## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_cAd-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cAd-T1-TRNA-1_B23WHTKLT4_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 21 05:55:43 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 72832010982 71927995626 9564 65322854713 4780938104 1620180630 204012615 0 0 0 10501081 237442793 1097855 0.042353 0.957647 0 0.90817 0.066468 0.022525 0.002836 0.974638 0.962541 0 0.520676 0.500195 0.74946 0.756645 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.257281 1 0.29216 2 0.341072 3 0.396292 4 0.453429 5 0.507887 6 0.563676 7 0.615697 8 0.66932 9 0.722927 10 0.773618 11 0.824804 12 0.867184 13 0.904717 14 0.93831 15 0.968697 16 0.996648 17 1.024243 18 1.037857 19 1.049808 20 1.068186 21 1.08224 22 1.098687 23 1.106969 24 1.11556 25 1.120352 26 1.122881 27 1.131506 28 1.148075 29 1.150913 30 1.143823 31 1.143606 32 1.135965 33 1.152604 34 1.155513 35 1.164863 36 1.171259 37 1.176361 38 1.186079 39 1.18502 40 1.17476 41 1.175734 42 1.179577 43 1.185178 44 1.189064 45 1.198762 46 1.18913 47 1.186206 48 1.18549 49 1.186691 50 1.182756 51 1.172985 52 1.162636 53 1.162423 54 1.167125 55 1.171245 56 1.170035 57 1.172071 58 1.165957 59 1.161911 60 1.163695 61 1.166465 62 1.169193 63 1.165906 64 1.162452 65 1.159964 66 1.15847 67 1.153606 68 1.146994 69 1.139697 70 1.129687 71 1.115954 72 1.107317 73 1.096811 74 1.089177 75 1.080083 76 1.072938 77 1.064754 78 1.057467 79 1.047904 80 1.032033 81 1.017693 82 1.006831 83 0.992242 84 0.98148 85 0.958837 86 0.934051 87 0.921248 88 0.908752 89 0.894183 90 0.872668 91 0.838624 92 0.81499 93 0.787999 94 0.755888 95 0.721086 96 0.68302 97 0.65365 98 0.615447 99 0.576018 100 0.533084