## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT /dreamworld/ngs_data/NIPT/N28/IRs/N28.primary.bam --OUTPUT /dev/stdout --METRICS_FILE /dreamworld/ngs_data/NIPT/N28/N28.md_metrics.txt --REMOVE_DUPLICATES true --ASSUME_SORT_ORDER queryname --TMP_DIR /tmp/tmprwgpnvha --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 19:56:12 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-N28-001 1506 652958 8289 4820 378 112521 12860 0.172416 1836179 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.016733 443947 0 453331 2.0 1.729207 82543 12103 76004 3.0 2.228472 12184 360 9870 4.0 2.57833 1539 11 1092 5.0 2.823493 181 1 110 6.0 2.99529 32 0 21 7.0 3.115677 3 0 2 8.0 3.200037 5 0 4 9.0 3.259153 0 0 0 10.0 3.300578 0 0 0 11.0 3.329607 1 0 1 12.0 3.349948 0 0 0 13.0 3.364203 0 0 0 14.0 3.374192 0 0 0 15.0 3.381191 0 0 0 16.0 3.386096 1 0 1 17.0 3.389533 0 0 0 18.0 3.391942 0 0 0 19.0 3.39363 0 0 0 20.0 3.394812 0 0 0 21.0 3.395641 0 0 0 22.0 3.396222 0 0 0 23.0 3.396629 0 0 0 24.0 3.396914 0 0 0 25.0 3.397114 0 0 0 26.0 3.397254 0 0 0 27.0 3.397352 0 0 0 28.0 3.397421 0 0 0 29.0 3.397469 0 0 0 30.0 3.397503 0 0 0 31.0 3.397527 0 0 0 32.0 3.397543 1 0 1 33.0 3.397555 0 0 0 34.0 3.397563 0 0 0 35.0 3.397569 0 0 0 36.0 3.397573 0 0 0 37.0 3.397575 0 0 0 38.0 3.397577 0 0 0 39.0 3.397579 0 0 0 40.0 3.39758 0 0 0 41.0 3.39758 0 0 0 42.0 3.397581 0 0 0 43.0 3.397581 0 0 0 44.0 3.397581 0 0 0 45.0 3.397582 0 0 0 46.0 3.397582 0 0 0 47.0 3.397582 0 0 0 48.0 3.397582 0 0 0 49.0 3.397582 0 0 0 50.0 3.397582 0 0 0 51.0 3.397582 0 0 0 52.0 3.397582 0 0 0 53.0 3.397582 0 0 0 54.0 3.397582 0 0 0 55.0 3.397582 0 0 0 56.0 3.397582 0 0 0 57.0 3.397582 0 0 0 58.0 3.397582 0 0 0 59.0 3.397582 0 0 0 60.0 3.397582 0 0 0 61.0 3.397582 0 0 0 62.0 3.397582 0 0 0 63.0 3.397582 0 0 0 64.0 3.397582 0 0 0 65.0 3.397582 0 0 0 66.0 3.397582 0 0 0 67.0 3.397582 0 0 0 68.0 3.397582 0 0 0 69.0 3.397582 0 0 0 70.0 3.397582 0 0 0 71.0 3.397582 0 0 0 72.0 3.397582 0 0 0 73.0 3.397582 0 0 0 74.0 3.397582 0 0 0 75.0 3.397582 0 0 0 76.0 3.397582 0 0 0 77.0 3.397582 0 0 0 78.0 3.397582 0 0 0 79.0 3.397582 0 0 0 80.0 3.397582 0 0 0 81.0 3.397582 0 0 0 82.0 3.397582 0 0 0 83.0 3.397582 0 0 0 84.0 3.397582 0 0 0 85.0 3.397582 0 0 0 86.0 3.397582 0 0 0 87.0 3.397582 0 0 0 88.0 3.397582 0 0 0 89.0 3.397582 0 0 0 90.0 3.397582 0 0 0 91.0 3.397582 0 0 0 92.0 3.397582 0 0 0 93.0 3.397582 0 0 0 94.0 3.397582 0 0 0 95.0 3.397582 0 0 0 96.0 3.397582 0 0 0 97.0 3.397582 0 0 0 98.0 3.397582 0 0 0 99.0 3.397582 0 0 0 100.0 3.397582 0 0 0