## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354345.sorted.bam --OUTPUT SRX7354345.markdup.sorted.bam --METRICS_FILE SRX7354345.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 23:51:06 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 84238 48264211 6618306 8794340 60418 13485546 0 0.279793 69392599 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 29181120 29181120 2.0 1.498813 3930551 3930551 3.0 1.747628 779710 779710 4.0 1.871739 280140 280140 5.0 1.933648 146927 146927 6.0 1.964529 92304 92304 7.0 1.979933 63722 63722 8.0 1.987616 46549 46549 9.0 1.991449 35519 35519 10.0 1.993361 28111 28111 11.0 1.994314 22177 22177 12.0 1.99479 18377 18377 13.0 1.995027 15638 15638 14.0 1.995146 13162 13162 15.0 1.995205 11137 11137 16.0 1.995234 9743 9743 17.0 1.995249 8366 8366 18.0 1.995256 7472 7472 19.0 1.99526 6362 6362 20.0 1.995262 5793 5793 21.0 1.995263 5145 5145 22.0 1.995263 4598 4598 23.0 1.995263 4218 4218 24.0 1.995263 3805 3805 25.0 1.995263 3627 3627 26.0 1.995263 3269 3269 27.0 1.995263 2825 2825 28.0 1.995263 2757 2757 29.0 1.995263 2392 2392 30.0 1.995263 2239 2239 31.0 1.995263 2120 2120 32.0 1.995263 1955 1955 33.0 1.995263 1712 1712 34.0 1.995263 1675 1675 35.0 1.995263 1489 1489 36.0 1.995263 1459 1459 37.0 1.995263 1398 1398 38.0 1.995263 1319 1319 39.0 1.995263 1122 1122 40.0 1.995263 1071 1071 41.0 1.995263 1036 1036 42.0 1.995263 1003 1003 43.0 1.995263 895 895 44.0 1.995263 842 842 45.0 1.995263 841 841 46.0 1.995263 786 786 47.0 1.995263 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