## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354380.sorted.bam --OUTPUT SRX7354380.markdup.sorted.bam --METRICS_FILE SRX7354380.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 22:53:04 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 28776 32450754 4051924 3222682 21266 11450020 0 0.353014 34373639 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17972461 17972461 2.0 1.389045 1781799 1781799 3.0 1.540402 440825 440825 4.0 1.599286 207770 207770 5.0 1.622195 123946 123946 6.0 1.631107 83027 83027 7.0 1.634575 60438 60438 8.0 1.635924 45479 45479 9.0 1.636449 35641 35641 10.0 1.636653 28345 28345 11.0 1.636732 23336 23336 12.0 1.636763 19443 19443 13.0 1.636775 16415 16415 14.0 1.63678 14174 14174 15.0 1.636782 12352 12352 16.0 1.636782 10524 10524 17.0 1.636783 9160 9160 18.0 1.636783 8215 8215 19.0 1.636783 7193 7193 20.0 1.636783 6512 6512 21.0 1.636783 5967 5967 22.0 1.636783 5383 5383 23.0 1.636783 4927 4927 24.0 1.636783 4438 4438 25.0 1.636783 4161 4161 26.0 1.636783 3673 3673 27.0 1.636783 3431 3431 28.0 1.636783 3142 3142 29.0 1.636783 2955 2955 30.0 1.636783 2681 2681 31.0 1.636783 2565 2565 32.0 1.636783 2338 2338 33.0 1.636783 2185 2185 34.0 1.636783 2053 2053 35.0 1.636783 1900 1900 36.0 1.636783 1769 1769 37.0 1.636783 1654 1654 38.0 1.636783 1595 1595 39.0 1.636783 1427 1427 40.0 1.636783 1394 1394 41.0 1.636783 1312 1312 42.0 1.636783 1260 1260 43.0 1.636783 1146 1146 44.0 1.636783 1115 1115 45.0 1.636783 1052 1052 46.0 1.636783 968 968 47.0 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