## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354135.sorted.bam --OUTPUT SRX7354135.markdup.sorted.bam --METRICS_FILE SRX7354135.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 17:04:06 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 33766 32877541 4090272 5995000 25938 13123995 0 0.399368 29278931 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 15529604 15529604 2.0 1.325332 2749833 2749833 3.0 1.431174 634729 634729 4.0 1.465607 237022 237022 5.0 1.476809 128333 128333 6.0 1.480454 83501 83501 7.0 1.48164 59892 59892 8.0 1.482025 44973 44973 9.0 1.482151 35067 35067 10.0 1.482192 27983 27983 11.0 1.482205 22936 22936 12.0 1.482209 19366 19366 13.0 1.482211 16330 16330 14.0 1.482211 14093 14093 15.0 1.482211 12184 12184 16.0 1.482211 10417 10417 17.0 1.482211 9378 9378 18.0 1.482211 8276 8276 19.0 1.482211 7441 7441 20.0 1.482211 6495 6495 21.0 1.482211 5974 5974 22.0 1.482211 5422 5422 23.0 1.482211 4804 4804 24.0 1.482211 4470 4470 25.0 1.482211 4105 4105 26.0 1.482211 3657 3657 27.0 1.482211 3366 3366 28.0 1.482211 3128 3128 29.0 1.482211 3026 3026 30.0 1.482211 2742 2742 31.0 1.482211 2559 2559 32.0 1.482211 2281 2281 33.0 1.482211 2252 2252 34.0 1.482211 2067 2067 35.0 1.482211 1918 1918 36.0 1.482211 1882 1882 37.0 1.482211 1726 1726 38.0 1.482211 1627 1627 39.0 1.482211 1418 1418 40.0 1.482211 1444 1444 41.0 1.482211 1308 1308 42.0 1.482211 1292 1292 43.0 1.482211 1225 1225 44.0 1.482211 1150 1150 45.0 1.482211 1083 1083 46.0 1.482211 991 991 47.0 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