99396 7.0 1.837151 69954 69954 8.0 1.841377 51600 51600 9.0 1.843313 39525 39525 10.0 1.844199 31095 31095 11.0 1.844605 25341 25341 12.0 1.844791 20714 20714 13.0 1.844876 17612 17612 14.0 1.844915 14930 14930 15.0 1.844933 12594 12594 16.0 1.844941 11124 11124 17.0 1.844945 9813 9813 18.0 1.844946 8509 8509 19.0 1.844947 7584 7584 20.0 1.844948 6785 6785 21.0 1.844948 6077 6077 22.0 1.844948 5313 5313 23.0 1.844948 4836 4836 24.0 1.844948 4390 4390 25.0 1.844948 4018 4018 26.0 1.844948 3735 3735 27.0 1.844948 3420 3420 28.0 1.844948 3122 3122 29.0 1.844948 2885 2885 30.0 1.844948 2654 2654 31.0 1.844948 2507 2507 32.0 1.844948 2286 2286 33.0 1.844948 2168 2168 34.0 1.844948 2018 2018 35.0 1.844948 1833 1833 36.0 1.844948 1720 1720 37.0 1.844948 1603 1603 38.0 1.844948 1485 1485 39.0 1.844948 1430 1430 40.0 1.844948 1329 1329 41.0 1.844948 1288 1288 42.0 1.844948 1224 1224 43.0 1.844948 1154 1154 44.0 1.844948 1106 1106 45.0 1.844948 1048 1048 46.0 1.844948 949 949 47.0 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