## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354208.sorted.bam --OUTPUT SRX7354208.markdup.sorted.bam --METRICS_FILE SRX7354208.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 10:35:30 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 122804 56130702 8163584 2411982 98194 24646678 0 0.439488 43375764 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 24486187 24486187 2.0 1.274156 4327152 4327152 3.0 1.349318 1102693 1102693 4.0 1.369924 435680 435680 5.0 1.375573 239979 239979 6.0 1.377122 156560 156560 7.0 1.377547 111083 111083 8.0 1.377663 83298 83298 9.0 1.377695 65284 65284 10.0 1.377704 51900 51900 11.0 1.377706 42762 42762 12.0 1.377707 35597 35597 13.0 1.377707 30567 30567 14.0 1.377707 25889 25889 15.0 1.377707 22360 22360 16.0 1.377707 19413 19413 17.0 1.377707 17195 17195 18.0 1.377707 15319 15319 19.0 1.377707 13873 13873 20.0 1.377707 12272 12272 21.0 1.377707 11278 11278 22.0 1.377707 10122 10122 23.0 1.377707 9051 9051 24.0 1.377707 8275 8275 25.0 1.377707 7634 7634 26.0 1.377707 7029 7029 27.0 1.377707 6518 6518 28.0 1.377707 6109 6109 29.0 1.377707 5600 5600 30.0 1.377707 5222 5222 31.0 1.377707 5034 5034 32.0 1.377707 4430 4430 33.0 1.377707 4243 4243 34.0 1.377707 4023 4023 35.0 1.377707 3617 3617 36.0 1.377707 3464 3464 37.0 1.377707 3238 3238 38.0 1.377707 3116 3116 39.0 1.377707 2840 2840 40.0 1.377707 2766 2766 41.0 1.377707 2604 2604 42.0 1.377707 2450 2450 43.0 1.377707 2394 2394 44.0 1.377707 2208 2208 45.0 1.377707 2153 2153 46.0 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