## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT Hs746T_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT Hs746T_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 06:42:56 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 24930523616 24472772517 22680 21567898279 1651453337 1111688697 141709524 0 0 0 2881305 76579524 480926 0.036261 0.963739 0.000001 0.881302 0.067481 0.045426 0.00579 0.948783 0.931362 0 0.513117 0.587274 0.751056 0.897902 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.285291 1 0.323926 2 0.370533 3 0.429249 4 0.50079 5 0.570818 6 0.629542 7 0.689147 8 0.746691 9 0.79851 10 0.850025 11 0.902508 12 0.948464 13 0.98968 14 1.024382 15 1.058862 16 1.074695 17 1.09689 18 1.109336 19 1.12467 20 1.15035 21 1.172293 22 1.185772 23 1.196722 24 1.210381 25 1.213851 26 1.217622 27 1.217371 28 1.214468 29 1.208634 30 1.206762 31 1.207554 32 1.205226 33 1.203502 34 1.197974 35 1.195591 36 1.191758 37 1.185787 38 1.187085 39 1.184301 40 1.182812 41 1.179678 42 1.177468 43 1.176678 44 1.171259 45 1.171246 46 1.161645 47 1.155774 48 1.154322 49 1.156606 50 1.151277 51 1.146272 52 1.143717 53 1.142102 54 1.145724 55 1.141979 56 1.135984 57 1.133325 58 1.123118 59 1.114113 60 1.112431 61 1.10985 62 1.107426 63 1.103244 64 1.096573 65 1.09579 66 1.089143 67 1.077754 68 1.068394 69 1.062752 70 1.059604 71 1.053149 72 1.05301 73 1.042254 74 1.029447 75 1.025442 76 1.01868 77 1.006435 78 0.999032 79 0.99164 80 0.976127 81 0.957078 82 0.943371 83 0.92586 84 0.912929 85 0.904007 86 0.885173 87 0.872509 88 0.862009 89 0.841355 90 0.824012 91 0.800896 92 0.775288 93 0.751218 94 0.724939 95 0.701315 96 0.675424 97 0.647758 98 0.617113 99 0.586305 100 0.551251