## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354129.sorted.bam --OUTPUT SRX7354129.markdup.sorted.bam --METRICS_FILE SRX7354129.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: Fri Oct 27 17:41:01 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 54553 37797570 5351383 5564533 42162 12252536 0 0.324486 44869255 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21600499 21600499 2.0 1.430678 2513076 2513076 3.0 1.616162 563312 563312 4.0 1.696046 241367 241367 5.0 1.730451 138858 138858 6.0 1.745268 92141 92141 7.0 1.751649 65161 65161 8.0 1.754398 48682 48682 9.0 1.755581 37577 37577 10.0 1.756091 29698 29698 11.0 1.756311 24188 24188 12.0 1.756405 20056 20056 13.0 1.756446 16803 16803 14.0 1.756463 14455 14455 15.0 1.756471 12357 12357 16.0 1.756474 10512 10512 17.0 1.756476 9071 9071 18.0 1.756476 8175 8175 19.0 1.756476 7185 7185 20.0 1.756477 6503 6503 21.0 1.756477 5761 5761 22.0 1.756477 5279 5279 23.0 1.756477 4619 4619 24.0 1.756477 4248 4248 25.0 1.756477 3896 3896 26.0 1.756477 3355 3355 27.0 1.756477 3233 3233 28.0 1.756477 2925 2925 29.0 1.756477 2682 2682 30.0 1.756477 2457 2457 31.0 1.756477 2374 2374 32.0 1.756477 2217 2217 33.0 1.756477 2064 2064 34.0 1.756477 1876 1876 35.0 1.756477 1781 1781 36.0 1.756477 1641 1641 37.0 1.756477 1461 1461 38.0 1.756477 1357 1357 39.0 1.756477 1355 1355 40.0 1.756477 1284 1284 41.0 1.756477 1147 1147 42.0 1.756477 1053 1053 43.0 1.756477 1024 1024 44.0 1.756477 985 985 45.0 1.756477 984 984 46.0 1.756477 923 923 47.0 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