## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354106.sorted.bam --OUTPUT SRX7354106.markdup.sorted.bam --METRICS_FILE SRX7354106.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 15:16:23 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 70606 39748364 5679056 2190528 62771 25373883 0 0.638585 15593118 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 6862888 6862888 2.0 1.078152 3300649 3300649 3.0 1.08426 1721408 1721408 4.0 1.084737 918469 918469 5.0 1.084775 500836 500836 6.0 1.084778 285230 285230 7.0 1.084778 172410 172410 8.0 1.084778 112318 112318 9.0 1.084778 77860 77860 10.0 1.084778 57252 57252 11.0 1.084778 44301 44301 12.0 1.084778 35320 35320 13.0 1.084778 29257 29257 14.0 1.084778 24654 24654 15.0 1.084778 20413 20413 16.0 1.084778 17916 17916 17.0 1.084778 15201 15201 18.0 1.084778 13537 13537 19.0 1.084778 11896 11896 20.0 1.084778 10638 10638 21.0 1.084778 9427 9427 22.0 1.084778 8262 8262 23.0 1.084778 7585 7585 24.0 1.084778 7047 7047 25.0 1.084778 6308 6308 26.0 1.084778 5826 5826 27.0 1.084778 5287 5287 28.0 1.084778 4864 4864 29.0 1.084778 4464 4464 30.0 1.084778 4096 4096 31.0 1.084778 3835 3835 32.0 1.084778 3485 3485 33.0 1.084778 3259 3259 34.0 1.084778 3053 3053 35.0 1.084778 2815 2815 36.0 1.084778 2685 2685 37.0 1.084778 2454 2454 38.0 1.084778 2387 2387 39.0 1.084778 2197 2197 40.0 1.084778 2190 2190 41.0 1.084778 1916 1916 42.0 1.084778 1873 1873 43.0 1.084778 1663 1663 44.0 1.084778 1554 1554 45.0 1.084778 1587 1587 46.0 1.084778 1454 1454 47.0 1.084778 1325 1325 48.0 1.084778 1330 1330 49.0 1.084778 1307 1307 50.0 1.084778 1246 1246 51.0 1.084778 1133 1133 52.0 1.084778 1070 1070 53.0 1.084778 1095 1095 54.0 1.084778 983 983 55.0 1.084778 917 917 56.0 1.084778 907 907 57.0 1.084778 900 900 58.0 1.084778 820 820 59.0 1.084778 822 822 60.0 1.084778 755 755 61.0 1.084778 766 766 62.0 1.084778 721 721 63.0 1.084778 646 646 64.0 1.084778 640 640 65.0 1.084778 591 591 66.0 1.084778 566 566 67.0 1.084778 595 595 68.0 1.084778 535 535 69.0 1.084778 585 585 70.0 1.084778 516 516 71.0 1.084778 495 495 72.0 1.084778 465 465 73.0 1.084778 433 433 74.0 1.084778 463 463 75.0 1.084778 422 422 76.0 1.084778 395 395 77.0 1.084778 401 401 78.0 1.084778 377 377 79.0 1.084778 373 373 80.0 1.084778 357 357 81.0 1.084778 364 364 82.0 1.084778 335 335 83.0 1.084778 331 331 84.0 1.084778 311 311 85.0 1.084778 336 336 86.0 1.084778 303 303 87.0 1.084778 297 297 88.0 1.084778 271 271 89.0 1.084778 291 291 90.0 1.084778 279 279 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