## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT H1-H3K9me2_R1.target.filtered.sorted.bam --OUTPUT H1-H3K9me2_R1.target.markdup.bam --METRICS_FILE H1-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 15:18:02 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 13983368 0 0 0 438416 2000 0.031353 219273965 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000139 13119006 0 13120856 2.0 1.938488 414178 2000 412469 3.0 2.818866 11328 0 11196 4.0 3.644854 360 0 351 5.0 4.419812 33 0 33 6.0 5.146893 16 0 16 7.0 5.829055 10 0 10 8.0 6.469072 6 0 6 9.0 7.069549 4 0 4 10.0 7.632928 2 0 2 11.0 8.161501 1 0 1 12.0 8.657419 4 0 4 13.0 9.122699 1 0 1 14.0 9.559234 0 0 0 15.0 9.968799 1 0 1 16.0 10.353062 1 0 1 17.0 10.713584 0 0 0 18.0 11.051833 0 0 0 19.0 11.369185 0 0 0 20.0 11.666931 0 0 0 21.0 11.946282 0 0 0 22.0 12.208375 0 0 0 23.0 12.454276 0 0 0 24.0 12.684984 0 0 0 25.0 12.90144 0 0 0 26.0 13.104522 0 0 0 27.0 13.295059 0 0 0 28.0 13.473823 0 0 0 29.0 13.641544 0 0 0 30.0 13.798903 0 0 0 31.0 13.94654 0 0 0 32.0 14.085056 0 0 0 33.0 14.215014 0 0 0 34.0 14.336944 0 0 0 35.0 14.451341 0 0 0 36.0 14.55867 0 0 0 37.0 14.659368 0 0 0 38.0 14.753846 0 0 0 39.0 14.842486 0 0 0 40.0 14.92565 0 0 0 41.0 15.003676 0 0 0 42.0 15.076882 0 0 0 43.0 15.145565 0 0 0 44.0 15.210005 1 0 1 45.0 15.270464 0 0 0 46.0 15.327187 0 0 0 47.0 15.380406 0 0 0 48.0 15.430337 0 0 0 49.0 15.477184 0 0 0 50.0 15.521136 0 0 0 51.0 15.562373 0 0 0 52.0 15.601062 0 0 0 53.0 15.637361 0 0 0 54.0 15.671418 0 0 0 55.0 15.70337 0 0 0 56.0 15.733349 0 0 0 57.0 15.761475 0 0 0 58.0 15.787864 0 0 0 59.0 15.812622 0 0 0 60.0 15.835851 0 0 0 61.0 15.857644 0 0 0 62.0 15.878092 0 0 0 63.0 15.897276 0 0 0 64.0 15.915274 0 0 0 65.0 15.932161 0 0 0 66.0 15.948005 0 0 0 67.0 15.96287 0 0 0 68.0 15.976816 0 0 0 69.0 15.989901 0 0 0 70.0 16.002177 0 0 0 71.0 16.013695 0 0 0 72.0 16.024502 0 0 0 73.0 16.03464 0 0 0 74.0 16.044153 0 0 0 75.0 16.053078 0 0 0 76.0 16.061451 0 0 0 77.0 16.069307 0 0 0 78.0 16.076678 0 0 0 79.0 16.083593 0 0 0 80.0 16.090081 0 0 0 81.0 16.096168 0 0 0 82.0 16.101879 0 0 0 83.0 16.107238 0 0 0 84.0 16.112265 0 0 0 85.0 16.116982 0 0 0 86.0 16.121407 0 0 0 87.0 16.125559 0 0 0 88.0 16.129454 0 0 0 89.0 16.133109 0 0 0 90.0 16.136538 0 0 0 91.0 16.139755 0 0 0 92.0 16.142774 0 0 0 93.0 16.145605 0 0 0 94.0 16.148262 0 0 0 95.0 16.150755 0 0 0 96.0 16.153094 0 0 0 97.0 16.155288 0 0 0 98.0 16.157347 0 0 0 99.0 16.159278 0 0 0 100.0 16.161091 0 0 0