## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354092.sorted.bam --OUTPUT SRX7354092.markdup.sorted.bam --METRICS_FILE SRX7354092.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: Sun Oct 29 00:58:19 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 37366 41704046 6481845 4842098 27126 13589724 0 0.32604 49165260 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23873926 23873926 2.0 1.428167 2746253 2746253 3.0 1.611494 593483 593483 4.0 1.689988 248577 248577 5.0 1.723597 142771 142771 6.0 1.737987 93306 93306 7.0 1.744149 66277 66277 8.0 1.746787 49351 49351 9.0 1.747916 38430 38430 10.0 1.7484 30100 30100 11.0 1.748607 24815 24815 12.0 1.748696 20705 20705 13.0 1.748734 17141 17141 14.0 1.74875 14709 14709 15.0 1.748757 12716 12716 16.0 1.74876 11136 11136 17.0 1.748761 9996 9996 18.0 1.748762 8650 8650 19.0 1.748762 7684 7684 20.0 1.748762 6643 6643 21.0 1.748762 6095 6095 22.0 1.748762 5552 5552 23.0 1.748762 5002 5002 24.0 1.748762 4542 4542 25.0 1.748762 4187 4187 26.0 1.748762 3800 3800 27.0 1.748762 3621 3621 28.0 1.748762 3154 3154 29.0 1.748762 2920 2920 30.0 1.748762 2776 2776 31.0 1.748762 2501 2501 32.0 1.748762 2367 2367 33.0 1.748762 2278 2278 34.0 1.748762 2006 2006 35.0 1.748762 1954 1954 36.0 1.748762 1789 1789 37.0 1.748762 1725 1725 38.0 1.748762 1700 1700 39.0 1.748762 1477 1477 40.0 1.748762 1388 1388 41.0 1.748762 1332 1332 42.0 1.748762 1298 1298 43.0 1.748762 1219 1219 44.0 1.748762 1077 1077 45.0 1.748762 1138 1138 46.0 1.748762 1019 1019 47.0 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