## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L09_RNA_01_B23LG7FLT4_1_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 22:44:28 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 64910845571 63892087958 92536 56163808435 4294219526 2979145884 454821577 0 0 0 10368632 227062108 1250443 0.04367 0.95633 0.000001 0.879042 0.067211 0.046628 0.007119 0.946252 0.931401 0 0.716454 0.351894 0.581184 0.697881 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.30916 1 0.338627 2 0.390178 3 0.448595 4 0.494249 5 0.534246 6 0.582843 7 0.631933 8 0.686447 9 0.733298 10 0.761298 11 0.798775 12 0.843168 13 0.878009 14 0.907369 15 0.928813 16 0.943808 17 0.947281 18 0.954913 19 0.976276 20 0.993895 21 1.008001 22 1.032715 23 1.054063 24 1.069956 25 1.077948 26 1.079746 27 1.082807 28 1.098448 29 1.101155 30 1.092406 31 1.107853 32 1.115166 33 1.122504 34 1.117796 35 1.11892 36 1.123264 37 1.132696 38 1.147865 39 1.154807 40 1.161186 41 1.172986 42 1.178167 43 1.177765 44 1.173914 45 1.176972 46 1.162788 47 1.156648 48 1.15648 49 1.16807 50 1.188106 51 1.195451 52 1.194539 53 1.200893 54 1.204284 55 1.196766 56 1.201353 57 1.201753 58 1.19499 59 1.199378 60 1.212603 61 1.214855 62 1.210386 63 1.195051 64 1.185445 65 1.170177 66 1.157494 67 1.149095 68 1.146117 69 1.145371 70 1.133691 71 1.122615 72 1.113268 73 1.10811 74 1.114436 75 1.120154 76 1.130739 77 1.127094 78 1.109476 79 1.088353 80 1.069298 81 1.047609 82 1.034653 83 1.018695 84 1.010965 85 1.000016 86 0.990349 87 0.981013 88 0.96322 89 0.936964 90 0.904554 91 0.86652 92 0.828937 93 0.791587 94 0.759725 95 0.728755 96 0.689947 97 0.645369 98 0.598016 99 0.551414 100 0.505823