## 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-01eb49-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-01eb49-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 20:33:04 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 77186172197 76217441612 2758 68951715091 5385062636 1645061482 235599645 0 0 0 8152717 236919951 1478916 0.033267 0.966733 0 0.904671 0.070654 0.021584 0.003091 0.975325 0.963084 0 0.523139 0.635645 0.672479 1.041947 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.277763 1 0.332303 2 0.410995 3 0.487122 4 0.564133 5 0.638294 6 0.708801 7 0.774212 8 0.842992 9 0.902595 10 0.951185 11 0.997841 12 1.043671 13 1.082781 14 1.112358 15 1.128876 16 1.1454 17 1.161467 18 1.169227 19 1.18086 20 1.201465 21 1.221603 22 1.233546 23 1.240659 24 1.242526 25 1.239942 26 1.238458 27 1.234043 28 1.231169 29 1.226455 30 1.223898 31 1.219906 32 1.20932 33 1.207684 34 1.199655 35 1.197521 36 1.198224 37 1.195055 38 1.195028 39 1.190101 40 1.18479 41 1.176917 42 1.179606 43 1.18672 44 1.182694 45 1.18876 46 1.187047 47 1.188743 48 1.186413 49 1.183248 50 1.180383 51 1.171391 52 1.157921 53 1.149689 54 1.148926 55 1.144443 56 1.137052 57 1.130926 58 1.120656 59 1.112368 60 1.108657 61 1.103762 62 1.102719 63 1.09094 64 1.082936 65 1.080204 66 1.066815 67 1.049051 68 1.042297 69 1.033982 70 1.024169 71 1.009464 72 1.001972 73 0.990884 74 0.978561 75 0.968629 76 0.956008 77 0.946035 78 0.941631 79 0.932524 80 0.911944 81 0.895222 82 0.884677 83 0.871554 84 0.856822 85 0.844978 86 0.828167 87 0.811792 88 0.790983 89 0.771297 90 0.749225 91 0.732471 92 0.711681 93 0.68651 94 0.658295 95 0.631658 96 0.605447 97 0.580614 98 0.551033 99 0.521081 100 0.489825