## 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_29.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_29_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 17:59:44 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 24937433734 24646143521 15114 21285437470 2018988911 1200570246 141131780 0 0 0 1930412 77287923 322461 0.024368 0.975632 0.000001 0.863642 0.081919 0.048712 0.005726 0.945561 0.934516 0 0.517149 0.557462 0.770135 0.783701 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.279304 1 0.317132 2 0.369636 3 0.42901 4 0.494221 5 0.558633 6 0.62107 7 0.679786 8 0.732497 9 0.783961 10 0.827599 11 0.874956 12 0.923962 13 0.963327 14 0.990945 15 1.013864 16 1.036014 17 1.051214 18 1.065267 19 1.081496 20 1.094843 21 1.112637 22 1.128827 23 1.141463 24 1.14795 25 1.150843 26 1.156208 27 1.162184 28 1.165508 29 1.164997 30 1.162306 31 1.162897 32 1.15371 33 1.152137 34 1.1479 35 1.148847 36 1.151124 37 1.145188 38 1.138677 39 1.137874 40 1.129859 41 1.129524 42 1.134718 43 1.137038 44 1.135089 45 1.143389 46 1.145158 47 1.143222 48 1.142514 49 1.149274 50 1.15575 51 1.153741 52 1.152387 53 1.15303 54 1.153813 55 1.155213 56 1.154296 57 1.155149 58 1.152824 59 1.150529 60 1.150124 61 1.152054 62 1.149453 63 1.144206 64 1.143722 65 1.145299 66 1.14371 67 1.141695 68 1.132517 69 1.1248 70 1.114689 71 1.107636 72 1.105075 73 1.094179 74 1.087121 75 1.076729 76 1.0637 77 1.046885 78 1.036544 79 1.024993 80 1.008424 81 0.990416 82 0.984703 83 0.973526 84 0.960784 85 0.953853 86 0.940439 87 0.92233 88 0.900837 89 0.880661 90 0.856988 91 0.83305 92 0.809662 93 0.781396 94 0.753076 95 0.722677 96 0.688353 97 0.652082 98 0.616129 99 0.577361 100 0.5331