## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354300.sorted.bam --OUTPUT SRX7354300.markdup.sorted.bam --METRICS_FILE SRX7354300.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 21:37:28 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 44134 34975247 4861409 9356718 33904 11464927 0 0.328079 40909277 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19626075 19626075 2.0 1.425306 2535047 2535047 3.0 1.606191 551871 551871 4.0 1.683123 225899 225899 5.0 1.715842 127184 127184 6.0 1.729758 83513 83513 7.0 1.735676 59606 59606 8.0 1.738193 44127 44127 9.0 1.739264 33962 33962 10.0 1.739719 26871 26871 11.0 1.739913 21950 21950 12.0 1.739995 18144 18144 13.0 1.74003 15276 15276 14.0 1.740045 13006 13006 15.0 1.740051 10975 10975 16.0 1.740054 9621 9621 17.0 1.740055 8488 8488 18.0 1.740056 7366 7366 19.0 1.740056 6651 6651 20.0 1.740056 5920 5920 21.0 1.740056 5129 5129 22.0 1.740056 4690 4690 23.0 1.740056 4248 4248 24.0 1.740056 3810 3810 25.0 1.740056 3562 3562 26.0 1.740056 3289 3289 27.0 1.740056 3043 3043 28.0 1.740056 2758 2758 29.0 1.740056 2456 2456 30.0 1.740056 2294 2294 31.0 1.740056 2181 2181 32.0 1.740056 1998 1998 33.0 1.740056 1889 1889 34.0 1.740056 1737 1737 35.0 1.740056 1647 1647 36.0 1.740056 1564 1564 37.0 1.740056 1435 1435 38.0 1.740056 1328 1328 39.0 1.740056 1196 1196 40.0 1.740056 1257 1257 41.0 1.740056 1114 1114 42.0 1.740056 1048 1048 43.0 1.740056 984 984 44.0 1.740056 966 966 45.0 1.740056 872 872 46.0 1.740056 858 858 47.0 1.740056 750 750 48.0 1.740056 764 764 49.0 1.740056 694 694 50.0 1.740056 685 685 51.0 1.740056 640 640 52.0 1.740056 635 635 53.0 1.740056 581 581 54.0 1.740056 536 536 55.0 1.740056 559 559 56.0 1.740056 502 502 57.0 1.740056 494 494 58.0 1.740056 435 435 59.0 1.740056 466 466 60.0 1.740056 392 392 61.0 1.740056 400 400 62.0 1.740056 408 408 63.0 1.740056 404 404 64.0 1.740056 354 354 65.0 1.740056 339 339 66.0 1.740056 326 326 67.0 1.740056 319 319 68.0 1.740056 284 284 69.0 1.740056 282 282 70.0 1.740056 271 271 71.0 1.740056 239 239 72.0 1.740056 227 227 73.0 1.740056 244 244 74.0 1.740056 246 246 75.0 1.740056 232 232 76.0 1.740056 247 247 77.0 1.740056 220 220 78.0 1.740056 221 221 79.0 1.740056 180 180 80.0 1.740056 214 214 81.0 1.740056 193 193 82.0 1.740056 159 159 83.0 1.740056 206 206 84.0 1.740056 175 175 85.0 1.740056 165 165 86.0 1.740056 149 149 87.0 1.740056 159 159 88.0 1.740056 158 158 89.0 1.740056 155 155 90.0 1.740056 140 140 91.0 1.740056 137 137 92.0 1.740056 132 132 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