## 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_30.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_30_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 17:59:45 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 24687358998 24389095993 30636 21077925903 2000827338 1169578559 140733557 0 0 0 2630280 76636561 338231 0.033183 0.966817 0.000001 0.864236 0.082038 0.047955 0.00577 0.946273 0.934841 0 0.528227 0.551521 0.764174 0.802392 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.281114 1 0.31688 2 0.368274 3 0.425625 4 0.48907 5 0.554015 6 0.615326 7 0.673552 8 0.722364 9 0.769764 10 0.81429 11 0.861209 12 0.909971 13 0.951289 14 0.981538 15 1.006895 16 1.030126 17 1.047621 18 1.063716 19 1.081684 20 1.0966 21 1.115017 22 1.131936 23 1.146892 24 1.155445 25 1.159281 26 1.166993 27 1.174715 28 1.182354 29 1.182244 30 1.181051 31 1.181802 32 1.17192 33 1.169837 34 1.166302 35 1.164938 36 1.162895 37 1.155287 38 1.147573 39 1.142789 40 1.135506 41 1.131473 42 1.133519 43 1.135627 44 1.132011 45 1.139778 46 1.137129 47 1.133485 48 1.134722 49 1.140042 50 1.14675 51 1.145926 52 1.144004 53 1.144118 54 1.147949 55 1.151456 56 1.152763 57 1.15231 58 1.153092 59 1.146801 60 1.145103 61 1.148626 62 1.146897 63 1.141794 64 1.140838 65 1.141235 66 1.136854 67 1.130103 68 1.121574 69 1.114385 70 1.105187 71 1.098778 72 1.097257 73 1.086914 74 1.077984 75 1.073118 76 1.063067 77 1.042947 78 1.034483 79 1.024397 80 1.010194 81 0.993848 82 0.989029 83 0.974916 84 0.961927 85 0.956712 86 0.943788 87 0.925867 88 0.906898 89 0.888513 90 0.868259 91 0.844448 92 0.822112 93 0.793532 94 0.761221 95 0.726644 96 0.690782 97 0.654264 98 0.617653 99 0.57816 100 0.534373