## 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-ac6a71-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ac6a71-R1_B23WHYVLT4_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: Sat May 16 11:54:46 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 76846636706 76032998083 2688 69074102806 4750532748 2027155745 181204096 0 0 0 2925007 245104235 1712165 0.011793 0.988207 0 0.908475 0.06248 0.026662 0.002383 0.970955 0.960675 0 0.55424 0.505195 0.719647 0.778602 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.276796 1 0.309741 2 0.364181 3 0.429276 4 0.479583 5 0.527644 6 0.586792 7 0.637674 8 0.682584 9 0.731137 10 0.781103 11 0.829979 12 0.882204 13 0.923302 14 0.961838 15 0.993798 16 1.021453 17 1.0399 18 1.06361 19 1.083664 20 1.104534 21 1.123108 22 1.138641 23 1.155457 24 1.158413 25 1.161977 26 1.168458 27 1.176909 28 1.189034 29 1.196422 30 1.199094 31 1.197134 32 1.195205 33 1.191532 34 1.184011 35 1.188035 36 1.194418 37 1.185291 38 1.185054 39 1.184862 40 1.183952 41 1.180458 42 1.177635 43 1.182411 44 1.183899 45 1.187615 46 1.176032 47 1.179259 48 1.176114 49 1.177687 50 1.184641 51 1.181697 52 1.172975 53 1.173349 54 1.17404 55 1.168576 56 1.165613 57 1.159426 58 1.151688 59 1.142957 60 1.140023 61 1.146338 62 1.145151 63 1.14388 64 1.14162 65 1.135303 66 1.124239 67 1.114955 68 1.109005 69 1.109195 70 1.101656 71 1.089666 72 1.084704 73 1.081327 74 1.078867 75 1.070648 76 1.055928 77 1.042711 78 1.036205 79 1.020161 80 1.004599 81 0.9895 82 0.975059 83 0.958694 84 0.94098 85 0.928585 86 0.911396 87 0.902181 88 0.883947 89 0.86111 90 0.835206 91 0.805098 92 0.783175 93 0.749859 94 0.723118 95 0.696754 96 0.665257 97 0.631594 98 0.596185 99 0.561999 100 0.524204