## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0001_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: Thu May 28 22:31:05 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 71994076008 71026416966 50991 59075160820 7668177300 3789610614 493417241 0 0 0 6070415 207428914 1413477 0.028433 0.971567 0.000001 0.831735 0.107962 0.053355 0.006947 0.939697 0.927067 0 0.518579 0.574039 0.740441 0.861951 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.271586 1 0.311231 2 0.375073 3 0.441407 4 0.510254 5 0.579045 6 0.647563 7 0.710991 8 0.765509 9 0.815424 10 0.860742 11 0.913085 12 0.962254 13 1.004056 14 1.037293 15 1.070111 16 1.097664 17 1.11185 18 1.123369 19 1.136858 20 1.153968 21 1.168967 22 1.177269 23 1.183771 24 1.192402 25 1.200371 26 1.204279 27 1.206508 28 1.202515 29 1.200204 30 1.191076 31 1.187688 32 1.17527 33 1.175735 34 1.17546 35 1.177934 36 1.179674 37 1.170671 38 1.162539 39 1.164026 40 1.16543 41 1.164079 42 1.164891 43 1.163613 44 1.15878 45 1.164349 46 1.163616 47 1.160991 48 1.154259 49 1.155883 50 1.158329 51 1.153982 52 1.147886 53 1.149087 54 1.15007 55 1.145204 56 1.140422 57 1.137532 58 1.129172 59 1.122028 60 1.122368 61 1.12595 62 1.124707 63 1.117884 64 1.115664 65 1.110522 66 1.103029 67 1.096785 68 1.084038 69 1.073674 70 1.060701 71 1.050083 72 1.044759 73 1.03751 74 1.032239 75 1.021856 76 1.009796 77 0.99643 78 0.9894 79 0.980887 80 0.96374 81 0.94449 82 0.936947 83 0.920467 84 0.909163 85 0.901416 86 0.889606 87 0.881072 88 0.865306 89 0.847373 90 0.828511 91 0.803312 92 0.781881 93 0.758967 94 0.734771 95 0.706444 96 0.67627 97 0.645804 98 0.613007 99 0.577364 100 0.534225