## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1_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 22:38:54 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 65699774023 64408551876 68327 57503225957 3951400314 2405168432 548688846 0 0 0 13521829 221408848 1276664 0.057557 0.942443 0.000001 0.892789 0.061349 0.037342 0.008519 0.954138 0.935386 0 0.829445 0.351681 0.442953 0.927271 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.346179 1 0.379623 2 0.437992 3 0.502589 4 0.548428 5 0.594598 6 0.658157 7 0.717703 8 0.784476 9 0.836059 10 0.873427 11 0.901661 12 0.929575 13 0.965425 14 0.996285 15 1.018742 16 1.029859 17 1.0369 18 1.045121 19 1.054833 20 1.077442 21 1.093182 22 1.09918 23 1.106456 24 1.115747 25 1.125744 26 1.132399 27 1.140361 28 1.151237 29 1.145564 30 1.1411 31 1.148892 32 1.156331 33 1.17 34 1.153712 35 1.157289 36 1.177074 37 1.19208 38 1.203158 39 1.19859 40 1.189029 41 1.200708 42 1.193611 43 1.190714 44 1.189544 45 1.189928 46 1.19078 47 1.202628 48 1.19449 49 1.185982 50 1.186204 51 1.188134 52 1.176317 53 1.170015 54 1.168308 55 1.157247 56 1.147475 57 1.14866 58 1.144275 59 1.145724 60 1.16683 61 1.170244 62 1.165526 63 1.141607 64 1.128419 65 1.118375 66 1.111068 67 1.100609 68 1.095654 69 1.080229 70 1.061983 71 1.052128 72 1.04825 73 1.044032 74 1.043775 75 1.037621 76 1.038126 77 1.041234 78 1.035844 79 1.024011 80 1.005375 81 0.987581 82 0.96958 83 0.961578 84 0.953295 85 0.939273 86 0.923831 87 0.915704 88 0.898945 89 0.881479 90 0.853568 91 0.819923 92 0.772527 93 0.730119 94 0.685148 95 0.648099 96 0.613444 97 0.57914 98 0.544112 99 0.507896 100 0.465669