## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT A673_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT A673_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 22:29:53 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 73512628841 72663627768 51628 63401253105 4907562830 3772507766 582252439 0 0 0 4262143 232994193 1478218 0.017964 0.982036 0.000001 0.872531 0.067538 0.051917 0.008013 0.940069 0.929212 0 0.522925 0.568471 0.738335 0.855042 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.265351 1 0.303736 2 0.358457 3 0.424417 4 0.499753 5 0.567696 6 0.634558 7 0.697342 8 0.758177 9 0.812681 10 0.863417 11 0.910421 12 0.957356 13 0.996806 14 1.031007 15 1.056095 16 1.086471 17 1.108444 18 1.114296 19 1.126032 20 1.140215 21 1.155113 22 1.164137 23 1.177132 24 1.179018 25 1.180686 26 1.180834 27 1.184669 28 1.182176 29 1.173978 30 1.162687 31 1.155112 32 1.160863 33 1.15579 34 1.151099 35 1.150131 36 1.148389 37 1.141318 38 1.140379 39 1.143678 40 1.146425 41 1.149027 42 1.154927 43 1.15557 44 1.149062 45 1.141804 46 1.126414 47 1.1203 48 1.121004 49 1.125158 50 1.130781 51 1.127355 52 1.133137 53 1.134197 54 1.139103 55 1.139917 56 1.133411 57 1.135535 58 1.135754 59 1.132471 60 1.128708 61 1.130469 62 1.130235 63 1.125516 64 1.122841 65 1.115269 66 1.109845 67 1.107018 68 1.108608 69 1.111656 70 1.102182 71 1.093159 72 1.084916 73 1.075781 74 1.073888 75 1.065911 76 1.054233 77 1.041258 78 1.034734 79 1.027252 80 1.016666 81 1.005578 82 0.994881 83 0.970117 84 0.956029 85 0.945741 86 0.932703 87 0.917167 88 0.896243 89 0.872992 90 0.850966 91 0.826483 92 0.797893 93 0.765276 94 0.724927 95 0.695001 96 0.66132 97 0.624251 98 0.583773 99 0.540376 100 0.496561