## 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_22.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_22_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 17:59:36 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 24839416276 24536207295 18125 21222216894 2018635509 1156370772 138965995 0 0 0 3180175 76197907 317455 0.040064 0.959936 0.000001 0.864935 0.082272 0.047129 0.005664 0.947206 0.935644 0 0.52478 0.562496 0.760916 0.835034 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.279124 1 0.314561 2 0.368731 3 0.429341 4 0.494055 5 0.560463 6 0.624559 7 0.684957 8 0.737389 9 0.788198 10 0.834231 11 0.882693 12 0.929096 13 0.966858 14 0.996298 15 1.021037 16 1.046058 17 1.06461 18 1.07909 19 1.097012 20 1.109489 21 1.127009 22 1.14139 23 1.153763 24 1.159894 25 1.162728 26 1.169003 27 1.174476 28 1.179485 29 1.178714 30 1.174395 31 1.17269 32 1.164054 33 1.162042 34 1.159004 35 1.157052 36 1.154224 37 1.144869 38 1.136639 39 1.134367 40 1.125411 41 1.12304 42 1.127907 43 1.130857 44 1.126179 45 1.134723 46 1.131708 47 1.130192 48 1.132121 49 1.139647 50 1.145146 51 1.142694 52 1.140008 53 1.139965 54 1.142407 55 1.145952 56 1.146841 57 1.146076 58 1.143565 59 1.141655 60 1.14091 61 1.146503 62 1.144906 63 1.138525 64 1.136669 65 1.137195 66 1.132315 67 1.1264 68 1.119811 69 1.113351 70 1.100997 71 1.094886 72 1.092982 73 1.083556 74 1.077006 75 1.07192 76 1.061691 77 1.045407 78 1.037776 79 1.028513 80 1.013301 81 0.995679 82 0.989253 83 0.975232 84 0.963536 85 0.956602 86 0.943851 87 0.926205 88 0.905287 89 0.887575 90 0.863497 91 0.838547 92 0.815829 93 0.78692 94 0.754871 95 0.72226 96 0.685694 97 0.649509 98 0.612572 99 0.573289 100 0.528627