## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT DE-CTCF_R1.target.filtered.sorted.bam --OUTPUT DE-CTCF_R1.target.markdup.bam --METRICS_FILE DE-CTCF_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 15:09:16 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 9953349 0 0 0 302881 1440 0.03043 160944078 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.00014 9356826 0 9358142 2.0 1.940302 285033 1440 283838 3.0 2.824082 8192 0 8074 4.0 3.654862 321 0 318 5.0 4.43582 59 0 59 6.0 5.169944 15 0 15 7.0 5.860043 2 0 2 8.0 6.508756 8 0 8 9.0 7.118566 5 0 5 10.0 7.691806 4 0 4 11.0 8.230668 0 0 0 12.0 8.737215 2 0 2 13.0 9.213384 0 0 0 14.0 9.660998 0 0 0 15.0 10.081767 0 0 0 16.0 10.477304 0 0 0 17.0 10.84912 0 0 0 18.0 11.198638 0 0 0 19.0 11.527196 0 0 0 20.0 11.83605 0 0 0 21.0 12.126382 0 0 0 22.0 12.399302 0 0 0 23.0 12.655856 0 0 0 24.0 12.897024 0 0 0 25.0 13.123729 1 0 1 26.0 13.336839 0 0 0 27.0 13.537169 0 0 0 28.0 13.725485 0 0 0 29.0 13.902507 0 0 0 30.0 14.068914 0 0 0 31.0 14.225341 0 0 0 32.0 14.372387 0 0 0 33.0 14.510615 0 0 0 34.0 14.640553 0 0 0 35.0 14.762699 0 0 0 36.0 14.877519 0 0 0 37.0 14.985454 0 0 0 38.0 15.086916 0 0 0 39.0 15.182294 0 0 0 40.0 15.271951 0 0 0 41.0 15.356232 0 0 0 42.0 15.435459 0 0 0 43.0 15.509934 0 0 0 44.0 15.579943 0 0 0 45.0 15.645754 0 0 0 46.0 15.707618 0 0 0 47.0 15.765771 0 0 0 48.0 15.820438 0 0 0 49.0 15.871826 0 0 0 50.0 15.920132 0 0 0 51.0 15.965542 0 0 0 52.0 16.008228 0 0 0 53.0 16.048354 0 0 0 54.0 16.086074 0 0 0 55.0 16.121532 0 0 0 56.0 16.154864 0 0 0 57.0 16.186196 0 0 0 58.0 16.21565 0 0 0 59.0 16.243337 0 0 0 60.0 16.269364 0 0 0 61.0 16.29383 0 0 0 62.0 16.316828 0 0 0 63.0 16.338448 0 0 0 64.0 16.358771 0 0 0 65.0 16.377875 0 0 0 66.0 16.395834 0 0 0 67.0 16.412715 0 0 0 68.0 16.428585 0 0 0 69.0 16.443502 0 0 0 70.0 16.457525 0 0 0 71.0 16.470707 0 0 0 72.0 16.483098 0 0 0 73.0 16.494747 0 0 0 74.0 16.505696 0 0 0 75.0 16.51599 0 0 0 76.0 16.525665 0 0 0 77.0 16.534761 0 0 0 78.0 16.543311 0 0 0 79.0 16.551348 0 0 0 80.0 16.558904 0 0 0 81.0 16.566006 0 0 0 82.0 16.572682 0 0 0 83.0 16.578958 0 0 0 84.0 16.584858 0 0 0 85.0 16.590404 0 0 0 86.0 16.595617 0 0 0 87.0 16.600518 0 0 0 88.0 16.605124 0 0 0 89.0 16.609455 0 0 0 90.0 16.613525 0 0 0 91.0 16.617352 0 0 0 92.0 16.620949 0 0 0 93.0 16.62433 0 0 0 94.0 16.627509 0 0 0 95.0 16.630497 0 0 0 96.0 16.633306 0 0 0 97.0 16.635946 0 0 0 98.0 16.638428 0 0 0 99.0 16.640761 0 0 0 100.0 16.642955 0 0 0