## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354115.sorted.bam --OUTPUT SRX7354115.markdup.sorted.bam --METRICS_FILE SRX7354115.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 17:44:17 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 27295 29814529 3820271 3143329 19300 8478928 0 0.284583 41920661 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17727823 17727823 2.0 1.491048 2502126 2502126 3.0 1.732176 510790 510790 4.0 1.850582 187036 187036 5.0 1.908725 100272 100272 6.0 1.937276 63838 63838 7.0 1.951295 44488 44488 8.0 1.95818 32391 32391 9.0 1.96156 24633 24633 10.0 1.96322 19229 19229 11.0 1.964036 15351 15351 12.0 1.964436 12671 12671 13.0 1.964632 10438 10438 14.0 1.964729 8655 8655 15.0 1.964776 7487 7487 16.0 1.9648 6285 6285 17.0 1.964811 5615 5615 18.0 1.964817 4874 4874 19.0 1.964819 4083 4083 20.0 1.964821 3817 3817 21.0 1.964821 3326 3326 22.0 1.964822 2891 2891 23.0 1.964822 2695 2695 24.0 1.964822 2333 2333 25.0 1.964822 2119 2119 26.0 1.964822 2014 2014 27.0 1.964822 1778 1778 28.0 1.964822 1562 1562 29.0 1.964822 1535 1535 30.0 1.964822 1331 1331 31.0 1.964822 1255 1255 32.0 1.964822 1130 1130 33.0 1.964822 1019 1019 34.0 1.964822 1002 1002 35.0 1.964822 888 888 36.0 1.964822 823 823 37.0 1.964822 749 749 38.0 1.964822 719 719 39.0 1.964822 694 694 40.0 1.964822 635 635 41.0 1.964822 633 633 42.0 1.964822 563 563 43.0 1.964822 551 551 44.0 1.964822 495 495 45.0 1.964822 465 465 46.0 1.964822 442 442 47.0 1.964822 418 418 48.0 1.964822 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