## 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_46.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_46_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 18:00:08 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 24414905357 24114347814 24617 20805826844 1997094789 1165420633 145980931 0 0 0 1368553 77656137 348427 0.017318 0.982682 0.000001 0.862799 0.082818 0.048329 0.006054 0.945616 0.933975 0 0.528523 0.568216 0.749297 0.833456 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.286465 1 0.321939 2 0.374825 3 0.434143 4 0.499015 5 0.565028 6 0.628123 7 0.690259 8 0.742445 9 0.79299 10 0.837737 11 0.883874 12 0.932178 13 0.972188 14 1.001024 15 1.024947 16 1.03976 17 1.054765 18 1.070748 19 1.089299 20 1.104896 21 1.126597 22 1.145316 23 1.157847 24 1.165036 25 1.16751 26 1.17552 27 1.183048 28 1.189482 29 1.187627 30 1.182758 31 1.182111 32 1.172489 33 1.170311 34 1.164001 35 1.162477 36 1.160295 37 1.15108 38 1.142133 39 1.138241 40 1.130684 41 1.126464 42 1.130757 43 1.132725 44 1.12882 45 1.135123 46 1.131491 47 1.126314 48 1.125987 49 1.132564 50 1.13886 51 1.1368 52 1.134879 53 1.135433 54 1.137267 55 1.140077 56 1.14042 57 1.138836 58 1.1365 59 1.134024 60 1.134165 61 1.138715 62 1.139398 63 1.134579 64 1.135343 65 1.13627 66 1.132616 67 1.128156 68 1.119827 69 1.111023 70 1.101594 71 1.095388 72 1.095623 73 1.084273 74 1.074737 75 1.069134 76 1.05681 77 1.037852 78 1.028585 79 1.017776 80 1.002959 81 0.986039 82 0.981385 83 0.967554 84 0.955342 85 0.951832 86 0.939921 87 0.923752 88 0.905103 89 0.887012 90 0.864274 91 0.839513 92 0.816583 93 0.789308 94 0.757781 95 0.723967 96 0.689534 97 0.652889 98 0.616244 99 0.576211 100 0.52966