## 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_13.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_13_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 17:59:22 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 25325462259 25031583134 10956 21589103804 2085241871 1207189011 150037492 0 0 0 2660860 76677903 315768 0.033538 0.966462 0 0.862475 0.083304 0.048227 0.005994 0.945779 0.934804 0 0.515153 0.579124 0.754539 0.837467 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.280161 1 0.317184 2 0.371862 3 0.433405 4 0.500667 5 0.567851 6 0.632059 7 0.692524 8 0.745211 9 0.795717 10 0.8415 11 0.889812 12 0.937648 13 0.97619 14 1.004099 15 1.027562 16 1.051536 17 1.069191 18 1.083756 19 1.100598 20 1.11838 21 1.135964 22 1.150246 23 1.163407 24 1.173452 25 1.176425 26 1.180769 27 1.18523 28 1.189753 29 1.187958 30 1.184563 31 1.185974 32 1.176415 33 1.172745 34 1.164752 35 1.16156 36 1.162008 37 1.155246 38 1.147444 39 1.143548 40 1.134826 41 1.130789 42 1.134403 43 1.133615 44 1.128462 45 1.137667 46 1.137118 47 1.135225 48 1.136193 49 1.14213 50 1.146238 51 1.142768 52 1.139253 53 1.139216 54 1.141016 55 1.144074 56 1.14627 57 1.146188 58 1.144089 59 1.14166 60 1.141301 61 1.144104 62 1.140713 63 1.135878 64 1.135852 65 1.136973 66 1.132439 67 1.128539 68 1.12088 69 1.112521 70 1.101334 71 1.093447 72 1.090316 73 1.078478 74 1.069988 75 1.063146 76 1.051993 77 1.035257 78 1.027677 79 1.016556 80 0.998935 81 0.980231 82 0.973813 83 0.962214 84 0.949729 85 0.942217 86 0.927143 87 0.910938 88 0.889266 89 0.868993 90 0.846525 91 0.822812 92 0.799269 93 0.77065 94 0.741946 95 0.710353 96 0.67443 97 0.638577 98 0.602921 99 0.562986 100 0.520257