## 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_11.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_11_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 25499659424 25201256278 10165 21895551729 2088270690 1073885337 143538357 0 0 0 1926085 77693853 329208 0.024191 0.975809 0 0.868828 0.082864 0.042612 0.005696 0.951692 0.940555 0 0.51171 0.575982 0.755254 0.851269 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.270342 1 0.309644 2 0.367576 3 0.434055 4 0.502571 5 0.569916 6 0.632717 7 0.694111 8 0.748638 9 0.800183 10 0.846594 11 0.89337 12 0.941313 13 0.984925 14 1.016594 15 1.043578 16 1.06187 17 1.076451 18 1.091364 19 1.110511 20 1.127448 21 1.145447 22 1.159825 23 1.169906 24 1.177845 25 1.181013 26 1.186366 27 1.191715 28 1.193658 29 1.192456 30 1.187819 31 1.184495 32 1.173408 33 1.170608 34 1.164869 35 1.163168 36 1.162227 37 1.153659 38 1.145259 39 1.14215 40 1.134519 41 1.131126 42 1.133913 43 1.13483 44 1.130045 45 1.138788 46 1.139089 47 1.13777 48 1.138368 49 1.145047 50 1.151259 51 1.147736 52 1.142755 53 1.141591 54 1.143025 55 1.143044 56 1.140041 57 1.137833 58 1.134472 59 1.126852 60 1.126365 61 1.133554 62 1.131753 63 1.1277 64 1.125967 65 1.126698 66 1.124478 67 1.121358 68 1.11479 69 1.106143 70 1.094526 71 1.085602 72 1.082552 73 1.072555 74 1.063403 75 1.055475 76 1.04367 77 1.024456 78 1.018923 79 1.011479 80 0.993494 81 0.974814 82 0.967598 83 0.953809 84 0.94207 85 0.937125 86 0.92436 87 0.908025 88 0.886463 89 0.867866 90 0.849909 91 0.828439 92 0.80635 93 0.779479 94 0.748249 95 0.717599 96 0.683413 97 0.648328 98 0.613192 99 0.572625 100 0.528335