## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-ffabe0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ffabe0-R1_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 20:19:57 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 71106528555 70238701174 5292 63204324011 4714445221 2087254039 232672611 0 0 0 7992283 240975439 1040131 0.032102 0.967898 0 0.89985 0.06712 0.029717 0.003313 0.966971 0.955169 0 0.530911 0.454591 0.759698 0.724733 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.294114 1 0.325595 2 0.3781 3 0.437855 4 0.483336 5 0.521943 6 0.576405 7 0.623063 8 0.671727 9 0.714862 10 0.75396 11 0.803114 12 0.849295 13 0.886615 14 0.918211 15 0.948888 16 0.976524 17 1.002092 18 1.025834 19 1.042684 20 1.057235 21 1.072124 22 1.084556 23 1.09908 24 1.104484 25 1.112807 26 1.11927 27 1.122495 28 1.130514 29 1.129986 30 1.132648 31 1.132208 32 1.132961 33 1.139058 34 1.136378 35 1.143872 36 1.147372 37 1.146616 38 1.145962 39 1.144969 40 1.143819 41 1.140818 42 1.153018 43 1.163234 44 1.169615 45 1.172746 46 1.173103 47 1.178026 48 1.17656 49 1.178276 50 1.178835 51 1.181664 52 1.178693 53 1.177668 54 1.177376 55 1.175924 56 1.176636 57 1.171 58 1.163637 59 1.156179 60 1.150561 61 1.153544 62 1.155215 63 1.147215 64 1.148984 65 1.150309 66 1.144492 67 1.141622 68 1.144897 69 1.146035 70 1.136255 71 1.129414 72 1.122134 73 1.115289 74 1.109898 75 1.105044 76 1.094666 77 1.084102 78 1.078672 79 1.065811 80 1.052056 81 1.037314 82 1.025028 83 1.00489 84 0.988371 85 0.973195 86 0.953225 87 0.945076 88 0.928793 89 0.913059 90 0.887575 91 0.866039 92 0.842993 93 0.812297 94 0.779737 95 0.745272 96 0.70673 97 0.668861 98 0.628738 99 0.58806 100 0.550145