## 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-9b89b4-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-9b89b4-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 20:42:02 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 72685728775 71907131528 3852 65672331781 4440348459 1533557321 260890115 0 0 0 10362829 240229515 1059271 0.041353 0.958647 0 0.913294 0.061751 0.021327 0.003628 0.975045 0.9646 0 0.549983 0.49032 0.727763 0.803507 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.304122 1 0.33665 2 0.387776 3 0.445431 4 0.4969 5 0.544748 6 0.597102 7 0.647687 8 0.697908 9 0.745918 10 0.788676 11 0.837021 12 0.888475 13 0.937502 14 0.974284 15 1.0022 16 1.030302 17 1.052179 18 1.066833 19 1.075176 20 1.08538 21 1.096592 22 1.113992 23 1.127655 24 1.139903 25 1.147974 26 1.157444 27 1.161546 28 1.167812 29 1.174596 30 1.182189 31 1.185486 32 1.180201 33 1.178212 34 1.170637 35 1.179264 36 1.18704 37 1.184778 38 1.187302 39 1.185826 40 1.182569 41 1.179167 42 1.179924 43 1.189452 44 1.191441 45 1.202453 46 1.205739 47 1.210676 48 1.20829 49 1.211024 50 1.198752 51 1.192377 52 1.188772 53 1.188387 54 1.187546 55 1.173018 56 1.162342 57 1.151053 58 1.145672 59 1.140723 60 1.134618 61 1.133188 62 1.133557 63 1.128108 64 1.127953 65 1.127923 66 1.121063 67 1.116786 68 1.112596 69 1.107328 70 1.101322 71 1.092864 72 1.085445 73 1.076118 74 1.065903 75 1.057448 76 1.04848 77 1.035037 78 1.022015 79 1.009759 80 0.994632 81 0.980216 82 0.967754 83 0.952789 84 0.939208 85 0.927848 86 0.909552 87 0.896146 88 0.880104 89 0.861137 90 0.839008 91 0.812802 92 0.782318 93 0.753644 94 0.725551 95 0.698248 96 0.665246 97 0.63172 98 0.596099 99 0.559435 100 0.520967