## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT H1-H3K27me3_R1.target.filtered.sorted.bam --OUTPUT H1-H3K27me3_R1.target.markdup.bam --METRICS_FILE H1-H3K27me3_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 15:04:40 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 8996537 0 0 0 319298 1627 0.035491 124329933 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000174 8381003 0 8382485 2.0 1.930532 277109 1627 275750 3.0 2.795948 16208 0 16104 4.0 3.600953 2245 0 2227 5.0 4.349766 478 0 479 6.0 5.046308 118 0 116 7.0 5.694229 41 0 41 8.0 6.296922 20 0 20 9.0 6.857545 10 0 10 10.0 7.379034 4 0 4 11.0 7.864121 1 0 1 12.0 8.315347 1 0 1 13.0 8.735075 0 0 0 14.0 9.125504 1 0 1 15.0 9.48868 0 0 0 16.0 9.826505 0 0 0 17.0 10.140748 0 0 0 18.0 10.433055 0 0 0 19.0 10.704959 0 0 0 20.0 10.957882 0 0 0 21.0 11.19315 0 0 0 22.0 11.411995 0 0 0 23.0 11.615565 0 0 0 24.0 11.804924 0 0 0 25.0 11.981065 0 0 0 26.0 12.14491 0 0 0 27.0 12.297319 0 0 0 28.0 12.439089 0 0 0 29.0 12.570962 0 0 0 30.0 12.693631 0 0 0 31.0 12.807736 0 0 0 32.0 12.913877 0 0 0 33.0 13.012608 0 0 0 34.0 13.104448 0 0 0 35.0 13.189877 0 0 0 36.0 13.269342 0 0 0 37.0 13.343261 0 0 0 38.0 13.412019 0 0 0 39.0 13.475979 0 0 0 40.0 13.535473 0 0 0 41.0 13.590814 0 0 0 42.0 13.642293 0 0 0 43.0 13.690178 0 0 0 44.0 13.73472 0 0 0 45.0 13.776153 0 0 0 46.0 13.814694 0 0 0 47.0 13.850545 0 0 0 48.0 13.883893 0 0 0 49.0 13.914913 0 0 0 50.0 13.943768 0 0 0 51.0 13.970609 0 0 0 52.0 13.995576 0 0 0 53.0 14.0188 0 0 0 54.0 14.040404 0 0 0 55.0 14.060499 0 0 0 56.0 14.079191 0 0 0 57.0 14.096579 0 0 0 58.0 14.112753 0 0 0 59.0 14.127798 0 0 0 60.0 14.141792 0 0 0 61.0 14.15481 0 0 0 62.0 14.166919 0 0 0 63.0 14.178183 0 0 0 64.0 14.188661 0 0 0 65.0 14.198407 0 0 0 66.0 14.207473 0 0 0 67.0 14.215906 0 0 0 68.0 14.22375 0 0 0 69.0 14.231047 0 0 0 70.0 14.237834 0 0 0 71.0 14.244148 0 0 0 72.0 14.250021 0 0 0 73.0 14.255484 0 0 0 74.0 14.260566 0 0 0 75.0 14.265293 0 0 0 76.0 14.26969 0 0 0 77.0 14.27378 0 0 0 78.0 14.277584 0 0 0 79.0 14.281123 0 0 0 80.0 14.284415 0 0 0 81.0 14.287477 0 0 0 82.0 14.290326 0 0 0 83.0 14.292975 0 0 0 84.0 14.29544 0 0 0 85.0 14.297732 0 0 0 86.0 14.299865 0 0 0 87.0 14.301849 0 0 0 88.0 14.303694 0 0 0 89.0 14.30541 0 0 0 90.0 14.307007 0 0 0 91.0 14.308492 0 0 0 92.0 14.309873 0 0 0 93.0 14.311158 0 0 0 94.0 14.312354 0 0 0 95.0 14.313466 0 0 0 96.0 14.3145 0 0 0 97.0 14.315462 0 0 0 98.0 14.316357 0 0 0 99.0 14.317189 0 0 0 100.0 14.317964 0 0 0