## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354172.sorted.bam --OUTPUT SRX7354172.markdup.sorted.bam --METRICS_FILE SRX7354172.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: Fri Oct 27 17:03:18 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 29223 31082532 3800012 3049015 22010 11467286 0 0.369111 30959268 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16668178 16668178 2.0 1.366418 1772215 1772215 3.0 1.50068 408360 408360 4.0 1.549875 189004 189004 5.0 1.567902 114029 114029 6.0 1.574507 77508 77508 7.0 1.576927 56736 56736 8.0 1.577814 43394 43394 9.0 1.578139 33964 33964 10.0 1.578258 27455 27455 11.0 1.578302 23072 23072 12.0 1.578318 19137 19137 13.0 1.578323 16167 16167 14.0 1.578326 14003 14003 15.0 1.578326 12152 12152 16.0 1.578327 10566 10566 17.0 1.578327 9453 9453 18.0 1.578327 8262 8262 19.0 1.578327 7560 7560 20.0 1.578327 6592 6592 21.0 1.578327 5981 5981 22.0 1.578327 5597 5597 23.0 1.578327 4975 4975 24.0 1.578327 4591 4591 25.0 1.578327 4147 4147 26.0 1.578327 3858 3858 27.0 1.578327 3550 3550 28.0 1.578327 3156 3156 29.0 1.578327 2929 2929 30.0 1.578327 2781 2781 31.0 1.578327 2618 2618 32.0 1.578327 2393 2393 33.0 1.578327 2161 2161 34.0 1.578327 2074 2074 35.0 1.578327 2006 2006 36.0 1.578327 1858 1858 37.0 1.578327 1735 1735 38.0 1.578327 1653 1653 39.0 1.578327 1549 1549 40.0 1.578327 1455 1455 41.0 1.578327 1364 1364 42.0 1.578327 1285 1285 43.0 1.578327 1186 1186 44.0 1.578327 1162 1162 45.0 1.578327 1167 1167 46.0 1.578327 1090 1090 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