## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354182.sorted.bam --OUTPUT SRX7354182.markdup.sorted.bam --METRICS_FILE SRX7354182.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: Sun Oct 29 12:17:43 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 79401 35826008 4422264 18366931 61173 12047919 0 0.33677 40499192 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18762370 18762370 2.0 1.412875 3405354 3405354 3.0 1.583341 772234 772234 4.0 1.653722 269947 269947 5.0 1.68278 138049 138049 6.0 1.694778 86585 86585 7.0 1.699731 60151 60151 8.0 1.701777 44269 44269 9.0 1.702621 33965 33965 10.0 1.70297 26986 26986 11.0 1.703114 21461 21461 12.0 1.703173 17999 17999 13.0 1.703197 14869 14869 14.0 1.703208 12358 12358 15.0 1.703212 10544 10544 16.0 1.703214 9219 9219 17.0 1.703214 8047 8047 18.0 1.703215 6905 6905 19.0 1.703215 6302 6302 20.0 1.703215 5346 5346 21.0 1.703215 4821 4821 22.0 1.703215 4335 4335 23.0 1.703215 3823 3823 24.0 1.703215 3532 3532 25.0 1.703215 3137 3137 26.0 1.703215 2959 2959 27.0 1.703215 2584 2584 28.0 1.703215 2359 2359 29.0 1.703215 2258 2258 30.0 1.703215 1960 1960 31.0 1.703215 1861 1861 32.0 1.703215 1751 1751 33.0 1.703215 1616 1616 34.0 1.703215 1447 1447 35.0 1.703215 1306 1306 36.0 1.703215 1283 1283 37.0 1.703215 1179 1179 38.0 1.703215 1120 1120 39.0 1.703215 1029 1029 40.0 1.703215 987 987 41.0 1.703215 919 919 42.0 1.703215 836 836 43.0 1.703215 802 802 44.0 1.703215 737 737 45.0 1.703215 627 627 46.0 1.703215 705 705 47.0 1.703215 635 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