## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-H4K20me3_R1.target.filtered.sorted.bam --OUTPUT DE-H4K20me3_R1.target.markdup.bam --METRICS_FILE DE-H4K20me3_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 15:10:46 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 13961712 0 0 0 308010 1665 0.022061 313406943 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000117 13355001 0 13356568 2.0 1.956658 291551 1665 290079 3.0 2.871522 6275 0 6183 4.0 3.746525 458 0 455 5.0 4.583404 168 0 168 6.0 5.383819 84 0 84 7.0 6.14936 49 0 49 8.0 6.881546 32 0 32 9.0 7.58183 24 0 24 10.0 8.251603 19 0 19 11.0 8.892193 9 0 9 12.0 9.504872 6 0 6 13.0 10.090857 14 0 14 14.0 10.65131 3 0 3 15.0 11.187344 1 0 1 16.0 11.700023 1 0 1 17.0 12.190363 1 0 1 18.0 12.65934 0 0 0 19.0 13.107883 1 0 1 20.0 13.536883 1 0 1 21.0 13.947191 0 0 0 22.0 14.339621 0 0 0 23.0 14.714954 1 0 1 24.0 15.073933 0 0 0 25.0 15.417271 0 0 0 26.0 15.745649 0 0 0 27.0 16.05972 0 0 0 28.0 16.360107 0 0 0 29.0 16.647406 1 0 1 30.0 16.922187 0 0 0 31.0 17.184995 0 0 0 32.0 17.436353 1 0 1 33.0 17.676759 0 0 0 34.0 17.906691 0 0 0 35.0 18.126604 0 0 0 36.0 18.336936 0 0 0 37.0 18.538103 1 0 1 38.0 18.730505 0 0 0 39.0 18.914525 0 0 0 40.0 19.090526 0 0 0 41.0 19.258859 0 0 0 42.0 19.419858 0 0 0 43.0 19.573842 0 0 0 44.0 19.721117 0 0 0 45.0 19.861974 0 0 0 46.0 19.996695 0 0 0 47.0 20.125546 0 0 0 48.0 20.248783 0 0 0 49.0 20.36665 0 0 0 50.0 20.479382 0 0 0 51.0 20.587201 0 0 0 52.0 20.690324 0 0 0 53.0 20.788953 0 0 0 54.0 20.883284 0 0 0 55.0 20.973506 0 0 0 56.0 21.059797 0 0 0 57.0 21.142328 0 0 0 58.0 21.221263 0 0 0 59.0 21.296759 0 0 0 60.0 21.368965 0 0 0 61.0 21.438025 0 0 0 62.0 21.504077 0 0 0 63.0 21.56725 0 0 0 64.0 21.627671 0 0 0 65.0 21.685459 0 0 0 66.0 21.74073 0 0 0 67.0 21.793592 0 0 0 68.0 21.844151 0 0 0 69.0 21.892508 0 0 0 70.0 21.938757 0 0 0 71.0 21.982991 0 0 0 72.0 22.025298 0 0 0 73.0 22.065762 0 0 0 74.0 22.104462 0 0 0 75.0 22.141477 0 0 0 76.0 22.176878 0 0 0 77.0 22.210737 0 0 0 78.0 22.243121 0 0 0 79.0 22.274094 0 0 0 80.0 22.303718 0 0 0 81.0 22.33205 0 0 0 82.0 22.359148 0 0 0 83.0 22.385066 0 0 0 84.0 22.409854 0 0 0 85.0 22.433563 0 0 0 86.0 22.456238 0 0 0 87.0 22.477925 0 0 0 88.0 22.498668 0 0 0 89.0 22.518506 0 0 0 90.0 22.53748 0 0 0 91.0 22.555628 0 0 0 92.0 22.572985 0 0 0 93.0 22.589585 0 0 0 94.0 22.605463 0 0 0 95.0 22.620648 0 0 0 96.0 22.635172 0 0 0 97.0 22.649063 0 0 0 98.0 22.662349 0 0 0 99.0 22.675056 0 0 0 100.0 22.687209 0 0 0