## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT U118MG_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_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: Fri Feb 27 07:06:09 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 25318608506 25002969966 11440 22333503691 1561639789 951741643 156073403 0 0 0 2015266 78379102 491090 0.025067 0.974933 0 0.893234 0.062458 0.038065 0.006242 0.955692 0.943778 0 0.502844 0.618884 0.740758 0.973814 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.321514 1 0.365031 2 0.420761 3 0.488574 4 0.548612 5 0.607177 6 0.671907 7 0.734991 8 0.791354 9 0.850589 10 0.899077 11 0.948822 12 0.994233 13 1.033858 14 1.067325 15 1.102185 16 1.130707 17 1.143909 18 1.1503 19 1.153967 20 1.168677 21 1.187835 22 1.195544 23 1.210082 24 1.211016 25 1.212355 26 1.212732 27 1.206637 28 1.200222 29 1.188973 30 1.18515 31 1.180954 32 1.176781 33 1.179105 34 1.17301 35 1.174331 36 1.16984 37 1.164249 38 1.164788 39 1.164784 40 1.165119 41 1.166223 42 1.163392 43 1.163369 44 1.159247 45 1.158913 46 1.158527 47 1.156061 48 1.152123 49 1.154099 50 1.152989 51 1.157164 52 1.154535 53 1.151476 54 1.154733 55 1.155815 56 1.14873 57 1.142673 58 1.135632 59 1.119973 60 1.107706 61 1.102896 62 1.104135 63 1.102082 64 1.092219 65 1.08496 66 1.080868 67 1.069785 68 1.062151 69 1.056343 70 1.04888 71 1.038734 72 1.035819 73 1.022121 74 1.007831 75 0.999813 76 0.99094 77 0.973712 78 0.96531 79 0.956284 80 0.944088 81 0.931972 82 0.92185 83 0.903961 84 0.89301 85 0.88454 86 0.869642 87 0.854389 88 0.838026 89 0.821892 90 0.807174 91 0.780879 92 0.75724 93 0.732814 94 0.705902 95 0.682748 96 0.660938 97 0.633734 98 0.609597 99 0.582778 100 0.550841