## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354299.sorted.bam --OUTPUT SRX7354299.markdup.sorted.bam --METRICS_FILE SRX7354299.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 22:43:08 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 47354 44083363 5602778 5094696 36934 15201686 0 0.345073 48176152 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23788821 23788821 2.0 1.400498 3295201 3295201 3.0 1.560897 736370 736370 4.0 1.625137 302501 302501 5.0 1.650865 171268 171268 6.0 1.661169 111369 111369 7.0 1.665296 79294 79294 8.0 1.666948 58504 58504 9.0 1.66761 45335 45335 10.0 1.667875 35742 35742 11.0 1.667982 29061 29061 12.0 1.668024 23911 23911 13.0 1.668041 20406 20406 14.0 1.668048 16927 16927 15.0 1.668051 14821 14821 16.0 1.668052 12813 12813 17.0 1.668052 11078 11078 18.0 1.668052 9790 9790 19.0 1.668052 8608 8608 20.0 1.668052 7522 7522 21.0 1.668052 6785 6785 22.0 1.668052 6141 6141 23.0 1.668052 5593 5593 24.0 1.668052 5067 5067 25.0 1.668052 4660 4660 26.0 1.668052 4224 4224 27.0 1.668052 3971 3971 28.0 1.668052 3465 3465 29.0 1.668052 3291 3291 30.0 1.668052 3113 3113 31.0 1.668052 2790 2790 32.0 1.668052 2566 2566 33.0 1.668052 2334 2334 34.0 1.668052 2169 2169 35.0 1.668052 2056 2056 36.0 1.668052 2009 2009 37.0 1.668052 1868 1868 38.0 1.668052 1638 1638 39.0 1.668052 1603 1603 40.0 1.668052 1502 1502 41.0 1.668052 1464 1464 42.0 1.668052 1335 1335 43.0 1.668052 1245 1245 44.0 1.668052 1246 1246 45.0 1.668052 1210 1210 46.0 1.668052 987 987 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