## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354132.sorted.bam --OUTPUT SRX7354132.markdup.sorted.bam --METRICS_FILE SRX7354132.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: Sun Oct 29 00:19:06 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 28390 40164887 5070774 2767706 21710 16213658 0 0.403805 35190720 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19153207 19153207 2.0 1.319388 3084715 3084715 3.0 1.421397 702523 702523 4.0 1.453977 273272 273272 5.0 1.464383 152504 152504 6.0 1.467706 99913 99913 7.0 1.468768 72225 72225 8.0 1.469107 54579 54579 9.0 1.469215 42765 42765 10.0 1.46925 34248 34248 11.0 1.469261 28131 28131 12.0 1.469264 23678 23678 13.0 1.469265 20172 20172 14.0 1.469266 17081 17081 15.0 1.469266 15034 15034 16.0 1.469266 13206 13206 17.0 1.469266 11767 11767 18.0 1.469266 10140 10140 19.0 1.469266 9175 9175 20.0 1.469266 8235 8235 21.0 1.469266 7494 7494 22.0 1.469266 6722 6722 23.0 1.469266 6182 6182 24.0 1.469266 5617 5617 25.0 1.469266 5147 5147 26.0 1.469266 4777 4777 27.0 1.469266 4429 4429 28.0 1.469266 4016 4016 29.0 1.469266 3582 3582 30.0 1.469266 3450 3450 31.0 1.469266 3222 3222 32.0 1.469266 2998 2998 33.0 1.469266 2866 2866 34.0 1.469266 2640 2640 35.0 1.469266 2362 2362 36.0 1.469266 2443 2443 37.0 1.469266 2175 2175 38.0 1.469266 2015 2015 39.0 1.469266 1986 1986 40.0 1.469266 1779 1779 41.0 1.469266 1765 1765 42.0 1.469266 1626 1626 43.0 1.469266 1592 1592 44.0 1.469266 1502 1502 45.0 1.469266 1439 1439 46.0 1.469266 1318 1318 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