## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354253.sorted.bam --OUTPUT SRX7354253.markdup.sorted.bam --METRICS_FILE SRX7354253.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 19:21:55 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 17118 30535104 4287957 1130136 14629 20654235 0 0.676459 10441558 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 3206386 3206386 2.0 1.053698 2477229 2477229 3.0 1.056581 1725819 1725819 4.0 1.056736 1046448 1046448 5.0 1.056744 574116 574116 6.0 1.056745 299162 299162 7.0 1.056745 156928 156928 8.0 1.056745 87783 87783 9.0 1.056745 54518 54518 10.0 1.056745 37503 37503 11.0 1.056745 27689 27689 12.0 1.056745 21368 21368 13.0 1.056745 17513 17513 14.0 1.056745 14599 14599 15.0 1.056745 12135 12135 16.0 1.056745 10494 10494 17.0 1.056745 8921 8921 18.0 1.056745 7927 7927 19.0 1.056745 6934 6934 20.0 1.056745 6060 6060 21.0 1.056745 5567 5567 22.0 1.056745 4921 4921 23.0 1.056745 4650 4650 24.0 1.056745 4063 4063 25.0 1.056745 3730 3730 26.0 1.056745 3237 3237 27.0 1.056745 2937 2937 28.0 1.056745 2759 2759 29.0 1.056745 2485 2485 30.0 1.056745 2431 2431 31.0 1.056745 2180 2180 32.0 1.056745 2033 2033 33.0 1.056745 1848 1848 34.0 1.056745 1840 1840 35.0 1.056745 1557 1557 36.0 1.056745 1548 1548 37.0 1.056745 1468 1468 38.0 1.056745 1407 1407 39.0 1.056745 1252 1252 40.0 1.056745 1189 1189 41.0 1.056745 1106 1106 42.0 1.056745 1012 1012 43.0 1.056745 973 973 44.0 1.056745 949 949 45.0 1.056745 868 868 46.0 1.056745 774 774 47.0 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