## 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_28.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_28_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 18:10:55 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 25179939820 24894101122 12249 21525848519 2037853335 1190736056 139650963 0 0 0 1870379 77490325 342961 0.023568 0.976432 0 0.864697 0.081861 0.047832 0.00561 0.946558 0.935812 0 0.510742 0.57395 0.773226 0.8267 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.277686 1 0.314765 2 0.367985 3 0.427761 4 0.490771 5 0.553704 6 0.616138 7 0.675784 8 0.726614 9 0.777922 10 0.820686 11 0.865496 12 0.915728 13 0.957209 14 0.986306 15 1.010876 16 1.034648 17 1.051745 18 1.072174 19 1.088412 20 1.100877 21 1.120731 22 1.134113 23 1.145416 24 1.153379 25 1.156482 26 1.163875 27 1.17205 28 1.17487 29 1.173204 30 1.17068 31 1.170759 32 1.161578 33 1.159115 34 1.153493 35 1.154862 36 1.156137 37 1.147249 38 1.139854 39 1.13679 40 1.127907 41 1.127265 42 1.132156 43 1.137581 44 1.13824 45 1.146494 46 1.149149 47 1.149197 48 1.148982 49 1.154783 50 1.160952 51 1.158761 52 1.156022 53 1.157023 54 1.157045 55 1.158296 56 1.157283 57 1.158104 58 1.155782 59 1.154247 60 1.154454 61 1.155555 62 1.152966 63 1.146096 64 1.144574 65 1.144594 66 1.142559 67 1.138998 68 1.130585 69 1.123146 70 1.112502 71 1.105001 72 1.101604 73 1.089891 74 1.081996 75 1.074537 76 1.062539 77 1.044909 78 1.035473 79 1.023414 80 1.005739 81 0.988388 82 0.98299 83 0.971291 84 0.95627 85 0.949047 86 0.935295 87 0.917274 88 0.897162 89 0.877257 90 0.853135 91 0.829327 92 0.806866 93 0.778397 94 0.747957 95 0.715214 96 0.679368 97 0.643985 98 0.609023 99 0.570758 100 0.525077