## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT /dreamworld/ngs_data/NIPT/N40/IRs/N40.primary.bam --OUTPUT /dev/stdout --METRICS_FILE /dreamworld/ngs_data/NIPT/N40/N40.md_metrics.txt --REMOVE_DUPLICATES true --ASSUME_SORT_ORDER queryname --TMP_DIR /tmp/tmpchr7qe_l --VERBOSITY ERROR --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 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --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 --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Sep 09 20:25:33 KRAT 2022 ## 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 LIB-N40-003 2236 660691 9596 7352 652 136060 13738 0.206081 1487613 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.016873 411861 0 420874 2.0 1.669078 93255 12866 87873 3.0 2.087392 16375 402 13620 4.0 2.355691 2632 20 1936 5.0 2.527773 417 2 269 6.0 2.638144 69 0 43 7.0 2.708934 13 0 7 8.0 2.754338 6 0 6 9.0 2.783459 2 0 2 10.0 2.802137 0 0 0 11.0 2.814116 1 0 1 12.0 2.8218 0 0 0 13.0 2.826728 0 0 0 14.0 2.829889 0 0 0 15.0 2.831916 0 0 0 16.0 2.833216 0 0 0 17.0 2.83405 0 0 0 18.0 2.834585 0 0 0 19.0 2.834928 0 0 0 20.0 2.835148 0 0 0 21.0 2.835289 0 0 0 22.0 2.83538 0 0 0 23.0 2.835438 0 0 0 24.0 2.835475 0 0 0 25.0 2.835499 0 0 0 26.0 2.835514 0 0 0 27.0 2.835524 0 0 0 28.0 2.83553 0 0 0 29.0 2.835534 0 0 0 30.0 2.835537 0 0 0 31.0 2.835539 0 0 0 32.0 2.83554 0 0 0 33.0 2.83554 0 0 0 34.0 2.835541 0 0 0 35.0 2.835541 0 0 0 36.0 2.835541 0 0 0 37.0 2.835541 0 0 0 38.0 2.835541 0 0 0 39.0 2.835541 0 0 0 40.0 2.835541 0 0 0 41.0 2.835542 0 0 0 42.0 2.835542 0 0 0 43.0 2.835542 0 0 0 44.0 2.835542 0 0 0 45.0 2.835542 0 0 0 46.0 2.835542 0 0 0 47.0 2.835542 0 0 0 48.0 2.835542 0 0 0 49.0 2.835542 0 0 0 50.0 2.835542 0 0 0 51.0 2.835542 0 0 0 52.0 2.835542 0 0 0 53.0 2.835542 0 0 0 54.0 2.835542 0 0 0 55.0 2.835542 0 0 0 56.0 2.835542 0 0 0 57.0 2.835542 0 0 0 58.0 2.835542 0 0 0 59.0 2.835542 0 0 0 60.0 2.835542 0 0 0 61.0 2.835542 0 0 0 62.0 2.835542 0 0 0 63.0 2.835542 0 0 0 64.0 2.835542 0 0 0 65.0 2.835542 0 0 0 66.0 2.835542 0 0 0 67.0 2.835542 0 0 0 68.0 2.835542 0 0 0 69.0 2.835542 0 0 0 70.0 2.835542 0 0 0 71.0 2.835542 0 0 0 72.0 2.835542 0 0 0 73.0 2.835542 0 0 0 74.0 2.835542 0 0 0 75.0 2.835542 0 0 0 76.0 2.835542 0 0 0 77.0 2.835542 0 0 0 78.0 2.835542 0 0 0 79.0 2.835542 0 0 0 80.0 2.835542 0 0 0 81.0 2.835542 0 0 0 82.0 2.835542 0 0 0 83.0 2.835542 0 0 0 84.0 2.835542 0 0 0 85.0 2.835542 0 0 0 86.0 2.835542 0 0 0 87.0 2.835542 0 0 0 88.0 2.835542 0 0 0 89.0 2.835542 0 0 0 90.0 2.835542 0 0 0 91.0 2.835542 0 0 0 92.0 2.835542 0 0 0 93.0 2.835542 0 0 0 94.0 2.835542 0 0 0 95.0 2.835542 0 0 0 96.0 2.835542 0 0 0 97.0 2.835542 0 0 0 98.0 2.835542 0 0 0 99.0 2.835542 0 0 0 100.0 2.835542 0 0 0