## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354283.sorted.bam --OUTPUT SRX7354283.markdup.sorted.bam --METRICS_FILE SRX7354283.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 20:10:55 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 44429 42608922 5011940 2996667 35628 16070350 0 0.377381 41148219 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21319919 21319919 2.0 1.355049 3401276 3401276 3.0 1.481109 779193 779193 4.0 1.525867 301265 301265 5.0 1.541758 163839 163839 6.0 1.5474 105777 105777 7.0 1.549403 74256 74256 8.0 1.550115 54832 54832 9.0 1.550367 42733 42733 10.0 1.550457 33987 33987 11.0 1.550489 27735 27735 12.0 1.5505 23139 23139 13.0 1.550504 19092 19092 14.0 1.550505 16417 16417 15.0 1.550506 14163 14163 16.0 1.550506 12413 12413 17.0 1.550506 10790 10790 18.0 1.550506 9551 9551 19.0 1.550506 8704 8704 20.0 1.550506 7628 7628 21.0 1.550506 6941 6941 22.0 1.550506 6177 6177 23.0 1.550506 5752 5752 24.0 1.550506 5214 5214 25.0 1.550506 4863 4863 26.0 1.550506 4346 4346 27.0 1.550506 3946 3946 28.0 1.550506 3641 3641 29.0 1.550506 3435 3435 30.0 1.550506 3057 3057 31.0 1.550506 2935 2935 32.0 1.550506 2734 2734 33.0 1.550506 2599 2599 34.0 1.550506 2391 2391 35.0 1.550506 2200 2200 36.0 1.550506 2077 2077 37.0 1.550506 1960 1960 38.0 1.550506 1947 1947 39.0 1.550506 1792 1792 40.0 1.550506 1574 1574 41.0 1.550506 1554 1554 42.0 1.550506 1470 1470 43.0 1.550506 1321 1321 44.0 1.550506 1271 1271 45.0 1.550506 1195 1195 46.0 1.550506 1167 1167 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