## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354215.sorted.bam --OUTPUT SRX7354215.markdup.sorted.bam --METRICS_FILE SRX7354215.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 20:14:44 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 28890 35211699 4367082 3278352 20828 13018959 0 0.369878 34965781 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18761464 18761464 2.0 1.365301 2131738 2131738 3.0 1.498746 473464 473464 4.0 1.547494 206505 206505 5.0 1.565301 122321 122321 6.0 1.571806 82540 82540 7.0 1.574183 60038 60038 8.0 1.575051 45458 45458 9.0 1.575368 35791 35791 10.0 1.575484 29247 29247 11.0 1.575526 24276 24276 12.0 1.575542 20205 20205 13.0 1.575547 17384 17384 14.0 1.575549 14866 14866 15.0 1.57555 13029 13029 16.0 1.57555 11455 11455 17.0 1.57555 9928 9928 18.0 1.57555 8923 8923 19.0 1.57555 7830 7830 20.0 1.57555 7261 7261 21.0 1.57555 6474 6474 22.0 1.57555 5915 5915 23.0 1.57555 5402 5402 24.0 1.57555 5062 5062 25.0 1.57555 4509 4509 26.0 1.57555 4056 4056 27.0 1.57555 3770 3770 28.0 1.57555 3545 3545 29.0 1.57555 3318 3318 30.0 1.57555 3096 3096 31.0 1.57555 2856 2856 32.0 1.57555 2619 2619 33.0 1.57555 2451 2451 34.0 1.57555 2342 2342 35.0 1.57555 2186 2186 36.0 1.57555 2023 2023 37.0 1.57555 1916 1916 38.0 1.57555 1777 1777 39.0 1.57555 1645 1645 40.0 1.57555 1619 1619 41.0 1.57555 1509 1509 42.0 1.57555 1448 1448 43.0 1.57555 1430 1430 44.0 1.57555 1271 1271 45.0 1.57555 1205 1205 46.0 1.57555 1192 1192 47.0 1.57555 1127 1127 48.0 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