## 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-e08fa3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-e08fa3-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 20:47:08 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 74452321102 73595029625 4316 67262446746 4510590012 1619945354 202043197 0 0 0 6864544 241037261 1235522 0.027691 0.972309 0 0.913954 0.061289 0.022012 0.002745 0.975243 0.964013 0 0.508515 0.57789 0.742335 0.89424 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.267599 1 0.310294 2 0.362979 3 0.42899 4 0.495094 5 0.559254 6 0.622878 7 0.682079 8 0.738409 9 0.792397 10 0.840173 11 0.883537 12 0.926884 13 0.9686 14 1.004796 15 1.030656 16 1.054667 17 1.0795 18 1.099755 19 1.115737 20 1.132374 21 1.147972 22 1.154046 23 1.164773 24 1.171796 25 1.175068 26 1.17954 27 1.180693 28 1.185652 29 1.187114 30 1.18397 31 1.182144 32 1.179555 33 1.178558 34 1.174706 35 1.179425 36 1.182559 37 1.178999 38 1.180976 39 1.18113 40 1.174241 41 1.176082 42 1.179499 43 1.179266 44 1.172905 45 1.180575 46 1.169872 47 1.165777 48 1.164061 49 1.160494 50 1.165391 51 1.156709 52 1.153691 53 1.161031 54 1.167835 55 1.170016 56 1.166538 57 1.163256 58 1.157051 59 1.143674 60 1.133538 61 1.128867 62 1.126889 63 1.124807 64 1.124012 65 1.117079 66 1.113279 67 1.106035 68 1.103603 69 1.096315 70 1.087038 71 1.073961 72 1.067717 73 1.064579 74 1.058134 75 1.048532 76 1.041234 77 1.031605 78 1.029271 79 1.021417 80 1.001171 81 0.987395 82 0.971999 83 0.953583 84 0.941252 85 0.922316 86 0.900478 87 0.884635 88 0.861134 89 0.84084 90 0.815589 91 0.792788 92 0.768942 93 0.740983 94 0.710738 95 0.679825 96 0.649439 97 0.617491 98 0.58311 99 0.548573 100 0.511725