## 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: Thu May 28 22:48:48 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 74816601244 73469374693 62578 64750911723 4958344967 3332904776 427150649 0 0 0 8635749 229952589 1406655 0.036195 0.963805 0.000001 0.881332 0.067489 0.045365 0.005814 0.948821 0.931735 0 0.511314 0.586698 0.758283 0.903962 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.287922 1 0.327028 2 0.373654 3 0.432055 4 0.502487 5 0.5738 6 0.634907 7 0.696252 8 0.753895 9 0.804299 10 0.851669 11 0.902692 12 0.946849 13 0.985934 14 1.018419 15 1.051446 16 1.075847 17 1.100706 18 1.111025 19 1.122902 20 1.147307 21 1.170067 22 1.18364 23 1.194353 24 1.207498 25 1.209947 26 1.21331 27 1.212932 28 1.211878 29 1.207481 30 1.207892 31 1.208393 32 1.205413 33 1.204347 34 1.198329 35 1.19672 36 1.193 37 1.185272 38 1.186629 39 1.184389 40 1.182765 41 1.179074 42 1.177409 43 1.176574 44 1.171103 45 1.171103 46 1.164103 47 1.157642 48 1.154775 49 1.155987 50 1.149437 51 1.143972 52 1.142282 53 1.142232 54 1.145265 55 1.14288 56 1.13711 57 1.134639 58 1.124478 59 1.115036 60 1.112942 61 1.108084 62 1.106322 63 1.10305 64 1.09728 65 1.096128 66 1.089427 67 1.078873 68 1.069267 69 1.063652 70 1.059824 71 1.052435 72 1.051855 73 1.041179 74 1.028285 75 1.024843 76 1.01796 77 1.007459 78 1.000017 79 0.991644 80 0.973918 81 0.955856 82 0.943614 83 0.92715 84 0.912825 85 0.903353 86 0.884172 87 0.871129 88 0.860031 89 0.840235 90 0.823326 91 0.800945 92 0.77639 93 0.75264 94 0.726082 95 0.7017 96 0.675465 97 0.647296 98 0.617455 99 0.58675 100 0.550932