## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_HD834_01_RNA_0001_23LGNLLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD834_01_RNA_0001_23LGNLLT4_2_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: Sat May 16 10:14:44 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 78860246573 78015190491 33603 68796067599 5373619711 3374001348 471468230 0 0 0 7368116 234424275 1515306 0.030473 0.969527 0 0.881829 0.068879 0.043248 0.006043 0.950708 0.940521 0 0.488005 0.641866 0.766543 0.970731 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.302165 1 0.345694 2 0.402351 3 0.46927 4 0.54127 5 0.612683 6 0.679341 7 0.741945 8 0.7983 9 0.847302 10 0.897025 11 0.943574 12 0.986646 13 1.02539 14 1.052984 15 1.079772 16 1.10753 17 1.133026 18 1.141653 19 1.150194 20 1.158771 21 1.173522 22 1.178685 23 1.191876 24 1.202586 25 1.200168 26 1.197562 27 1.195257 28 1.194183 29 1.190775 30 1.186681 31 1.183485 32 1.179919 33 1.179307 34 1.175269 35 1.174898 36 1.168359 37 1.160628 38 1.154908 39 1.154552 40 1.157106 41 1.15654 42 1.150801 43 1.150477 44 1.149197 45 1.14924 46 1.146578 47 1.14537 48 1.145629 49 1.148066 50 1.146778 51 1.145981 52 1.141733 53 1.13692 54 1.139262 55 1.129501 56 1.119896 57 1.119527 58 1.110934 59 1.106652 60 1.099481 61 1.097544 62 1.100982 63 1.09363 64 1.091072 65 1.087159 66 1.086386 67 1.079899 68 1.071185 69 1.06236 70 1.04949 71 1.036053 72 1.034911 73 1.03242 74 1.024696 75 1.021669 76 1.012119 77 0.997877 78 0.992479 79 0.984727 80 0.970977 81 0.959059 82 0.947226 83 0.93516 84 0.916524 85 0.90698 86 0.893006 87 0.880772 88 0.865046 89 0.845706 90 0.825886 91 0.804663 92 0.779804 93 0.751886 94 0.726326 95 0.700991 96 0.674528 97 0.647058 98 0.615082 99 0.585 100 0.546598