## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-H3K9me2_R1.target.filtered.sorted.bam --OUTPUT DE-H3K9me2_R1.target.markdup.bam --METRICS_FILE DE-H3K9me2_R1.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORT_ORDER coordinate --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --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 --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 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 5 --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: Thu Jun 15 15:09:15 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 0 8991824 0 0 0 191601 1538 0.021308 209620061 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000167 8612155 0 8613601 2.0 1.958339 184756 1538 183397 3.0 2.876278 3193 0 3111 4.0 3.755674 84 0 79 5.0 4.598145 17 0 17 6.0 5.405242 5 0 5 7.0 6.17845 5 0 5 8.0 6.919191 5 0 5 9.0 7.62883 1 0 1 10.0 8.308672 0 0 0 11.0 8.959968 0 0 0 12.0 9.583917 0 0 0 13.0 10.181668 0 0 0 14.0 10.754319 0 0 0 15.0 11.302925 0 0 0 16.0 11.828496 0 0 0 17.0 12.331999 0 0 0 18.0 12.814361 1 0 1 19.0 13.276469 0 0 0 20.0 13.719173 0 0 0 21.0 14.143289 0 0 0 22.0 14.549596 0 0 0 23.0 14.938843 0 0 0 24.0 15.311747 0 0 0 25.0 15.668992 1 0 1 26.0 16.011237 0 0 0 27.0 16.339112 0 0 0 28.0 16.65322 0 0 0 29.0 16.954138 0 0 0 30.0 17.242422 0 0 0 31.0 17.5186 0 0 0 32.0 17.783183 0 0 0 33.0 18.036655 0 0 0 34.0 18.279485 0 0 0 35.0 18.512119 0 0 0 36.0 18.734984 0 0 0 37.0 18.948492 0 0 0 38.0 19.153035 0 0 0 39.0 19.348989 0 0 0 40.0 19.536716 0 0 0 41.0 19.71656 0 0 0 42.0 19.888852 0 0 0 43.0 20.053911 0 0 0 44.0 20.212038 0 0 0 45.0 20.363526 0 0 0 46.0 20.508654 0 0 0 47.0 20.647687 0 0 0 48.0 20.780883 0 0 0 49.0 20.908486 0 0 0 50.0 21.030731 0 0 0 51.0 21.147843 0 0 0 52.0 21.260038 0 0 0 53.0 21.367521 0 0 0 54.0 21.470492 0 0 0 55.0 21.569139 0 0 0 56.0 21.663644 0 0 0 57.0 21.754181 0 0 0 58.0 21.840916 0 0 0 59.0 21.92401 0 0 0 60.0 22.003614 0 0 0 61.0 22.079876 0 0 0 62.0 22.152936 0 0 0 63.0 22.222928 0 0 0 64.0 22.289981 0 0 0 65.0 22.354219 0 0 0 66.0 22.415759 0 0 0 67.0 22.474716 0 0 0 68.0 22.531197 0 0 0 69.0 22.585306 0 0 0 70.0 22.637143 0 0 0 71.0 22.686804 0 0 0 72.0 22.73438 0 0 0 73.0 22.779958 0 0 0 74.0 22.823622 0 0 0 75.0 22.865452 0 0 0 76.0 22.905527 0 0 0 77.0 22.943918 0 0 0 78.0 22.980698 0 0 0 79.0 23.015933 0 0 0 80.0 23.049689 0 0 0 81.0 23.082028 0 0 0 82.0 23.113008 0 0 0 83.0 23.142688 0 0 0 84.0 23.171122 0 0 0 85.0 23.198361 0 0 0 86.0 23.224457 0 0 0 87.0 23.249457 0 0 0 88.0 23.273408 0 0 0 89.0 23.296353 0 0 0 90.0 23.318334 0 0 0 91.0 23.339392 0 0 0 92.0 23.359567 0 0 0 93.0 23.378894 0 0 0 94.0 23.397409 0 0 0 95.0 23.415147 0 0 0 96.0 23.432141 0 0 0 97.0 23.44842 0 0 0 98.0 23.464017 0 0 0 99.0 23.478958 0 0 0 100.0 23.493272 0 0 0