## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354349.sorted.bam --OUTPUT SRX7354349.markdup.sorted.bam --METRICS_FILE SRX7354349.markdup.sorted.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORTED true --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Homo_sapiens_assembly38_noALT_noHLA_noDecoy_patched_ERCC92.fasta --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 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Oct 30 23:22:50 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 151771 44934915 6639057 7240043 123503 19841260 0 0.442183 34427611 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 15087343 15087343 2.0 1.271118 6088053 6088053 3.0 1.344623 2242347 2242347 4.0 1.364552 820970 820970 5.0 1.369955 330775 330775 6.0 1.37142 156643 156643 7.0 1.371817 87472 87472 8.0 1.371925 56613 56613 9.0 1.371954 39558 39558 10.0 1.371962 29273 29273 11.0 1.371964 22502 22502 12.0 1.371965 17732 17732 13.0 1.371965 14388 14388 14.0 1.371965 11642 11642 15.0 1.371965 9741 9741 16.0 1.371965 8160 8160 17.0 1.371965 6977 6977 18.0 1.371965 5885 5885 19.0 1.371965 5200 5200 20.0 1.371965 4573 4573 21.0 1.371965 3940 3940 22.0 1.371965 3562 3562 23.0 1.371965 3130 3130 24.0 1.371965 2867 2867 25.0 1.371965 2480 2480 26.0 1.371965 2296 2296 27.0 1.371965 1993 1993 28.0 1.371965 1901 1901 29.0 1.371965 1651 1651 30.0 1.371965 1505 1505 31.0 1.371965 1347 1347 32.0 1.371965 1234 1234 33.0 1.371965 1145 1145 34.0 1.371965 1062 1062 35.0 1.371965 958 958 36.0 1.371965 896 896 37.0 1.371965 875 875 38.0 1.371965 752 752 39.0 1.371965 733 733 40.0 1.371965 681 681 41.0 1.371965 633 633 42.0 1.371965 548 548 43.0 1.371965 558 558 44.0 1.371965 514 514 45.0 1.371965 461 461 46.0 1.371965 479 479 47.0 1.371965 402 402 48.0 1.371965 378 378 49.0 1.371965 387 387 50.0 1.371965 369 369 51.0 1.371965 334 334 52.0 1.371965 325 325 53.0 1.371965 301 301 54.0 1.371965 296 296 55.0 1.371965 257 257 56.0 1.371965 234 234 57.0 1.371965 231 231 58.0 1.371965 252 252 59.0 1.371965 233 233 60.0 1.371965 188 188 61.0 1.371965 209 209 62.0 1.371965 161 161 63.0 1.371965 197 197 64.0 1.371965 168 168 65.0 1.371965 173 173 66.0 1.371965 176 176 67.0 1.371965 143 143 68.0 1.371965 128 128 69.0 1.371965 133 133 70.0 1.371965 128 128 71.0 1.371965 124 124 72.0 1.371965 106 106 73.0 1.371965 127 127 74.0 1.371965 121 121 75.0 1.371965 119 119 76.0 1.371965 90 90 77.0 1.371965 88 88 78.0 1.371965 105 105 79.0 1.371965 78 78 80.0 1.371965 84 84 81.0 1.371965 92 92 82.0 1.371965 85 85 83.0 1.371965 76 76 84.0 1.371965 77 77 85.0 1.371965 73 73 86.0 1.371965 60 60 87.0 1.371965 61 61 88.0 1.371965 62 62 89.0 1.371965 57 57 90.0 1.371965 54 54 91.0 1.371965 59 59 92.0 1.371965 55 55 93.0 1.371965 56 56 94.0 1.371965 60 60 95.0 1.371965 46 46 96.0 1.371965 48 48 97.0 1.371965 54 54 98.0 1.371965 46 46 99.0 1.371965 37 37 100.0 1.371965 39 39 101.0 0 36 36 102.0 0 33 33 103.0 0 45 45 104.0 0 44 44 105.0 0 22 22 106.0 0 24 24 107.0 0 41 41 108.0 0 36 36 109.0 0 27 27 110.0 0 19 19 111.0 0 24 24 112.0 0 22 22 113.0 0 23 23 114.0 0 32 32 115.0 0 29 29 116.0 0 26 26 117.0 0 28 28 118.0 0 24 24 119.0 0 12 12 120.0 0 29 29 121.0 0 27 27 122.0 0 14 14 123.0 0 24 24 124.0 0 18 18 125.0 0 23 23 126.0 0 27 27 127.0 0 15 15 128.0 0 17 17 129.0 0 19 19 130.0 0 12 12 131.0 0 22 22 132.0 0 16 16 133.0 0 19 19 134.0 0 15 15 135.0 0 12 12 136.0 0 18 18 137.0 0 7 7 138.0 0 15 15 139.0 0 16 16 140.0 0 16 16 141.0 0 16 16 142.0 0 8 8 143.0 0 14 14 144.0 0 12 12 145.0 0 8 8 146.0 0 9 9 147.0 0 13 13 148.0 0 14 14 149.0 0 10 10 150.0 0 7 7 151.0 0 7 7 152.0 0 10 10 153.0 0 10 10 154.0 0 13 13 155.0 0 13 13 156.0 0 5 5 157.0 0 9 9 158.0 0 6 6 159.0 0 12 12 160.0 0 3 3 161.0 0 5 5 162.0 0 10 10 163.0 0 4 4 164.0 0 8 8 165.0 0 7 7 166.0 0 8 8 167.0 0 6 6 168.0 0 9 9 169.0 0 10 10 170.0 0 7 7 171.0 0 9 9 172.0 0 8 8 173.0 0 8 8 174.0 0 5 5 175.0 0 9 9 176.0 0 2 2 177.0 0 3 3 178.0 0 7 7 179.0 0 4 4 180.0 0 7 7 181.0 0 7 7 182.0 0 4 4 184.0 0 6 6 185.0 0 3 3 186.0 0 3 3 187.0 0 6 6 188.0 0 5 5 189.0 0 7 7 190.0 0 3 3 191.0 0 4 4 192.0 0 6 6 193.0 0 3 3 194.0 0 5 5 195.0 0 6 6 196.0 0 2 2 197.0 0 7 7 198.0 0 1 1 199.0 0 3 3 200.0 0 2 2 201.0 0 4 4 202.0 0 2 2 203.0 0 4 4 204.0 0 1 1 205.0 0 4 4 206.0 0 3 3 207.0 0 3 3 208.0 0 8 8 209.0 0 1 1 210.0 0 4 4 211.0 0 4 4 212.0 0 2 2 213.0 0 2 2 214.0 0 6 6 215.0 0 6 6 216.0 0 2 2 217.0 0 4 4 218.0 0 2 2 219.0 0 1 1 220.0 0 2 2 221.0 0 2 2 222.0 0 5 5 223.0 0 4 4 224.0 0 3 3 225.0 0 2 2 227.0 0 1 1 228.0 0 1 1 229.0 0 2 2 230.0 0 1 1 231.0 0 1 1 232.0 0 2 2 236.0 0 1 1 237.0 0 2 2 238.0 0 2 2 239.0 0 1 1 240.0 0 4 4 241.0 0 1 1 243.0 0 1 1 244.0 0 2 2 245.0 0 1 1 246.0 0 3 3 247.0 0 4 4 248.0 0 1 1 249.0 0 3 3 250.0 0 2 2 251.0 0 2 2 252.0 0 1 1 253.0 0 5 5 256.0 0 1 1 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