## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT ColoN_FFPE_L01_RNA_01_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT ColoN_FFPE_L01_RNA_01_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 23:20:43 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 56761207306 55306523980 105311 48496876852 4026578131 2089452194 693511492 0 0 0 24667815 165626026 1026884 0.12963 0.87037 0.000002 0.876874 0.072805 0.037779 0.012539 0.949679 0.925341 0 0.723922 0.371341 0.545485 0.68523 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.266165 1 0.298882 2 0.354021 3 0.416918 4 0.481854 5 0.554294 6 0.621565 7 0.677243 8 0.734293 9 0.780035 10 0.82826 11 0.872173 12 0.920653 13 0.970143 14 1.015508 15 1.049507 16 1.070384 17 1.081603 18 1.088048 19 1.094825 20 1.117212 21 1.128006 22 1.134201 23 1.141824 24 1.156299 25 1.167156 26 1.175845 27 1.181711 28 1.1905 29 1.178989 30 1.168631 31 1.165304 32 1.167716 33 1.161866 34 1.155848 35 1.16283 36 1.162431 37 1.149289 38 1.146759 39 1.149877 40 1.15197 41 1.161692 42 1.166396 43 1.175935 44 1.183438 45 1.184954 46 1.189151 47 1.193222 48 1.18526 49 1.187088 50 1.177729 51 1.178315 52 1.167795 53 1.16351 54 1.164828 55 1.172832 56 1.167908 57 1.154289 58 1.15399 59 1.155255 60 1.154697 61 1.160057 62 1.168874 63 1.151252 64 1.146639 65 1.131084 66 1.118491 67 1.113101 68 1.104772 69 1.097585 70 1.084536 71 1.070678 72 1.065929 73 1.064659 74 1.059827 75 1.063522 76 1.066444 77 1.059727 78 1.045669 79 1.032527 80 1.015088 81 0.996518 82 0.976149 83 0.966178 84 0.94498 85 0.919005 86 0.892277 87 0.879418 88 0.866333 89 0.846636 90 0.824494 91 0.797901 92 0.772579 93 0.742902 94 0.71374 95 0.675229 96 0.63674 97 0.613025 98 0.577642 99 0.545329 100 0.512918