## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354062.sorted.bam --OUTPUT SRX7354062.markdup.sorted.bam --METRICS_FILE SRX7354062.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: Sat Oct 28 15:18:14 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 28717 35074928 4262483 3702861 20968 13899242 0 0.396409 31567530 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16411682 16411682 2.0 1.329194 3169901 3169901 3.0 1.437563 726053 726053 4.0 1.473237 256791 256791 5.0 1.484981 134696 134696 6.0 1.488847 85333 85333 7.0 1.49012 60717 60717 8.0 1.490539 45999 45999 9.0 1.490676 34977 34977 10.0 1.490722 28051 28051 11.0 1.490737 22991 22991 12.0 1.490742 19239 19239 13.0 1.490743 16355 16355 14.0 1.490744 13808 13808 15.0 1.490744 11917 11917 16.0 1.490744 10713 10713 17.0 1.490744 9232 9232 18.0 1.490744 8213 8213 19.0 1.490744 7273 7273 20.0 1.490744 6499 6499 21.0 1.490744 5944 5944 22.0 1.490744 5325 5325 23.0 1.490744 4853 4853 24.0 1.490744 4426 4426 25.0 1.490744 4083 4083 26.0 1.490744 3694 3694 27.0 1.490744 3478 3478 28.0 1.490744 3111 3111 29.0 1.490744 3037 3037 30.0 1.490744 2652 2652 31.0 1.490744 2420 2420 32.0 1.490744 2296 2296 33.0 1.490744 2155 2155 34.0 1.490744 2036 2036 35.0 1.490744 1889 1889 36.0 1.490744 1738 1738 37.0 1.490744 1682 1682 38.0 1.490744 1545 1545 39.0 1.490744 1474 1474 40.0 1.490744 1409 1409 41.0 1.490744 1379 1379 42.0 1.490744 1286 1286 43.0 1.490744 1195 1195 44.0 1.490744 1154 1154 45.0 1.490744 1073 1073 46.0 1.490744 986 986 47.0 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