## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 786-O_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT 786-O_FFPE_RNA_0001_B23LG7FLT4_3_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 22:29:51 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 74964079438 74079971155 59028 65474369033 5040942730 3074463386 490136978 0 0 0 6531206 231369619 1417014 0.027453 0.972547 0.000001 0.883834 0.068047 0.041502 0.006616 0.951881 0.940655 0 0.509273 0.578141 0.764816 0.855336 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.297736 1 0.331188 2 0.379438 3 0.436639 4 0.500038 5 0.561304 6 0.61818 7 0.675906 8 0.739715 9 0.804117 10 0.862205 11 0.919808 12 0.964654 13 1.002184 14 1.032229 15 1.053745 16 1.07288 17 1.097847 18 1.116062 19 1.134007 20 1.152822 21 1.171361 22 1.181655 23 1.192083 24 1.196881 25 1.193484 26 1.187563 27 1.18394 28 1.182724 29 1.177007 30 1.174966 31 1.181281 32 1.181988 33 1.180152 34 1.172985 35 1.171946 36 1.169153 37 1.161215 38 1.157221 39 1.155115 40 1.15503 41 1.158589 42 1.161375 43 1.159891 44 1.157449 45 1.166694 46 1.157979 47 1.156878 48 1.156025 49 1.154576 50 1.152926 51 1.150658 52 1.144114 53 1.136061 54 1.135961 55 1.135876 56 1.130668 57 1.1242 58 1.11862 59 1.11364 60 1.106086 61 1.107889 62 1.112487 63 1.110696 64 1.107122 65 1.104306 66 1.09972 67 1.096019 68 1.085825 69 1.080308 70 1.074263 71 1.064024 72 1.057376 73 1.049317 74 1.04111 75 1.034145 76 1.022546 77 1.01352 78 1.012612 79 1.001177 80 0.986403 81 0.975871 82 0.966282 83 0.946697 84 0.934436 85 0.922526 86 0.907263 87 0.892613 88 0.874626 89 0.857329 90 0.837414 91 0.814167 92 0.79211 93 0.767742 94 0.739822 95 0.709998 96 0.68125 97 0.658039 98 0.629745 99 0.598449 100 0.560268