## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354099.sorted.bam --OUTPUT SRX7354099.markdup.sorted.bam --METRICS_FILE SRX7354099.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 15:16:33 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 44182 32701198 4411598 4158452 35385 14104878 0 0.431576 25966584 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 13510712 13510712 2.0 1.283836 3147421 3147421 3.0 1.3644 886869 886869 4.0 1.387266 345870 345870 5.0 1.393757 179907 179907 6.0 1.395599 111571 111571 7.0 1.396122 75550 75550 8.0 1.39627 54534 54534 9.0 1.396312 40890 40890 10.0 1.396324 31742 31742 11.0 1.396328 25302 25302 12.0 1.396329 20801 20801 13.0 1.396329 17246 17246 14.0 1.396329 14417 14417 15.0 1.396329 12218 12218 16.0 1.396329 10361 10361 17.0 1.396329 8991 8991 18.0 1.396329 7918 7918 19.0 1.396329 6870 6870 20.0 1.396329 6268 6268 21.0 1.396329 5471 5471 22.0 1.396329 4968 4968 23.0 1.396329 4460 4460 24.0 1.396329 3990 3990 25.0 1.396329 3724 3724 26.0 1.396329 3356 3356 27.0 1.396329 3061 3061 28.0 1.396329 2838 2838 29.0 1.396329 2492 2492 30.0 1.396329 2329 2329 31.0 1.396329 2157 2157 32.0 1.396329 1976 1976 33.0 1.396329 1878 1878 34.0 1.396329 1733 1733 35.0 1.396329 1581 1581 36.0 1.396329 1488 1488 37.0 1.396329 1321 1321 38.0 1.396329 1371 1371 39.0 1.396329 1254 1254 40.0 1.396329 1202 1202 41.0 1.396329 1123 1123 42.0 1.396329 1014 1014 43.0 1.396329 971 971 44.0 1.396329 973 973 45.0 1.396329 866 866 46.0 1.396329 815 815 47.0 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