## 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-f2fa3a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f2fa3a-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 20:30:59 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 68404020237 67507963961 7200 62026764738 3705734863 1582759820 192697340 0 0 0 9672219 241115053 853103 0.038567 0.961433 0 0.918807 0.054893 0.023446 0.002854 0.9737 0.960945 0 0.565091 0.445184 0.74194 0.75557 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.261847 1 0.289112 2 0.329862 3 0.386745 4 0.439295 5 0.48266 6 0.536284 7 0.586358 8 0.642524 9 0.696505 10 0.748539 11 0.798675 12 0.850077 13 0.895027 14 0.932419 15 0.969075 16 0.99749 17 1.022705 18 1.041046 19 1.057608 20 1.074579 21 1.092794 22 1.11297 23 1.130616 24 1.136892 25 1.145314 26 1.150011 27 1.154739 28 1.163582 29 1.16833 30 1.16797 31 1.167991 32 1.16174 33 1.166854 34 1.166086 35 1.177451 36 1.181515 37 1.183719 38 1.18482 39 1.182885 40 1.181928 41 1.183519 42 1.191456 43 1.197439 44 1.201868 45 1.208543 46 1.205822 47 1.201163 48 1.197342 49 1.197781 50 1.190929 51 1.185175 52 1.178177 53 1.180714 54 1.186329 55 1.188521 56 1.192493 57 1.1922 58 1.180141 59 1.169411 60 1.157017 61 1.152719 62 1.151371 63 1.142067 64 1.144203 65 1.140857 66 1.129884 67 1.127537 68 1.125963 69 1.119213 70 1.110509 71 1.104619 72 1.096653 73 1.088571 74 1.08069 75 1.075011 76 1.068292 77 1.059973 78 1.060557 79 1.051901 80 1.03307 81 1.012507 82 0.996656 83 0.975583 84 0.957899 85 0.942024 86 0.925348 87 0.921971 88 0.908527 89 0.893904 90 0.874192 91 0.846756 92 0.819949 93 0.78718 94 0.752706 95 0.718379 96 0.682668 97 0.64713 98 0.61188 99 0.575602 100 0.539931