## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354385.sorted.bam --OUTPUT SRX7354385.markdup.sorted.bam --METRICS_FILE SRX7354385.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 23:44:24 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 38576 38446171 4591120 4978660 30021 16432819 0 0.4276 30950248 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 15858153 15858153 2.0 1.28875 4067703 4067703 3.0 1.372127 1037101 1037101 4.0 1.396202 345278 345278 5.0 1.403154 165936 165936 6.0 1.405161 101762 101762 7.0 1.405741 70357 70357 8.0 1.405908 51941 51941 9.0 1.405957 40077 40077 10.0 1.40597 32118 32118 11.0 1.405975 25895 25895 12.0 1.405976 21469 21469 13.0 1.405976 18336 18336 14.0 1.405976 15453 15453 15.0 1.405976 13275 13275 16.0 1.405976 11411 11411 17.0 1.405976 10253 10253 18.0 1.405976 9037 9037 19.0 1.405976 8185 8185 20.0 1.405976 7280 7280 21.0 1.405976 6641 6641 22.0 1.405976 5729 5729 23.0 1.405976 5258 5258 24.0 1.405976 4864 4864 25.0 1.405976 4496 4496 26.0 1.405976 4086 4086 27.0 1.405976 3722 3722 28.0 1.405976 3404 3404 29.0 1.405976 3142 3142 30.0 1.405976 2924 2924 31.0 1.405976 2768 2768 32.0 1.405976 2508 2508 33.0 1.405976 2342 2342 34.0 1.405976 2219 2219 35.0 1.405976 2052 2052 36.0 1.405976 1913 1913 37.0 1.405976 1761 1761 38.0 1.405976 1702 1702 39.0 1.405976 1592 1592 40.0 1.405976 1486 1486 41.0 1.405976 1402 1402 42.0 1.405976 1343 1343 43.0 1.405976 1344 1344 44.0 1.405976 1195 1195 45.0 1.405976 1175 1175 46.0 1.405976 1117 1117 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