## 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_0005_23KMKGLT4_17.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_17_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: Mon Mar 09 18:10:57 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 25511860340 25216458537 8834 22128169205 2026613372 927427309 134239817 0 0 0 1941959 78098482 342917 0.024262 0.975738 0 0.877529 0.080369 0.036779 0.005323 0.957897 0.946806 0 0.508196 0.611664 0.742798 0.906993 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.268544 1 0.307742 2 0.369229 3 0.439273 4 0.511812 5 0.583095 6 0.64853 7 0.7119 8 0.768518 9 0.825368 10 0.875307 11 0.926079 12 0.980365 13 1.023292 14 1.056031 15 1.082403 16 1.094595 17 1.107352 18 1.127013 19 1.145192 20 1.155568 21 1.171205 22 1.181927 23 1.192779 24 1.200508 25 1.202257 26 1.203897 27 1.20477 28 1.200291 29 1.192381 30 1.185231 31 1.1796 32 1.166815 33 1.167128 34 1.164302 35 1.162392 36 1.163861 37 1.155776 38 1.147354 39 1.146029 40 1.139246 41 1.137018 42 1.139964 43 1.140488 44 1.136592 45 1.148141 46 1.145898 47 1.144438 48 1.143838 49 1.150195 50 1.157253 51 1.155894 52 1.152201 53 1.151687 54 1.150721 55 1.152185 56 1.149979 57 1.147543 58 1.143459 59 1.132656 60 1.126394 61 1.124627 62 1.119346 63 1.113285 64 1.108807 65 1.108051 66 1.105544 67 1.10229 68 1.096538 69 1.088619 70 1.07925 71 1.072285 72 1.067498 73 1.058856 74 1.050024 75 1.042399 76 1.030572 77 1.013929 78 1.008275 79 1.001259 80 0.985195 81 0.966499 82 0.957087 83 0.941371 84 0.925493 85 0.915703 86 0.899248 87 0.880274 88 0.857076 89 0.83558 90 0.819744 91 0.795919 92 0.77374 93 0.746513 94 0.721055 95 0.688174 96 0.654983 97 0.621642 98 0.58634 99 0.548015 100 0.504336