## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354067.sorted.bam --OUTPUT SRX7354067.markdup.sorted.bam --METRICS_FILE SRX7354067.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 16:57:17 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 25078 29619433 4144222 2359404 17891 10720346 0 0.362085 30296224 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16496697 16496697 2.0 1.37619 1263126 1263126 3.0 1.517709 374856 374856 4.0 1.570947 190096 190096 5.0 1.590975 116960 116960 6.0 1.598509 78999 78999 7.0 1.601343 57802 57802 8.0 1.602409 43428 43428 9.0 1.60281 34248 34248 10.0 1.602961 27245 27245 11.0 1.603018 22429 22429 12.0 1.603039 18641 18641 13.0 1.603047 15827 15827 14.0 1.60305 13543 13543 15.0 1.603052 11808 11808 16.0 1.603052 10250 10250 17.0 1.603052 9080 9080 18.0 1.603052 7981 7981 19.0 1.603052 7281 7281 20.0 1.603052 6453 6453 21.0 1.603052 5760 5760 22.0 1.603052 5155 5155 23.0 1.603052 4688 4688 24.0 1.603052 4296 4296 25.0 1.603052 3899 3899 26.0 1.603052 3624 3624 27.0 1.603052 3353 3353 28.0 1.603052 3132 3132 29.0 1.603052 2693 2693 30.0 1.603052 2656 2656 31.0 1.603052 2402 2402 32.0 1.603052 2358 2358 33.0 1.603052 2135 2135 34.0 1.603052 1937 1937 35.0 1.603052 1861 1861 36.0 1.603052 1864 1864 37.0 1.603052 1670 1670 38.0 1.603052 1548 1548 39.0 1.603052 1438 1438 40.0 1.603052 1421 1421 41.0 1.603052 1340 1340 42.0 1.603052 1200 1200 43.0 1.603052 1147 1147 44.0 1.603052 1049 1049 45.0 1.603052 984 984 46.0 1.603052 991 991 47.0 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