## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_HD789_01_RNA_13_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_01_RNA_13_A23YTGFLT4_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: Wed Jun 03 20:13:05 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 79407815385 78713344590 3891 71512996344 5249264206 1730910983 220169166 0 0 0 3162682 245363471 1452223 0.012726 0.987274 0 0.908524 0.066688 0.02199 0.002797 0.975213 0.966684 0 0.48518 0.623674 0.753534 0.881479 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.270579 1 0.311568 2 0.366736 3 0.436354 4 0.51253 5 0.585423 6 0.650211 7 0.714125 8 0.772673 9 0.825529 10 0.873645 11 0.920594 12 0.969124 13 1.006146 14 1.03126 15 1.054943 16 1.077455 17 1.101985 18 1.116387 19 1.131807 20 1.150258 21 1.164376 22 1.168097 23 1.170705 24 1.172872 25 1.169996 26 1.172146 27 1.170915 28 1.167915 29 1.162043 30 1.155763 31 1.152264 32 1.146552 33 1.145367 34 1.143381 35 1.148217 36 1.148617 37 1.146571 38 1.141914 39 1.138195 40 1.136371 41 1.140653 42 1.144337 43 1.14775 44 1.148318 45 1.147168 46 1.139774 47 1.13704 48 1.137912 49 1.139403 50 1.141165 51 1.138602 52 1.137589 53 1.140909 54 1.147159 55 1.1474 56 1.143082 57 1.145792 58 1.147776 59 1.1403 60 1.139272 61 1.137252 62 1.135511 63 1.129658 64 1.122006 65 1.118131 66 1.124914 67 1.123305 68 1.120712 69 1.116431 70 1.105662 71 1.099112 72 1.096002 73 1.086296 74 1.07807 75 1.072079 76 1.060449 77 1.04136 78 1.031379 79 1.021851 80 0.99686 81 0.977343 82 0.969091 83 0.953027 84 0.934233 85 0.916624 86 0.897314 87 0.883672 88 0.867789 89 0.846693 90 0.830564 91 0.806962 92 0.780524 93 0.753595 94 0.725198 95 0.696484 96 0.663695 97 0.627989 98 0.589141 99 0.55278 100 0.517005