## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354279.sorted.bam --OUTPUT SRX7354279.markdup.sorted.bam --METRICS_FILE SRX7354279.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 21:44:14 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 85099 46093401 8633996 4694751 62749 15643854 0 0.339762 51466652 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21635519 21635519 2.0 1.408364 6017775 6017775 3.0 1.575124 1655690 1655690 4.0 1.643223 524540 524540 5.0 1.671033 214256 214256 6.0 1.682389 112470 112470 7.0 1.687026 69529 69529 8.0 1.68892 46553 46553 9.0 1.689693 33154 33154 10.0 1.690009 24540 24540 11.0 1.690138 18819 18819 12.0 1.690191 14736 14736 13.0 1.690212 11808 11808 14.0 1.690221 9401 9401 15.0 1.690225 7734 7734 16.0 1.690226 6621 6621 17.0 1.690227 5444 5444 18.0 1.690227 4616 4616 19.0 1.690227 3929 3929 20.0 1.690227 3358 3358 21.0 1.690227 2876 2876 22.0 1.690227 2485 2485 23.0 1.690227 2204 2204 24.0 1.690227 1941 1941 25.0 1.690227 1660 1660 26.0 1.690227 1447 1447 27.0 1.690227 1355 1355 28.0 1.690227 1236 1236 29.0 1.690227 1070 1070 30.0 1.690227 979 979 31.0 1.690227 875 875 32.0 1.690227 739 739 33.0 1.690227 756 756 34.0 1.690227 659 659 35.0 1.690227 618 618 36.0 1.690227 524 524 37.0 1.690227 484 484 38.0 1.690227 428 428 39.0 1.690227 416 416 40.0 1.690227 375 375 41.0 1.690227 351 351 42.0 1.690227 344 344 43.0 1.690227 292 292 44.0 1.690227 281 281 45.0 1.690227 272 272 46.0 1.690227 261 261 47.0 1.690227 216 216 48.0 1.690227 197 197 49.0 1.690227 212 212 50.0 1.690227 190 190 51.0 1.690227 176 176 52.0 1.690227 146 146 53.0 1.690227 143 143 54.0 1.690227 142 142 55.0 1.690227 126 126 56.0 1.690227 119 119 57.0 1.690227 114 114 58.0 1.690227 118 118 59.0 1.690227 104 104 60.0 1.690227 104 104 61.0 1.690227 81 81 62.0 1.690227 103 103 63.0 1.690227 72 72 64.0 1.690227 58 58 65.0 1.690227 72 72 66.0 1.690227 67 67 67.0 1.690227 61 61 68.0 1.690227 65 65 69.0 1.690227 54 54 70.0 1.690227 61 61 71.0 1.690227 51 51 72.0 1.690227 41 41 73.0 1.690227 40 40 74.0 1.690227 48 48 75.0 1.690227 43 43 76.0 1.690227 31 31 77.0 1.690227 30 30 78.0 1.690227 34 34 79.0 1.690227 33 33 80.0 1.690227 28 28 81.0 1.690227 24 24 82.0 1.690227 29 29 83.0 1.690227 25 25 84.0 1.690227 35 35 85.0 1.690227 26 26 86.0 1.690227 27 27 87.0 1.690227 23 23 88.0 1.690227 31 31 89.0 1.690227 27 27 90.0 1.690227 20 20 91.0 1.690227 29 29 92.0 1.690227 19 19 93.0 1.690227 17 17 94.0 1.690227 19 19 95.0 1.690227 24 24 96.0 1.690227 24 24 97.0 1.690227 21 21 98.0 1.690227 17 17 99.0 1.690227 15 15 100.0 1.690227 14 14 101.0 0 16 16 102.0 0 13 13 103.0 0 12 12 104.0 0 10 10 105.0 0 12 12 106.0 0 13 13 107.0 0 14 14 108.0 0 10 10 109.0 0 11 11 110.0 0 8 8 111.0 0 9 9 112.0 0 8 8 113.0 0 13 13 114.0 0 8 8 115.0 0 13 13 116.0 0 9 9 117.0 0 13 13 118.0 0 10 10 119.0 0 2 2 120.0 0 6 6 121.0 0 7 7 122.0 0 4 4 123.0 0 7 7 124.0 0 4 4 125.0 0 8 8 126.0 0 8 8 127.0 0 3 3 128.0 0 5 5 129.0 0 12 12 130.0 0 6 6 131.0 0 7 7 132.0 0 6 6 133.0 0 3 3 134.0 0 3 3 135.0 0 4 4 136.0 0 5 5 137.0 0 4 4 138.0 0 7 7 139.0 0 2 2 140.0 0 4 4 141.0 0 4 4 143.0 0 7 7 144.0 0 4 4 145.0 0 1 1 146.0 0 6 6 147.0 0 6 6 148.0 0 2 2 149.0 0 2 2 150.0 0 3 3 151.0 0 5 5 152.0 0 3 3 153.0 0 1 1 155.0 0 1 1 156.0 0 7 7 157.0 0 2 2 158.0 0 1 1 159.0 0 1 1 160.0 0 2 2 163.0 0 3 3 164.0 0 7 7 165.0 0 4 4 166.0 0 4 4 167.0 0 2 2 169.0 0 2 2 171.0 0 2 2 172.0 0 2 2 176.0 0 3 3 177.0 0 2 2 179.0 0 2 2 183.0 0 2 2 184.0 0 1 1 186.0 0 1 1 188.0 0 1 1 189.0 0 2 2 190.0 0 7 7 191.0 0 1 1 192.0 0 1 1 193.0 0 2 2 194.0 0 1 1 196.0 0 1 1 197.0 0 1 1 198.0 0 2 2 199.0 0 2 2 204.0 0 1 1 205.0 0 1 1 206.0 0 2 2 207.0 0 1 1 208.0 0 2 2 209.0 0 1 1 211.0 0 3 3 212.0 0 3 3 213.0 0 1 1 214.0 0 1 1 215.0 0 2 2 217.0 0 1 1 222.0 0 2 2 230.0 0 1 1 232.0 0 1 1 234.0 0 1 1 240.0 0 1 1 241.0 0 1 1 243.0 0 1 1 247.0 0 1 1 251.0 0 1 1 265.0 0 1 1 276.0 0 2 2 292.0 0 1 1 293.0 0 1 1 294.0 0 1 1 301.0 0 1 1 319.0 0 1 1 329.0 0 1 1 335.0 0 1 1 346.0 0 1 1 361.0 0 1 1 384.0 0 1 1 448.0 0 1 1 530.0 0 1 1 551.0 0 1 1 626.0 0 1 1