## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354368.sorted.bam --OUTPUT SRX7354368.markdup.sorted.bam --METRICS_FILE SRX7354368.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 22:05:22 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 39276 37136460 5499303 3059134 26278 10800180 0 0.291024 50751966 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23396691 23396691 2.0 1.481079 1746113 1746113 3.0 1.712515 425193 425193 4.0 1.823854 200518 200518 5.0 1.877417 119475 119475 6.0 1.903185 79550 79550 7.0 1.915582 57341 57341 8.0 1.921545 43291 43291 9.0 1.924414 33647 33647 10.0 1.925795 27175 27175 11.0 1.926459 22158 22158 12.0 1.926778 18596 18596 13.0 1.926932 15628 15628 14.0 1.927006 13189 13189 15.0 1.927041 11642 11642 16.0 1.927058 10052 10052 17.0 1.927067 8573 8573 18.0 1.927071 7776 7776 19.0 1.927072 6962 6962 20.0 1.927073 6173 6173 21.0 1.927074 5605 5605 22.0 1.927074 5031 5031 23.0 1.927074 4597 4597 24.0 1.927074 4150 4150 25.0 1.927074 3750 3750 26.0 1.927074 3393 3393 27.0 1.927074 3222 3222 28.0 1.927074 2965 2965 29.0 1.927074 2702 2702 30.0 1.927074 2494 2494 31.0 1.927074 2316 2316 32.0 1.927074 2166 2166 33.0 1.927074 2018 2018 34.0 1.927074 1941 1941 35.0 1.927074 1840 1840 36.0 1.927074 1616 1616 37.0 1.927074 1600 1600 38.0 1.927074 1429 1429 39.0 1.927074 1327 1327 40.0 1.927074 1306 1306 41.0 1.927074 1172 1172 42.0 1.927074 1149 1149 43.0 1.927074 1058 1058 44.0 1.927074 1037 1037 45.0 1.927074 1010 1010 46.0 1.927074 921 921 47.0 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