## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_27.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_27_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --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 Mar 09 17:59:53 GMT 2026 ## METRICS CLASS picard.analysis.RnaSeqMetrics PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS NUM_R1_TRANSCRIPT_STRAND_READS NUM_R2_TRANSCRIPT_STRAND_READS NUM_UNEXPLAINED_READS PCT_R1_TRANSCRIPT_STRAND_READS PCT_R2_TRANSCRIPT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP 25371409783 25086504404 13480 21753949794 2052992347 1135366919 144181864 0 0 0 1905419 77486358 369277 0.024 0.976 0.000001 0.867157 0.081837 0.045258 0.005747 0.948994 0.938337 0 0.510351 0.573951 0.763571 0.834812 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.271413 1 0.308804 2 0.363898 3 0.425415 4 0.491279 5 0.555944 6 0.618402 7 0.679975 8 0.735352 9 0.787616 10 0.831389 11 0.877628 12 0.92712 13 0.967907 14 0.995547 15 1.022225 16 1.046424 17 1.063363 18 1.082077 19 1.098787 20 1.111218 21 1.129084 22 1.142421 23 1.152264 24 1.159834 25 1.16366 26 1.170708 27 1.177061 28 1.178867 29 1.175172 30 1.170755 31 1.167841 32 1.158511 33 1.156612 34 1.154272 35 1.153968 36 1.153921 37 1.149871 38 1.143053 39 1.142451 40 1.135789 41 1.135531 42 1.139198 43 1.141448 44 1.137721 45 1.147239 46 1.148834 47 1.147744 48 1.146482 49 1.152431 50 1.160625 51 1.159726 52 1.157493 53 1.157813 54 1.158276 55 1.160126 56 1.157724 57 1.1561 58 1.152265 59 1.145334 60 1.145795 61 1.149919 62 1.147079 63 1.140874 64 1.138638 65 1.140185 66 1.138915 67 1.134508 68 1.126162 69 1.117853 70 1.109245 71 1.101938 72 1.098925 73 1.088104 74 1.077299 75 1.068691 76 1.057426 77 1.039169 78 1.031518 79 1.020986 80 1.001254 81 0.9814 82 0.974147 83 0.959861 84 0.9478 85 0.941335 86 0.92834 87 0.910186 88 0.887962 89 0.867349 90 0.847576 91 0.825746 92 0.803594 93 0.77684 94 0.746004 95 0.713734 96 0.678409 97 0.641876 98 0.606113 99 0.566501 100 0.522834