## 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_20.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_20_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 17:59:43 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 24834336950 24533896299 16662 21270884267 2017703887 1106156511 139134972 0 0 0 2292657 77159025 316368 0.028856 0.971144 0.000001 0.867 0.082241 0.045087 0.005671 0.949241 0.937758 0 0.519994 0.578371 0.775761 0.846929 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.27852 1 0.31651 2 0.373086 3 0.435182 4 0.50225 5 0.56899 6 0.63277 7 0.692704 8 0.74648 9 0.797208 10 0.842745 11 0.89098 12 0.941752 13 0.9796 14 1.010943 15 1.038707 16 1.056115 17 1.070849 18 1.086062 19 1.102993 20 1.114238 21 1.131693 22 1.147134 23 1.159774 24 1.167 25 1.169304 26 1.174474 27 1.179161 28 1.183785 29 1.182586 30 1.178328 31 1.177072 32 1.167718 33 1.165345 34 1.162034 35 1.161242 36 1.158902 37 1.151268 38 1.142236 39 1.13826 40 1.131409 41 1.127307 42 1.129849 43 1.131559 44 1.127303 45 1.137505 46 1.137872 47 1.13536 48 1.135038 49 1.141602 50 1.146013 51 1.141988 52 1.138038 53 1.13818 54 1.140653 55 1.142806 56 1.140592 57 1.139551 58 1.136585 59 1.131501 60 1.131029 61 1.137307 62 1.135062 63 1.130293 64 1.12844 65 1.133002 66 1.133388 67 1.129032 68 1.120381 69 1.112155 70 1.099762 71 1.092783 72 1.090352 73 1.079717 74 1.07253 75 1.066085 76 1.054278 77 1.034961 78 1.026467 79 1.017892 80 1.001907 81 0.983519 82 0.976217 83 0.960989 84 0.949006 85 0.943333 86 0.93111 87 0.915008 88 0.89474 89 0.877524 90 0.859517 91 0.837146 92 0.814052 93 0.784909 94 0.752828 95 0.719991 96 0.684073 97 0.647167 98 0.609296 99 0.568388 100 0.523625