## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354333.sorted.bam --OUTPUT SRX7354333.markdup.sorted.bam --METRICS_FILE SRX7354333.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 23:48:21 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 123180 93111872 13339599 15040988 111653 69392551 0 0.745367 24239638 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 6244545 6244545 2.0 1.021466 4897194 4897194 3.0 1.021926 3754318 3754318 4.0 1.021936 2752817 2752817 5.0 1.021936 1931896 1931896 6.0 1.021936 1301239 1301239 7.0 1.021936 848211 848211 8.0 1.021936 541991 541991 9.0 1.021936 345368 345368 10.0 1.021936 225566 225566 11.0 1.021936 152177 152177 12.0 1.021936 107212 107212 13.0 1.021936 78829 78829 14.0 1.021936 61788 61788 15.0 1.021936 49219 49219 16.0 1.021936 40418 40418 17.0 1.021936 33735 33735 18.0 1.021936 28965 28965 19.0 1.021936 24915 24915 20.0 1.021936 21743 21743 21.0 1.021936 19430 19430 22.0 1.021936 17067 17067 23.0 1.021936 15280 15280 24.0 1.021936 13830 13830 25.0 1.021936 12438 12438 26.0 1.021936 11097 11097 27.0 1.021936 10436 10436 28.0 1.021936 9227 9227 29.0 1.021936 8614 8614 30.0 1.021936 7985 7985 31.0 1.021936 7358 7358 32.0 1.021936 6801 6801 33.0 1.021936 6156 6156 34.0 1.021936 5854 5854 35.0 1.021936 5406 5406 36.0 1.021936 5095 5095 37.0 1.021936 4679 4679 38.0 1.021936 4500 4500 39.0 1.021936 4146 4146 40.0 1.021936 4045 4045 41.0 1.021936 3672 3672 42.0 1.021936 3405 3405 43.0 1.021936 3232 3232 44.0 1.021936 3157 3157 45.0 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