## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT ColoN_FFPE_L06_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT ColoN_FFPE_L06_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: Sat May 16 08:38:26 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 1873887217 1791474927 301650 1346102358 151619391 235315138 58136390 0 0 0 408256 6158453 56577 0.062171 0.937829 0.000168 0.751393 0.084634 0.131353 0.032452 0.836027 0.799259 0 0.898374 0.337879 0.39689 0.479552 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.31616 1 0.359503 2 0.431498 3 0.507597 4 0.579535 5 0.649564 6 0.694369 7 0.743487 8 0.79396 9 0.838848 10 0.875731 11 0.917833 12 0.954513 13 0.988751 14 1.023473 15 1.026473 16 1.034586 17 1.027728 18 1.019664 19 1.032745 20 1.050621 21 1.07422 22 1.083046 23 1.10568 24 1.119183 25 1.121403 26 1.130098 27 1.136207 28 1.145611 29 1.139222 30 1.144012 31 1.148845 32 1.147904 33 1.156961 34 1.147455 35 1.142568 36 1.136163 37 1.136985 38 1.135709 39 1.134354 40 1.131663 41 1.149003 42 1.150917 43 1.152159 44 1.150433 45 1.151847 46 1.133016 47 1.126222 48 1.130103 49 1.123643 50 1.110917 51 1.106396 52 1.105178 53 1.120391 54 1.139978 55 1.14316 56 1.143217 57 1.135918 58 1.120925 59 1.112433 60 1.104776 61 1.111447 62 1.109092 63 1.093018 64 1.090679 65 1.08881 66 1.094825 67 1.090883 68 1.095665 69 1.095131 70 1.084969 71 1.071837 72 1.075734 73 1.071022 74 1.072881 75 1.076975 76 1.069887 77 1.056882 78 1.049919 79 1.036988 80 1.024985 81 1.020569 82 1.016652 83 1.018585 84 1.023529 85 1.017181 86 0.996579 87 0.974321 88 0.950296 89 0.92375 90 0.892581 91 0.87738 92 0.833047 93 0.788951 94 0.755273 95 0.720964 96 0.683618 97 0.640674 98 0.591576 99 0.547672 100 0.560766