## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354051.sorted.bam --OUTPUT SRX7354051.markdup.sorted.bam --METRICS_FILE SRX7354051.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: Fri Oct 27 16:59:42 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 41569 30770445 3988273 3812783 30996 10729116 0 0.34895 33125232 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 15731966 15731966 2.0 1.394983 2944050 2944050 3.0 1.550995 646492 646492 4.0 1.612616 226736 226736 5.0 1.636956 117939 117939 6.0 1.64657 74292 74292 7.0 1.650367 51426 51426 8.0 1.651867 37883 37883 9.0 1.652459 28771 28771 10.0 1.652693 22898 22898 11.0 1.652786 18498 18498 12.0 1.652822 15082 15082 13.0 1.652837 12606 12606 14.0 1.652842 10768 10768 15.0 1.652845 9209 9209 16.0 1.652845 7967 7967 17.0 1.652846 6911 6911 18.0 1.652846 6016 6016 19.0 1.652846 5357 5357 20.0 1.652846 4641 4641 21.0 1.652846 4255 4255 22.0 1.652846 3844 3844 23.0 1.652846 3414 3414 24.0 1.652846 3250 3250 25.0 1.652846 2863 2863 26.0 1.652846 2633 2633 27.0 1.652846 2411 2411 28.0 1.652846 2183 2183 29.0 1.652846 1995 1995 30.0 1.652846 1860 1860 31.0 1.652846 1697 1697 32.0 1.652846 1541 1541 33.0 1.652846 1481 1481 34.0 1.652846 1327 1327 35.0 1.652846 1260 1260 36.0 1.652846 1183 1183 37.0 1.652846 1119 1119 38.0 1.652846 989 989 39.0 1.652846 999 999 40.0 1.652846 901 901 41.0 1.652846 820 820 42.0 1.652846 828 828 43.0 1.652846 733 733 44.0 1.652846 699 699 45.0 1.652846 682 682 46.0 1.652846 652 652 47.0 1.652846 643 643 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