## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT RT4_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT RT4_FFPE_RNA_0001_B23LG7FLT4_2_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 28 22:44:26 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 75865500936 74981534655 56168 64565134814 5519819552 4319615977 576908144 0 0 0 6580796 229348764 1447392 0.027893 0.972107 0.000001 0.86108 0.073616 0.057609 0.007694 0.934696 0.923805 0 0.499381 0.54913 0.790476 0.758296 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.287609 1 0.322122 2 0.370789 3 0.429329 4 0.490226 5 0.551503 6 0.610362 7 0.662204 8 0.715932 9 0.76615 10 0.814745 11 0.858385 12 0.898206 13 0.92877 14 0.956454 15 0.98112 16 1.00298 17 1.027414 18 1.045684 19 1.060684 20 1.081018 21 1.098603 22 1.11963 23 1.134952 24 1.146365 25 1.148439 26 1.150012 27 1.155081 28 1.156376 29 1.156839 30 1.155328 31 1.156969 32 1.153567 33 1.156898 34 1.154857 35 1.155527 36 1.153202 37 1.152195 38 1.153217 39 1.156903 40 1.157248 41 1.152326 42 1.148279 43 1.149056 44 1.150919 45 1.151042 46 1.138086 47 1.133334 48 1.13482 49 1.145669 50 1.153312 51 1.152435 52 1.154959 53 1.160104 54 1.163596 55 1.160079 56 1.151509 57 1.148332 58 1.149421 59 1.14969 60 1.145978 61 1.147104 62 1.147801 63 1.142037 64 1.135256 65 1.129002 66 1.130005 67 1.122668 68 1.118468 69 1.111896 70 1.101426 71 1.092927 72 1.084422 73 1.074619 74 1.068496 75 1.067631 76 1.052486 77 1.039549 78 1.037307 79 1.027811 80 1.013542 81 0.999429 82 0.993294 83 0.979405 84 0.967068 85 0.961209 86 0.953083 87 0.944037 88 0.925686 89 0.908569 90 0.88374 91 0.861947 92 0.840727 93 0.816941 94 0.786022 95 0.753451 96 0.719432 97 0.683224 98 0.649252 99 0.615979 100 0.570798