## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354068.sorted.bam --OUTPUT SRX7354068.markdup.sorted.bam --METRICS_FILE SRX7354068.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 17:40:53 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 78325 33899710 6340284 2449813 68994 22624769 0 0.667649 11982755 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 4693035 4693035 2.0 1.059069 2631785 2631785 3.0 1.062559 1528193 1528193 4.0 1.062765 879060 879060 5.0 1.062777 505866 505866 6.0 1.062778 299088 299088 7.0 1.062778 181967 181967 8.0 1.062778 115644 115644 9.0 1.062778 77681 77681 10.0 1.062778 54496 54496 11.0 1.062778 40730 40730 12.0 1.062778 31515 31515 13.0 1.062778 25845 25845 14.0 1.062778 20915 20915 15.0 1.062778 17443 17443 16.0 1.062778 15112 15112 17.0 1.062778 13017 13017 18.0 1.062778 11129 11129 19.0 1.062778 9857 9857 20.0 1.062778 8770 8770 21.0 1.062778 7794 7794 22.0 1.062778 6846 6846 23.0 1.062778 6208 6208 24.0 1.062778 5632 5632 25.0 1.062778 5148 5148 26.0 1.062778 4575 4575 27.0 1.062778 4293 4293 28.0 1.062778 3916 3916 29.0 1.062778 3591 3591 30.0 1.062778 3357 3357 31.0 1.062778 3027 3027 32.0 1.062778 2927 2927 33.0 1.062778 2566 2566 34.0 1.062778 2505 2505 35.0 1.062778 2228 2228 36.0 1.062778 2076 2076 37.0 1.062778 1909 1909 38.0 1.062778 1825 1825 39.0 1.062778 1770 1770 40.0 1.062778 1688 1688 41.0 1.062778 1565 1565 42.0 1.062778 1404 1404 43.0 1.062778 1418 1418 44.0 1.062778 1290 1290 45.0 1.062778 1277 1277 46.0 1.062778 1149 1149 47.0 1.062778 1126 1126 48.0 1.062778 1053 1053 49.0 1.062778 1003 1003 50.0 1.062778 931 931 51.0 1.062778 866 866 52.0 1.062778 880 880 53.0 1.062778 808 808 54.0 1.062778 750 750 55.0 1.062778 738 738 56.0 1.062778 737 737 57.0 1.062778 682 682 58.0 1.062778 708 708 59.0 1.062778 607 607 60.0 1.062778 553 553 61.0 1.062778 595 595 62.0 1.062778 526 526 63.0 1.062778 581 581 64.0 1.062778 498 498 65.0 1.062778 558 558 66.0 1.062778 419 419 67.0 1.062778 426 426 68.0 1.062778 433 433 69.0 1.062778 416 416 70.0 1.062778 412 412 71.0 1.062778 408 408 72.0 1.062778 364 364 73.0 1.062778 362 362 74.0 1.062778 371 371 75.0 1.062778 349 349 76.0 1.062778 324 324 77.0 1.062778 313 313 78.0 1.062778 313 313 79.0 1.062778 323 323 80.0 1.062778 317 317 81.0 1.062778 272 272 82.0 1.062778 272 272 83.0 1.062778 283 283 84.0 1.062778 250 250 85.0 1.062778 236 236 86.0 1.062778 250 250 87.0 1.062778 235 235 88.0 1.062778 238 238 89.0 1.062778 208 208 90.0 1.062778 238 238 91.0 1.062778 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