## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354320.sorted.bam --OUTPUT SRX7354320.markdup.sorted.bam --METRICS_FILE SRX7354320.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 22:52:00 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 26707 30406980 4066335 2218915 18457 9196641 0 0.302622 39517017 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18394261 18394261 2.0 1.463261 1731967 1731967 3.0 1.677871 404940 404940 4.0 1.777292 184290 184290 5.0 1.823349 109087 109087 6.0 1.844686 72671 72671 7.0 1.85457 51579 51579 8.0 1.859149 38567 38567 9.0 1.861271 29910 29910 10.0 1.862253 23737 23737 11.0 1.862709 19238 19238 12.0 1.86292 15944 15944 13.0 1.863017 13322 13322 14.0 1.863063 11182 11182 15.0 1.863084 9543 9543 16.0 1.863093 8465 8465 17.0 1.863098 7215 7215 18.0 1.8631 6452 6452 19.0 1.863101 5768 5768 20.0 1.863101 5064 5064 21.0 1.863101 4706 4706 22.0 1.863102 4233 4233 23.0 1.863102 3743 3743 24.0 1.863102 3430 3430 25.0 1.863102 3154 3154 26.0 1.863102 2729 2729 27.0 1.863102 2536 2536 28.0 1.863102 2360 2360 29.0 1.863102 2163 2163 30.0 1.863102 2076 2076 31.0 1.863102 1873 1873 32.0 1.863102 1701 1701 33.0 1.863102 1593 1593 34.0 1.863102 1347 1347 35.0 1.863102 1380 1380 36.0 1.863102 1221 1221 37.0 1.863102 1214 1214 38.0 1.863102 1152 1152 39.0 1.863102 1042 1042 40.0 1.863102 986 986 41.0 1.863102 933 933 42.0 1.863102 837 837 43.0 1.863102 827 827 44.0 1.863102 788 788 45.0 1.863102 702 702 46.0 1.863102 725 725 47.0 1.863102 657 657 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