## 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_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_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: Fri Feb 27 08:05:06 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 25707036773 25367655839 19185 21092884976 2747854175 1353680564 173216939 0 0 0 2164155 73988345 519484 0.028419 0.971581 0.000001 0.831487 0.108321 0.053362 0.006828 0.939809 0.927401 0 0.519447 0.571776 0.743782 0.848222 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.273003 1 0.312334 2 0.375387 3 0.44211 4 0.512152 5 0.581619 6 0.65018 7 0.713851 8 0.768893 9 0.819083 10 0.864718 11 0.917466 12 0.967319 13 1.008106 14 1.041205 15 1.074025 16 1.095705 17 1.107242 18 1.119516 19 1.134735 20 1.151561 21 1.16653 22 1.174471 23 1.181021 24 1.189375 25 1.196973 26 1.200469 27 1.202662 28 1.199713 29 1.1982 30 1.187757 31 1.185084 32 1.174042 33 1.174352 34 1.17208 35 1.175604 36 1.176251 37 1.16747 38 1.159525 39 1.15891 40 1.157571 41 1.15546 42 1.155567 43 1.153844 44 1.148159 45 1.157038 46 1.157929 47 1.15676 48 1.150694 49 1.152296 50 1.155891 51 1.152418 52 1.147319 53 1.147269 54 1.145173 55 1.141671 56 1.138573 57 1.136885 58 1.128795 59 1.122445 60 1.122587 61 1.125076 62 1.124112 63 1.117009 64 1.114925 65 1.108993 66 1.100483 67 1.093677 68 1.080674 69 1.071263 70 1.060197 71 1.049109 72 1.04457 73 1.036995 74 1.03117 75 1.021796 76 1.011041 77 0.999104 78 0.992668 79 0.985939 80 0.969929 81 0.951241 82 0.944557 83 0.928992 84 0.918029 85 0.910939 86 0.899121 87 0.889134 88 0.872808 89 0.854703 90 0.833981 91 0.807477 92 0.78679 93 0.763284 94 0.738519 95 0.709558 96 0.679166 97 0.649025 98 0.616281 99 0.580699 100 0.537465