## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 786-O_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: Fri Feb 27 06:49:39 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 25136370399 24843155713 17876 21914932842 1692312657 1070988287 164904051 0 0 0 2601687 76666380 472660 0.032821 0.967179 0.000001 0.882132 0.06812 0.04311 0.006638 0.950251 0.939167 0 0.504807 0.573462 0.762199 0.837678 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.293218 1 0.325607 2 0.375152 3 0.432705 4 0.496829 5 0.558557 6 0.614739 7 0.668843 8 0.732797 9 0.796571 10 0.850497 11 0.906843 12 0.952856 13 0.991657 14 1.020461 15 1.041081 16 1.060179 17 1.088326 18 1.109858 19 1.127537 20 1.144988 21 1.161944 22 1.174608 23 1.186241 24 1.189866 25 1.185781 26 1.177997 27 1.173736 28 1.175503 29 1.171496 30 1.171608 31 1.177424 32 1.179359 33 1.175993 34 1.170766 35 1.170405 36 1.171942 37 1.166073 38 1.162951 39 1.162215 40 1.161777 41 1.163292 42 1.168544 43 1.16895 44 1.164882 45 1.173826 46 1.166272 47 1.164482 48 1.163561 49 1.16202 50 1.160111 51 1.160515 52 1.154237 53 1.145621 54 1.14675 55 1.145949 56 1.140073 57 1.132872 58 1.127175 59 1.122244 60 1.113403 61 1.114128 62 1.119913 63 1.117802 64 1.111916 65 1.107901 66 1.102407 67 1.097049 68 1.087179 69 1.083779 70 1.077771 71 1.069074 72 1.063352 73 1.054655 74 1.046408 75 1.040961 76 1.030048 77 1.020574 78 1.018818 79 1.008356 80 0.994929 81 0.982099 82 0.969688 83 0.950294 84 0.936323 85 0.924321 86 0.906986 87 0.89211 88 0.873321 89 0.8554 90 0.836023 91 0.811715 92 0.787517 93 0.759849 94 0.732868 95 0.704298 96 0.675914 97 0.651901 98 0.622212 99 0.589609 100 0.552154