## 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-5519ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-5519ab-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 20:16:00 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 71746182788 70992748228 8528 63649217002 4905076654 2061225983 377220061 0 0 0 13249398 237046611 1083167 0.052935 0.947065 0 0.896559 0.069093 0.029034 0.005314 0.965652 0.955511 0 0.569759 0.542086 0.725766 0.826679 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.321555 1 0.369274 2 0.430649 3 0.496235 4 0.561008 5 0.622133 6 0.681227 7 0.734374 8 0.791478 9 0.835484 10 0.876836 11 0.921704 12 0.964504 13 1.005 14 1.038561 15 1.052281 16 1.070496 17 1.088138 18 1.099488 19 1.116687 20 1.134323 21 1.148142 22 1.162251 23 1.17166 24 1.173756 25 1.174444 26 1.181751 27 1.19026 28 1.191343 29 1.183776 30 1.174116 31 1.174128 32 1.167122 33 1.16576 34 1.153637 35 1.145485 36 1.135974 37 1.130987 38 1.130246 39 1.1324 40 1.130893 41 1.134603 42 1.134235 43 1.135467 44 1.127845 45 1.130212 46 1.130015 47 1.12956 48 1.122995 49 1.126014 50 1.128906 51 1.121857 52 1.121174 53 1.11902 54 1.120185 55 1.121693 56 1.120581 57 1.118048 58 1.111763 59 1.109379 60 1.112374 61 1.113028 62 1.110139 63 1.102236 64 1.101082 65 1.103199 66 1.099957 67 1.094626 68 1.089735 69 1.083157 70 1.075559 71 1.065584 72 1.060485 73 1.055382 74 1.054091 75 1.048005 76 1.037091 77 1.02505 78 1.020448 79 1.010344 80 0.993924 81 0.976195 82 0.9673 83 0.959276 84 0.952654 85 0.943443 86 0.923221 87 0.913695 88 0.898434 89 0.87861 90 0.858125 91 0.831876 92 0.809031 93 0.779526 94 0.745866 95 0.717142 96 0.686005 97 0.652916 98 0.6192 99 0.5842 100 0.546519