## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354411.sorted.bam --OUTPUT SRX7354411.markdup.sorted.bam --METRICS_FILE SRX7354411.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 23:26:40 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 30051 36443652 4109397 3068627 21550 12895517 0 0.353998 38453224 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19925229 19925229 2.0 1.387616 2260259 2260259 3.0 1.537862 508885 508885 4.0 1.5961 221932 221932 5.0 1.618674 130844 130844 6.0 1.627424 87491 87491 7.0 1.630816 62889 62889 8.0 1.63213 47359 47359 9.0 1.63264 37242 37242 10.0 1.632838 29609 29609 11.0 1.632914 24749 24749 12.0 1.632944 20533 20533 13.0 1.632955 17363 17363 14.0 1.63296 14808 14808 15.0 1.632962 13041 13041 16.0 1.632962 11236 11236 17.0 1.632962 9934 9934 18.0 1.632963 8813 8813 19.0 1.632963 7616 7616 20.0 1.632963 6948 6948 21.0 1.632963 6239 6239 22.0 1.632963 5769 5769 23.0 1.632963 5253 5253 24.0 1.632963 4679 4679 25.0 1.632963 4282 4282 26.0 1.632963 3877 3877 27.0 1.632963 3563 3563 28.0 1.632963 3379 3379 29.0 1.632963 3047 3047 30.0 1.632963 2862 2862 31.0 1.632963 2632 2632 32.0 1.632963 2441 2441 33.0 1.632963 2331 2331 34.0 1.632963 2117 2117 35.0 1.632963 2062 2062 36.0 1.632963 1942 1942 37.0 1.632963 1721 1721 38.0 1.632963 1658 1658 39.0 1.632963 1538 1538 40.0 1.632963 1523 1523 41.0 1.632963 1456 1456 42.0 1.632963 1327 1327 43.0 1.632963 1295 1295 44.0 1.632963 1193 1193 45.0 1.632963 1091 1091 46.0 1.632963 1053 1053 47.0 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