## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354361.sorted.bam --OUTPUT SRX7354361.markdup.sorted.bam --METRICS_FILE SRX7354361.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: Tue Oct 31 00:50:34 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 20082 26911681 3358405 1221126 14170 9838619 0 0.365716 27146350 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14504120 14504120 2.0 1.371073 1557231 1557231 3.0 1.508769 361726 361726 4.0 1.559864 163922 163922 5.0 1.578824 98295 98295 6.0 1.58586 65955 65955 7.0 1.58847 48254 48254 8.0 1.589439 36393 36393 9.0 1.589799 28329 28329 10.0 1.589932 23030 23030 11.0 1.589981 18845 18845 12.0 1.59 15924 15924 13.0 1.590007 13418 13418 14.0 1.590009 11401 11401 15.0 1.59001 9941 9941 16.0 1.59001 8711 8711 17.0 1.590011 7739 7739 18.0 1.590011 6959 6959 19.0 1.590011 6012 6012 20.0 1.590011 5338 5338 21.0 1.590011 5067 5067 22.0 1.590011 4569 4569 23.0 1.590011 4042 4042 24.0 1.590011 3803 3803 25.0 1.590011 3383 3383 26.0 1.590011 3132 3132 27.0 1.590011 2848 2848 28.0 1.590011 2731 2731 29.0 1.590011 2423 2423 30.0 1.590011 2311 2311 31.0 1.590011 2101 2101 32.0 1.590011 2021 2021 33.0 1.590011 1904 1904 34.0 1.590011 1742 1742 35.0 1.590011 1639 1639 36.0 1.590011 1632 1632 37.0 1.590011 1437 1437 38.0 1.590011 1372 1372 39.0 1.590011 1258 1258 40.0 1.590011 1211 1211 41.0 1.590011 1101 1101 42.0 1.590011 1045 1045 43.0 1.590011 979 979 44.0 1.590011 1020 1020 45.0 1.590011 930 930 46.0 1.590011 884 884 47.0 1.590011 777 777 48.0 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