## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354121.sorted.bam --OUTPUT SRX7354121.markdup.sorted.bam --METRICS_FILE SRX7354121.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: Sat Oct 28 15:20:48 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 24310 34217632 4258810 3391698 18064 12479310 0 0.364838 34632291 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17187740 17187740 2.0 1.372311 3021656 3021656 3.0 1.510926 688213 688213 4.0 1.562534 253609 253609 5.0 1.581748 134886 134886 6.0 1.588901 86644 86644 7.0 1.591565 60499 60499 8.0 1.592556 44884 44884 9.0 1.592926 34492 34492 10.0 1.593063 27765 27765 11.0 1.593114 22209 22209 12.0 1.593133 18355 18355 13.0 1.59314 15499 15499 14.0 1.593143 13046 13046 15.0 1.593144 11146 11146 16.0 1.593144 9748 9748 17.0 1.593145 8528 8528 18.0 1.593145 7312 7312 19.0 1.593145 6666 6666 20.0 1.593145 5906 5906 21.0 1.593145 5183 5183 22.0 1.593145 4688 4688 23.0 1.593145 4253 4253 24.0 1.593145 3890 3890 25.0 1.593145 3554 3554 26.0 1.593145 3219 3219 27.0 1.593145 3076 3076 28.0 1.593145 2760 2760 29.0 1.593145 2530 2530 30.0 1.593145 2324 2324 31.0 1.593145 2157 2157 32.0 1.593145 1979 1979 33.0 1.593145 1885 1885 34.0 1.593145 1823 1823 35.0 1.593145 1609 1609 36.0 1.593145 1497 1497 37.0 1.593145 1478 1478 38.0 1.593145 1272 1272 39.0 1.593145 1206 1206 40.0 1.593145 1148 1148 41.0 1.593145 1096 1096 42.0 1.593145 1089 1089 43.0 1.593145 988 988 44.0 1.593145 962 962 45.0 1.593145 908 908 46.0 1.593145 821 821 47.0 1.593145 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