## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT NCI-H2228_FFPE_RNA_0001_B23LG7FLT4_3_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: Thu May 28 22:48:56 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 73313962819 72484022515 43706 64374786940 4696329490 2997690758 415171621 0 0 0 3188145 235884320 1423524 0.013335 0.986665 0.000001 0.888124 0.064791 0.041357 0.005728 0.952915 0.942128 0 0.537139 0.554605 0.76717 0.857342 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.261638 1 0.301166 2 0.353124 3 0.412815 4 0.474807 5 0.540675 6 0.607173 7 0.667497 8 0.725217 9 0.776869 10 0.827732 11 0.880753 12 0.92987 13 0.967166 14 0.994405 15 1.022197 16 1.055691 17 1.078748 18 1.087855 19 1.10766 20 1.122499 21 1.13339 22 1.142496 23 1.154933 24 1.157164 25 1.154909 26 1.161497 27 1.171606 28 1.18405 29 1.181742 30 1.174367 31 1.167749 32 1.169506 33 1.168378 34 1.163783 35 1.155917 36 1.154366 37 1.146368 38 1.141532 39 1.142677 40 1.148227 41 1.152581 42 1.159789 43 1.164407 44 1.163619 45 1.169711 46 1.164506 47 1.159082 48 1.154331 49 1.165807 50 1.173694 51 1.174615 52 1.168744 53 1.161235 54 1.162948 55 1.149828 56 1.146207 57 1.142857 58 1.13984 59 1.135737 60 1.13008 61 1.137785 62 1.145126 63 1.138896 64 1.128953 65 1.124984 66 1.117353 67 1.109633 68 1.096622 69 1.087291 70 1.072026 71 1.065948 72 1.06091 73 1.050626 74 1.049037 75 1.047411 76 1.042748 77 1.034455 78 1.032265 79 1.028471 80 1.016537 81 1.002346 82 0.993667 83 0.979261 84 0.963079 85 0.951946 86 0.935401 87 0.922731 88 0.905593 89 0.887358 90 0.864436 91 0.839285 92 0.81197 93 0.782747 94 0.7497 95 0.71531 96 0.683237 97 0.651602 98 0.615187 99 0.577101 100 0.53384