## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354102.sorted.bam --OUTPUT SRX7354102.markdup.sorted.bam --METRICS_FILE SRX7354102.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: Fri Oct 27 16:58:08 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 27787 30051643 5103402 3301137 20005 10359811 0 0.344907 32855363 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16919561 16919561 2.0 1.400651 1687966 1687966 3.0 1.561172 387503 387503 4.0 1.625485 176923 176923 5.0 1.651252 105686 105686 6.0 1.661576 71475 71475 7.0 1.665712 51700 51700 8.0 1.667369 39222 39222 9.0 1.668033 30560 30560 10.0 1.668299 24707 24707 11.0 1.668405 20376 20376 12.0 1.668448 16824 16824 13.0 1.668465 14361 14361 14.0 1.668472 11995 11995 15.0 1.668475 10611 10611 16.0 1.668476 9356 9356 17.0 1.668476 8352 8352 18.0 1.668477 7240 7240 19.0 1.668477 6555 6555 20.0 1.668477 5812 5812 21.0 1.668477 5336 5336 22.0 1.668477 4798 4798 23.0 1.668477 4341 4341 24.0 1.668477 3857 3857 25.0 1.668477 3539 3539 26.0 1.668477 3290 3290 27.0 1.668477 3067 3067 28.0 1.668477 2832 2832 29.0 1.668477 2586 2586 30.0 1.668477 2408 2408 31.0 1.668477 2287 2287 32.0 1.668477 2052 2052 33.0 1.668477 2017 2017 34.0 1.668477 1894 1894 35.0 1.668477 1722 1722 36.0 1.668477 1552 1552 37.0 1.668477 1446 1446 38.0 1.668477 1396 1396 39.0 1.668477 1327 1327 40.0 1.668477 1270 1270 41.0 1.668477 1140 1140 42.0 1.668477 1149 1149 43.0 1.668477 1015 1015 44.0 1.668477 1042 1042 45.0 1.668477 993 993 46.0 1.668477 908 908 47.0 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