## 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_23.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_23_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 17:59:37 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 25193876655 24891848253 13977 21506117335 2052177050 1194549424 138990467 0 0 0 2843291 76568688 331860 0.035804 0.964196 0.000001 0.863982 0.082444 0.04799 0.005584 0.946426 0.93508 0 0.517033 0.558932 0.76704 0.795294 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.280497 1 0.313793 2 0.364921 3 0.421493 4 0.483753 5 0.546755 6 0.609605 7 0.669338 8 0.720964 9 0.771054 10 0.816595 11 0.8654 12 0.91565 13 0.956048 14 0.989199 15 1.011763 16 1.03481 17 1.054137 18 1.069879 19 1.088042 20 1.100309 21 1.116761 22 1.130995 23 1.145404 24 1.156293 25 1.161111 26 1.168441 27 1.174351 28 1.179193 29 1.178609 30 1.176882 31 1.176541 32 1.167083 33 1.165409 34 1.16324 35 1.16324 36 1.162506 37 1.154114 38 1.145832 39 1.139529 40 1.129513 41 1.126571 42 1.130515 43 1.133497 44 1.130513 45 1.140088 46 1.140136 47 1.138712 48 1.140575 49 1.149363 50 1.155584 51 1.154884 52 1.152897 53 1.152024 54 1.152868 55 1.155733 56 1.156328 57 1.157364 58 1.154252 59 1.152654 60 1.149651 61 1.150925 62 1.146784 63 1.138492 64 1.136182 65 1.137076 66 1.133137 67 1.130446 68 1.125305 69 1.118823 70 1.107441 71 1.101224 72 1.099206 73 1.090965 74 1.084593 75 1.078151 76 1.067246 77 1.050321 78 1.042132 79 1.029106 80 1.011463 81 0.99454 82 0.988323 83 0.97653 84 0.964119 85 0.95619 86 0.942343 87 0.924602 88 0.906078 89 0.885841 90 0.86086 91 0.835757 92 0.811656 93 0.781688 94 0.751244 95 0.71765 96 0.681553 97 0.644588 98 0.608398 99 0.569813 100 0.526521