## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354174.sorted.bam --OUTPUT SRX7354174.markdup.sorted.bam --METRICS_FILE SRX7354174.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: Sat Oct 28 15:18:01 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 26145 24367368 3936006 2150599 19912 8585991 0 0.352576 25860018 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 13379704 13379704 2.0 1.389738 1363189 1363189 3.0 1.541634 381501 381501 4.0 1.600834 182412 182412 5.0 1.623906 107625 107625 6.0 1.632899 70602 70602 7.0 1.636403 49558 49558 8.0 1.637769 37119 37119 9.0 1.638301 28469 28469 10.0 1.638509 22475 22475 11.0 1.63859 18262 18262 12.0 1.638621 14860 14860 13.0 1.638634 12363 12363 14.0 1.638638 10605 10605 15.0 1.63864 9060 9060 16.0 1.638641 7808 7808 17.0 1.638641 6782 6782 18.0 1.638641 6065 6065 19.0 1.638641 5346 5346 20.0 1.638641 4681 4681 21.0 1.638641 4224 4224 22.0 1.638641 3850 3850 23.0 1.638641 3466 3466 24.0 1.638641 3084 3084 25.0 1.638641 2838 2838 26.0 1.638641 2601 2601 27.0 1.638641 2290 2290 28.0 1.638641 2162 2162 29.0 1.638641 1964 1964 30.0 1.638641 1813 1813 31.0 1.638641 1722 1722 32.0 1.638641 1546 1546 33.0 1.638641 1503 1503 34.0 1.638641 1367 1367 35.0 1.638641 1307 1307 36.0 1.638641 1193 1193 37.0 1.638641 1088 1088 38.0 1.638641 1067 1067 39.0 1.638641 920 920 40.0 1.638641 953 953 41.0 1.638641 828 828 42.0 1.638641 784 784 43.0 1.638641 749 749 44.0 1.638641 729 729 45.0 1.638641 706 706 46.0 1.638641 677 677 47.0 1.638641 610 610 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