## 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_2.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_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 07:06:58 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 25398174740 25069940474 13125 22409843680 1578269315 925524713 156289641 0 0 0 3657766 76791373 491081 0.045467 0.954533 0.000001 0.893893 0.062955 0.036918 0.006234 0.956848 0.944482 0 0.502233 0.619143 0.746177 0.964539 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.325479 1 0.369655 2 0.423573 3 0.491076 4 0.55258 5 0.613786 6 0.678153 7 0.741194 8 0.796924 9 0.857509 10 0.903902 11 0.953365 12 1.003068 13 1.040245 14 1.073876 15 1.110261 16 1.129394 17 1.141213 18 1.150712 19 1.156931 20 1.177767 21 1.19623 22 1.203215 23 1.216729 24 1.21736 25 1.215644 26 1.218268 27 1.216062 28 1.210015 29 1.197643 30 1.195268 31 1.194055 32 1.187137 33 1.188279 34 1.181752 35 1.184287 36 1.181483 37 1.176648 38 1.176322 39 1.173288 40 1.173244 41 1.17215 42 1.170232 43 1.169413 44 1.164228 45 1.163267 46 1.159261 47 1.155114 48 1.153417 49 1.1565 50 1.155151 51 1.159433 52 1.154543 53 1.151438 54 1.155233 55 1.157303 56 1.148928 57 1.142434 58 1.133515 59 1.119817 60 1.106165 61 1.099403 62 1.095707 63 1.090964 64 1.081911 65 1.074816 66 1.070955 67 1.061848 68 1.055425 69 1.04884 70 1.037955 71 1.02615 72 1.02372 73 1.011462 74 0.996401 75 0.987235 76 0.977698 77 0.956852 78 0.94734 79 0.940553 80 0.932615 81 0.920692 82 0.9109 83 0.893499 84 0.883751 85 0.875801 86 0.860549 87 0.843592 88 0.827994 89 0.809891 90 0.797161 91 0.775962 92 0.754606 93 0.73348 94 0.709704 95 0.685802 96 0.664885 97 0.637757 98 0.613371 99 0.585718 100 0.552539