## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354144.sorted.bam --OUTPUT SRX7354144.markdup.sorted.bam --METRICS_FILE SRX7354144.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: Sat Oct 28 15:19:12 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 36601 32655055 4258731 5777527 26054 9781277 0 0.299764 42972304 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19898364 19898364 2.0 1.467709 1842841 1842841 3.0 1.68646 414210 414210 4.0 1.788772 188999 188999 5.0 1.836625 112695 112695 6.0 1.859006 76241 76241 7.0 1.869473 54807 54807 8.0 1.874369 41228 41228 9.0 1.876659 31933 31933 10.0 1.87773 25521 25521 11.0 1.878231 21040 21040 12.0 1.878465 17531 17531 13.0 1.878575 14642 14642 14.0 1.878626 12625 12625 15.0 1.87865 10959 10959 16.0 1.878661 9475 9475 17.0 1.878666 8188 8188 18.0 1.878669 7101 7101 19.0 1.87867 6611 6611 20.0 1.878671 5642 5642 21.0 1.878671 5124 5124 22.0 1.878671 4685 4685 23.0 1.878671 4108 4108 24.0 1.878671 3572 3572 25.0 1.878671 3471 3471 26.0 1.878671 3028 3028 27.0 1.878671 2792 2792 28.0 1.878671 2521 2521 29.0 1.878671 2412 2412 30.0 1.878671 2217 2217 31.0 1.878671 2037 2037 32.0 1.878671 1895 1895 33.0 1.878671 1803 1803 34.0 1.878671 1676 1676 35.0 1.878671 1477 1477 36.0 1.878671 1404 1404 37.0 1.878671 1398 1398 38.0 1.878671 1247 1247 39.0 1.878671 1165 1165 40.0 1.878671 1043 1043 41.0 1.878671 1034 1034 42.0 1.878671 955 955 43.0 1.878671 935 935 44.0 1.878671 850 850 45.0 1.878671 779 779 46.0 1.878671 752 752 47.0 1.878671 688 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