## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT SRX7354057.sorted.bam --OUTPUT SRX7354057.markdup.sorted.bam --METRICS_FILE SRX7354057.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: Fri Oct 27 17:00:44 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 35182 36990630 5329694 2353108 26355 12828089 0 0.346984 40116535 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 20055616 20055616 2.0 1.397691 2643965 2643965 3.0 1.55585 589148 589148 4.0 1.618748 241421 241421 5.0 1.643762 138605 138605 6.0 1.65371 91352 91352 7.0 1.657666 64108 64108 8.0 1.659239 48487 48487 9.0 1.659865 37134 37134 10.0 1.660114 29646 29646 11.0 1.660213 24266 24266 12.0 1.660252 20065 20065 13.0 1.660268 17130 17130 14.0 1.660274 14499 14499 15.0 1.660276 12363 12363 16.0 1.660277 10738 10738 17.0 1.660278 9440 9440 18.0 1.660278 8228 8228 19.0 1.660278 7543 7543 20.0 1.660278 6757 6757 21.0 1.660278 6017 6017 22.0 1.660278 5394 5394 23.0 1.660278 4979 4979 24.0 1.660278 4445 4445 25.0 1.660278 3964 3964 26.0 1.660278 3699 3699 27.0 1.660278 3446 3446 28.0 1.660278 3051 3051 29.0 1.660278 2917 2917 30.0 1.660278 2607 2607 31.0 1.660278 2448 2448 32.0 1.660278 2180 2180 33.0 1.660278 2097 2097 34.0 1.660278 1996 1996 35.0 1.660278 1916 1916 36.0 1.660278 1710 1710 37.0 1.660278 1625 1625 38.0 1.660278 1527 1527 39.0 1.660278 1442 1442 40.0 1.660278 1458 1458 41.0 1.660278 1276 1276 42.0 1.660278 1253 1253 43.0 1.660278 1196 1196 44.0 1.660278 1082 1082 45.0 1.660278 1014 1014 46.0 1.660278 951 951 47.0 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