## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354407.sorted.bam --OUTPUT SRX7354407.markdup.sorted.bam --METRICS_FILE SRX7354407.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: Tue Oct 31 00:46:05 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 70360 52310149 6392050 8777822 55063 18477959 0 0.353527 55324990 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 27946452 27946452 2.0 1.388483 3792334 3792334 3.0 1.539401 853705 853705 4.0 1.598031 347612 347612 5.0 1.620807 195137 195137 6.0 1.629656 127810 127810 7.0 1.633093 90275 90275 8.0 1.634428 67458 67458 9.0 1.634947 52203 52203 10.0 1.635149 41622 41622 11.0 1.635227 33748 33748 12.0 1.635257 28460 28460 13.0 1.635269 23982 23982 14.0 1.635274 20063 20063 15.0 1.635276 17270 17270 16.0 1.635276 15255 15255 17.0 1.635276 13602 13602 18.0 1.635277 11858 11858 19.0 1.635277 10550 10550 20.0 1.635277 9379 9379 21.0 1.635277 8440 8440 22.0 1.635277 7587 7587 23.0 1.635277 7046 7046 24.0 1.635277 6262 6262 25.0 1.635277 5685 5685 26.0 1.635277 5345 5345 27.0 1.635277 4825 4825 28.0 1.635277 4507 4507 29.0 1.635277 4141 4141 30.0 1.635277 3831 3831 31.0 1.635277 3574 3574 32.0 1.635277 3356 3356 33.0 1.635277 3066 3066 34.0 1.635277 2873 2873 35.0 1.635277 2646 2646 36.0 1.635277 2473 2473 37.0 1.635277 2395 2395 38.0 1.635277 2226 2226 39.0 1.635277 2072 2072 40.0 1.635277 1986 1986 41.0 1.635277 1859 1859 42.0 1.635277 1808 1808 43.0 1.635277 1635 1635 44.0 1.635277 1585 1585 45.0 1.635277 1444 1444 46.0 1.635277 1368 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