## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354302.sorted.bam --OUTPUT SRX7354302.markdup.sorted.bam --METRICS_FILE SRX7354302.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 23:09:28 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 44880 32238826 4213915 9622506 34712 11162369 0 0.346537 35038964 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17813021 17813021 2.0 1.398485 1979024 1979024 3.0 1.557276 474337 474337 4.0 1.620551 216364 216364 5.0 1.645766 129052 129052 6.0 1.655813 86212 86212 7.0 1.659817 61459 61459 8.0 1.661412 45839 45839 9.0 1.662048 35606 35606 10.0 1.662302 28456 28456 11.0 1.662402 22976 22976 12.0 1.662443 18855 18855 13.0 1.662459 16019 16019 14.0 1.662465 13602 13602 15.0 1.662468 11755 11755 16.0 1.662469 10217 10217 17.0 1.662469 8991 8991 18.0 1.662469 7781 7781 19.0 1.662469 6998 6998 20.0 1.662469 6266 6266 21.0 1.662469 5503 5503 22.0 1.662469 4930 4930 23.0 1.662469 4566 4566 24.0 1.662469 4149 4149 25.0 1.662469 3706 3706 26.0 1.662469 3448 3448 27.0 1.662469 3182 3182 28.0 1.662469 2945 2945 29.0 1.662469 2686 2686 30.0 1.662469 2374 2374 31.0 1.662469 2212 2212 32.0 1.662469 2186 2186 33.0 1.662469 1947 1947 34.0 1.662469 1797 1797 35.0 1.662469 1711 1711 36.0 1.662469 1634 1634 37.0 1.662469 1456 1456 38.0 1.662469 1444 1444 39.0 1.662469 1300 1300 40.0 1.662469 1281 1281 41.0 1.662469 1179 1179 42.0 1.662469 1077 1077 43.0 1.662469 1038 1038 44.0 1.662469 1001 1001 45.0 1.662469 854 854 46.0 1.662469 872 872 47.0 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