## 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-bbc28d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-bbc28d-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 21:12:41 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 44925567191 44273932656 10216 38797730059 3897651982 1330891022 247649377 0 0 0 3879978 163329020 651757 0.023204 0.976796 0 0.876311 0.088035 0.03006 0.005594 0.964346 0.950358 0 0.58164 0.493559 0.74947 0.769421 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.242796 1 0.2799 2 0.330387 3 0.389282 4 0.452137 5 0.514285 6 0.576758 7 0.632761 8 0.689544 9 0.741277 10 0.785519 11 0.833261 12 0.887893 13 0.940239 14 0.976299 15 1.008755 16 1.031426 17 1.054011 18 1.068438 19 1.079357 20 1.088692 21 1.103005 22 1.116793 23 1.129257 24 1.131945 25 1.140189 26 1.137632 27 1.140113 28 1.147755 29 1.14511 30 1.143029 31 1.142764 32 1.138019 33 1.140225 34 1.128544 35 1.134719 36 1.138975 37 1.140536 38 1.146451 39 1.144894 40 1.139484 41 1.142605 42 1.151576 43 1.153675 44 1.157633 45 1.166714 46 1.169591 47 1.172767 48 1.16869 49 1.168723 50 1.172836 51 1.173786 52 1.163658 53 1.167007 54 1.173532 55 1.175522 56 1.171607 57 1.16382 58 1.152376 59 1.147507 60 1.139644 61 1.141064 62 1.14908 63 1.13852 64 1.144332 65 1.149159 66 1.141769 67 1.13347 68 1.132547 69 1.127489 70 1.11692 71 1.107744 72 1.109351 73 1.104949 74 1.09754 75 1.088877 76 1.081414 77 1.077993 78 1.0705 79 1.059247 80 1.049466 81 1.038728 82 1.026162 83 1.013157 84 0.99292 85 0.971749 86 0.952374 87 0.940342 88 0.921401 89 0.90958 90 0.886863 91 0.862101 92 0.833571 93 0.800849 94 0.764838 95 0.723899 96 0.682448 97 0.643686 98 0.600733 99 0.556561 100 0.516047