## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT A673_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT A673_FFPE_RNA_0001_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 22:28:57 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 75073905894 74237085342 49845 64761235662 5038798762 3849276793 587724280 0 0 0 4832977 232742082 1430561 0.020343 0.979657 0.000001 0.872357 0.067874 0.051851 0.007917 0.940231 0.929751 0 0.516854 0.57091 0.72931 0.870973 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.262125 1 0.301291 2 0.356363 3 0.42178 4 0.495339 5 0.561599 6 0.62714 7 0.69178 8 0.75248 9 0.806833 10 0.856988 11 0.902247 12 0.948204 13 0.988273 14 1.023745 15 1.04818 16 1.080165 17 1.104602 18 1.11208 19 1.123638 20 1.137124 21 1.153915 22 1.163711 23 1.178192 24 1.181736 25 1.185196 26 1.186423 27 1.19107 28 1.18789 29 1.180754 30 1.171454 31 1.163209 32 1.166676 33 1.161096 34 1.15475 35 1.154334 36 1.15231 37 1.144389 38 1.143947 39 1.147476 40 1.148759 41 1.151248 42 1.15712 43 1.158835 44 1.153968 45 1.147495 46 1.133067 47 1.127708 48 1.12871 49 1.132537 50 1.137754 51 1.132902 52 1.139248 53 1.141702 54 1.146108 55 1.146206 56 1.139775 57 1.139578 58 1.140878 59 1.138575 60 1.134617 61 1.135616 62 1.134231 63 1.127473 64 1.123839 65 1.116093 66 1.109961 67 1.106998 68 1.106669 69 1.10794 70 1.096912 71 1.087741 72 1.080597 73 1.071814 74 1.069493 75 1.063914 76 1.051868 77 1.039428 78 1.03395 79 1.027326 80 1.017999 81 1.006475 82 0.993429 83 0.967384 84 0.951921 85 0.941193 86 0.927203 87 0.910577 88 0.890361 89 0.868394 90 0.845863 91 0.820432 92 0.792351 93 0.760633 94 0.721403 95 0.692715 96 0.659615 97 0.622294 98 0.581534 99 0.53969 100 0.497697