## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_b7Z-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_b7Z-T1-TRNA-1_B23MHV2LT4_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: Sat May 23 00:23:00 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 79635603766 78716295065 4451 70210706229 6744632569 1509617982 251333834 0 0 0 6189148 238598895 1375644 0.025284 0.974716 0 0.891946 0.085683 0.019178 0.003193 0.977629 0.966343 0 0.500773 0.576196 0.733903 0.858646 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.246964 1 0.286537 2 0.344556 3 0.416885 4 0.486409 5 0.550062 6 0.610912 7 0.66139 8 0.715007 9 0.767675 10 0.817473 11 0.856997 12 0.887124 13 0.927762 14 0.964819 15 0.990824 16 1.014313 17 1.040945 18 1.06131 19 1.076896 20 1.097366 21 1.121405 22 1.136501 23 1.14821 24 1.158303 25 1.160185 26 1.164277 27 1.161702 28 1.163295 29 1.164537 30 1.168195 31 1.167791 32 1.162755 33 1.164153 34 1.160492 35 1.166973 36 1.169066 37 1.167002 38 1.169038 39 1.169018 40 1.168169 41 1.168852 42 1.172414 43 1.17956 44 1.176501 45 1.187772 46 1.191051 47 1.191817 48 1.186929 49 1.184504 50 1.175965 51 1.170377 52 1.168017 53 1.171831 54 1.181773 55 1.181486 56 1.177228 57 1.177033 58 1.176049 59 1.165859 60 1.154922 61 1.155657 62 1.154089 63 1.14508 64 1.146088 65 1.145459 66 1.138486 67 1.132121 68 1.125995 69 1.113592 70 1.104062 71 1.096089 72 1.092862 73 1.089312 74 1.081492 75 1.074784 76 1.06255 77 1.048714 78 1.041098 79 1.028927 80 1.00792 81 0.993946 82 0.981619 83 0.969721 84 0.955545 85 0.938572 86 0.912301 87 0.895897 88 0.877514 89 0.857068 90 0.833672 91 0.801511 92 0.775371 93 0.744978 94 0.714685 95 0.684231 96 0.652754 97 0.62982 98 0.592714 99 0.559112 100 0.520699