## 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-f0dbdf-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f0dbdf-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 20:22:04 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 74078246369 73219235164 8894 65995875240 5051348102 1895318686 276684242 0 0 0 8615289 238448131 1042466 0.034871 0.965129 0 0.901346 0.068989 0.025886 0.003779 0.970336 0.959083 0 0.545462 0.53887 0.701819 0.8582 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.272242 1 0.306668 2 0.370286 3 0.439501 4 0.512246 5 0.582366 6 0.644984 7 0.698484 8 0.754698 9 0.803542 10 0.843813 11 0.886943 12 0.932084 13 0.975242 14 1.005096 15 1.031079 16 1.058012 17 1.076148 18 1.082607 19 1.098022 20 1.111178 21 1.12448 22 1.145515 23 1.159327 24 1.169528 25 1.175073 26 1.178219 27 1.177789 28 1.176776 29 1.177042 30 1.182729 31 1.184524 32 1.179339 33 1.18569 34 1.178261 35 1.180758 36 1.182454 37 1.17726 38 1.172452 39 1.178011 40 1.177105 41 1.179915 42 1.177432 43 1.17569 44 1.176954 45 1.186162 46 1.182981 47 1.184288 48 1.183326 49 1.183448 50 1.181159 51 1.174212 52 1.162318 53 1.160157 54 1.162988 55 1.154257 56 1.140063 57 1.131608 58 1.123518 59 1.119791 60 1.111456 61 1.115003 62 1.111981 63 1.1076 64 1.102789 65 1.104697 66 1.106643 67 1.103257 68 1.097885 69 1.09002 70 1.07562 71 1.064568 72 1.062841 73 1.056823 74 1.052996 75 1.044471 76 1.035824 77 1.02408 78 1.017414 79 1.009202 80 0.990992 81 0.974616 82 0.963496 83 0.94943 84 0.932214 85 0.919088 86 0.901359 87 0.890662 88 0.877837 89 0.857952 90 0.832857 91 0.808535 92 0.787972 93 0.762626 94 0.729992 95 0.697321 96 0.667614 97 0.634577 98 0.600355 99 0.568392 100 0.533407