## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_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: Sat May 16 08:40:16 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 2783493764 2656532186 287432 2132599602 236291649 233795966 53557537 0 0 0 1051056 8841250 72271 0.10625 0.89375 0.000108 0.802776 0.088947 0.088008 0.020161 0.891723 0.85105 0 0.84501 0.33767 0.429097 0.542658 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.346115 1 0.385099 2 0.444356 3 0.506786 4 0.571284 5 0.644299 6 0.712896 7 0.7846 8 0.851349 9 0.906349 10 0.937696 11 0.968439 12 1.002592 13 1.0336 14 1.061555 15 1.068016 16 1.076085 17 1.068767 18 1.068878 19 1.075212 20 1.085802 21 1.103306 22 1.117909 23 1.133375 24 1.139429 25 1.146958 26 1.153062 27 1.165615 28 1.1848 29 1.189459 30 1.198642 31 1.197124 32 1.196318 33 1.208692 34 1.192772 35 1.195618 36 1.200848 37 1.190612 38 1.180619 39 1.164591 40 1.158835 41 1.157133 42 1.160995 43 1.166972 44 1.171696 45 1.17476 46 1.178643 47 1.195773 48 1.195579 49 1.18741 50 1.168279 51 1.158374 52 1.152649 53 1.147318 54 1.147638 55 1.147762 56 1.139395 57 1.130511 58 1.120862 59 1.102633 60 1.107952 61 1.111297 62 1.101203 63 1.090963 64 1.092295 65 1.089472 66 1.093877 67 1.0837 68 1.075856 69 1.073416 70 1.063371 71 1.043198 72 1.043781 73 1.050447 74 1.049965 75 1.038728 76 1.030074 77 1.023122 78 1.004969 79 0.988657 80 0.979884 81 0.966139 82 0.936219 83 0.922781 84 0.91281 85 0.901568 86 0.883265 87 0.869952 88 0.849792 89 0.833242 90 0.812667 91 0.787805 92 0.742163 93 0.697292 94 0.666826 95 0.643108 96 0.618857 97 0.587605 98 0.55443 99 0.521034 100 0.518339