## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354238.sorted.bam --OUTPUT SRX7354238.markdup.sorted.bam --METRICS_FILE SRX7354238.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 12:14:38 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 18977 27785923 3417449 3010313 13951 10408742 0 0.374728 27091022 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14316526 14316526 2.0 1.358563 1922840 1922840 3.0 1.487131 441877 441877 4.0 1.53323 186938 186938 5.0 1.54976 108130 108130 6.0 1.555687 72045 72045 7.0 1.557812 51525 51525 8.0 1.558574 38211 38211 9.0 1.558847 30394 30394 10.0 1.558945 23954 23954 11.0 1.55898 19782 19782 12.0 1.558993 16202 16202 13.0 1.558997 13643 13643 14.0 1.558999 11828 11828 15.0 1.558999 10036 10036 16.0 1.559 8786 8786 17.0 1.559 7842 7842 18.0 1.559 6735 6735 19.0 1.559 6090 6090 20.0 1.559 5536 5536 21.0 1.559 4926 4926 22.0 1.559 4377 4377 23.0 1.559 4017 4017 24.0 1.559 3632 3632 25.0 1.559 3395 3395 26.0 1.559 3079 3079 27.0 1.559 2808 2808 28.0 1.559 2647 2647 29.0 1.559 2447 2447 30.0 1.559 2172 2172 31.0 1.559 2169 2169 32.0 1.559 1912 1912 33.0 1.559 1727 1727 34.0 1.559 1699 1699 35.0 1.559 1571 1571 36.0 1.559 1404 1404 37.0 1.559 1275 1275 38.0 1.559 1317 1317 39.0 1.559 1225 1225 40.0 1.559 1198 1198 41.0 1.559 1142 1142 42.0 1.559 1051 1051 43.0 1.559 973 973 44.0 1.559 961 961 45.0 1.559 873 873 46.0 1.559 818 818 47.0 1.559 793 793 48.0 1.559 771 771 49.0 1.559 709 709 50.0 1.559 683 683 51.0 1.559 619 619 52.0 1.559 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