## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[P09-female_bleached_K5.sorted.bam] OUTPUT=P09-female_bleached_K5.sorted.dedup.bam METRICS_FILE=P09-female_bleached_K5-picard_metrics.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT 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 ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Jul 18 15:59:53 PDT 2019 ## 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 581570 20931495 0 1320106 374065 7421918 512793 0.358536 22891644 ## HISTOGRAM java.lang.Double BIN VALUE all_sets optical_sets non_optical_sets 1.0 1.015384 9803789 0 9981085 2.0 1.422317 2364786 399194 2313955 3.0 1.585403 739364 38938 686186 4.0 1.650763 278085 6568 245223 5.0 1.676957 121705 1566 103849 6.0 1.687454 61650 614 52091 7.0 1.691662 34353 264 29509 8.0 1.693348 21918 147 19024 9.0 1.694023 14757 100 13331 10.0 1.694294 10698 57 9893 11.0 1.694403 8138 34 7582 12.0 1.694446 6381 23 5921 13.0 1.694464 5132 23 4808 14.0 1.694471 4179 21 4044 15.0 1.694473 3488 21 3312 16.0 1.694475 2888 9 2735 17.0 1.694475 2561 10 2480 18.0 1.694475 2217 3 2205 19.0 1.694475 1912 9 1786 20.0 1.694475 1769 6 1630 21.0 1.694475 1479 2 1427 22.0 1.694475 1332 5 1276 23.0 1.694475 1184 0 1162 24.0 1.694475 1051 0 963 25.0 1.694475 963 2 896 26.0 1.694475 802 2 787 27.0 1.694475 762 0 727 28.0 1.694475 735 1 742 29.0 1.694475 636 2 627 30.0 1.694475 586 2 565 31.0 1.694475 564 2 520 32.0 1.694475 513 2 463 33.0 1.694475 451 0 424 34.0 1.694475 436 0 410 35.0 1.694475 383 0 371 36.0 1.694475 365 1 361 37.0 1.694475 330 0 305 38.0 1.694475 320 1 302 39.0 1.694475 266 0 268 40.0 1.694475 285 2 271 41.0 1.694475 281 0 260 42.0 1.694475 238 0 247 43.0 1.694475 233 0 234 44.0 1.694475 212 0 229 45.0 1.694475 226 0 212 46.0 1.694475 210 1 173 47.0 1.694475 189 0 176 48.0 1.694475 176 0 176 49.0 1.694475 161 0 148 50.0 1.694475 151 0 152 51.0 1.694475 165 0 143 52.0 1.694475 147 0 158 53.0 1.694475 126 0 121 54.0 1.694475 114 0 127 55.0 1.694475 132 0 113 56.0 1.694475 136 0 117 57.0 1.694475 117 0 102 58.0 1.694475 89 0 100 59.0 1.694475 99 0 88 60.0 1.694475 116 0 95 61.0 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