## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354221.sorted.bam --OUTPUT SRX7354221.markdup.sorted.bam --METRICS_FILE SRX7354221.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 19:51:32 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 29765 36477526 4097649 3474061 21149 12722751 0 0.348931 39253629 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19615016 19615016 2.0 1.394839 2725195 2725195 3.0 1.550736 578635 578635 4.0 1.612291 228523 228523 5.0 1.636595 129677 129677 6.0 1.646191 85783 85783 7.0 1.64998 61072 61072 8.0 1.651476 46453 46453 9.0 1.652067 35987 35987 10.0 1.6523 28597 28597 11.0 1.652392 23595 23595 12.0 1.652428 19624 19624 13.0 1.652443 16776 16776 14.0 1.652448 14296 14296 15.0 1.652451 12369 12369 16.0 1.652452 10649 10649 17.0 1.652452 9221 9221 18.0 1.652452 8368 8368 19.0 1.652452 7329 7329 20.0 1.652452 6477 6477 21.0 1.652452 6005 6005 22.0 1.652452 5239 5239 23.0 1.652452 4792 4792 24.0 1.652452 4299 4299 25.0 1.652452 4055 4055 26.0 1.652452 3631 3631 27.0 1.652452 3336 3336 28.0 1.652452 3289 3289 29.0 1.652452 2826 2826 30.0 1.652452 2625 2625 31.0 1.652452 2338 2338 32.0 1.652452 2247 2247 33.0 1.652452 2088 2088 34.0 1.652452 1969 1969 35.0 1.652452 1784 1784 36.0 1.652452 1771 1771 37.0 1.652452 1555 1555 38.0 1.652452 1479 1479 39.0 1.652452 1423 1423 40.0 1.652452 1395 1395 41.0 1.652452 1269 1269 42.0 1.652452 1195 1195 43.0 1.652452 1048 1048 44.0 1.652452 1085 1085 45.0 1.652452 1085 1085 46.0 1.652452 962 962 47.0 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