## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0002_RNA_0001_B23WHTKLT4_1_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: Thu May 21 07:12:19 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 79938793133 79055730363 2026 69145605154 7317313025 2234381262 358428896 0 0 0 9681547 231681632 1312776 0.040112 0.959888 0 0.874644 0.092559 0.028263 0.004534 0.967203 0.956518 0 0.525476 0.556938 0.724549 0.783403 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.263262 1 0.303102 2 0.363857 3 0.424824 4 0.488145 5 0.556803 6 0.620632 7 0.678811 8 0.734334 9 0.790352 10 0.835017 11 0.885953 12 0.934495 13 0.978852 14 1.008444 15 1.036277 16 1.06245 17 1.079781 18 1.098175 19 1.118249 20 1.138061 21 1.155603 22 1.171807 23 1.18497 24 1.193802 25 1.200476 26 1.21103 27 1.213953 28 1.211453 29 1.211044 30 1.207331 31 1.207062 32 1.191191 33 1.192455 34 1.194089 35 1.193392 36 1.192309 37 1.183605 38 1.176121 39 1.170963 40 1.164361 41 1.165107 42 1.169048 43 1.170049 44 1.169231 45 1.179845 46 1.178535 47 1.172647 48 1.168279 49 1.166306 50 1.167548 51 1.163894 52 1.158265 53 1.15824 54 1.159101 55 1.158784 56 1.156417 57 1.147914 58 1.139741 59 1.136334 60 1.133539 61 1.134656 62 1.131186 63 1.119791 64 1.114762 65 1.114295 66 1.114505 67 1.112759 68 1.10505 69 1.092817 70 1.078905 71 1.067197 72 1.062556 73 1.053847 74 1.049313 75 1.041563 76 1.027823 77 1.010351 78 1.001695 79 0.992421 80 0.962962 81 0.939488 82 0.929689 83 0.915156 84 0.901403 85 0.891956 86 0.878156 87 0.874153 88 0.863778 89 0.84418 90 0.824473 91 0.803944 92 0.781275 93 0.757371 94 0.729484 95 0.700198 96 0.666471 97 0.634665 98 0.599233 99 0.561798 100 0.5237