## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354284.sorted.bam --OUTPUT SRX7354284.markdup.sorted.bam --METRICS_FILE SRX7354284.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 20:05:15 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 47430 30903913 3738161 6618840 39107 15751258 0 0.509926 18770495 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 9366837 9366837 2.0 1.192741 3398064 3398064 3.0 1.22989 1193472 1193472 4.0 1.23705 455385 455385 5.0 1.23843 206918 206918 6.0 1.238696 115197 115197 7.0 1.238747 74394 74394 8.0 1.238757 52312 52312 9.0 1.238759 39472 39472 10.0 1.238759 30896 30896 11.0 1.238759 25058 25058 12.0 1.238759 20539 20539 13.0 1.238759 17276 17276 14.0 1.238759 14449 14449 15.0 1.238759 12271 12271 16.0 1.238759 11042 11042 17.0 1.238759 9418 9418 18.0 1.238759 8352 8352 19.0 1.238759 7214 7214 20.0 1.238759 6563 6563 21.0 1.238759 5731 5731 22.0 1.238759 5095 5095 23.0 1.238759 4704 4704 24.0 1.238759 4159 4159 25.0 1.238759 3846 3846 26.0 1.238759 3551 3551 27.0 1.238759 3339 3339 28.0 1.238759 2999 2999 29.0 1.238759 2774 2774 30.0 1.238759 2553 2553 31.0 1.238759 2370 2370 32.0 1.238759 2241 2241 33.0 1.238759 2024 2024 34.0 1.238759 1873 1873 35.0 1.238759 1850 1850 36.0 1.238759 1674 1674 37.0 1.238759 1541 1541 38.0 1.238759 1407 1407 39.0 1.238759 1385 1385 40.0 1.238759 1222 1222 41.0 1.238759 1238 1238 42.0 1.238759 1175 1175 43.0 1.238759 1112 1112 44.0 1.238759 1006 1006 45.0 1.238759 968 968 46.0 1.238759 913 913 47.0 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