## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00121_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00121_B23WHTKLT4_2_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 21 05:43:04 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 77526248970 76707832116 3454 69240864606 5091134189 2148360858 227469009 0 0 0 6110430 242926248 1084712 0.024536 0.975464 0 0.902657 0.06637 0.028007 0.002965 0.969028 0.958798 0 0.501041 0.518258 0.753563 0.778687 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.319506 1 0.351654 2 0.402163 3 0.458743 4 0.503026 5 0.544951 6 0.602317 7 0.654067 8 0.702629 9 0.750695 10 0.798477 11 0.845264 12 0.887921 13 0.926761 14 0.959841 15 0.988329 16 1.013669 17 1.03263 18 1.050527 19 1.06896 20 1.084422 21 1.097238 22 1.114795 23 1.129354 24 1.139277 25 1.143524 26 1.147963 27 1.152747 28 1.158989 29 1.160548 30 1.16582 31 1.170925 32 1.171543 33 1.179249 34 1.180277 35 1.187234 36 1.188899 37 1.187101 38 1.191089 39 1.186996 40 1.183879 41 1.177761 42 1.178302 43 1.185146 44 1.181533 45 1.185832 46 1.184394 47 1.17976 48 1.173671 49 1.171504 50 1.159193 51 1.154311 52 1.1479 53 1.151315 54 1.149299 55 1.145583 56 1.145497 57 1.143657 58 1.137398 59 1.134757 60 1.128652 61 1.127657 62 1.127684 63 1.123718 64 1.118278 65 1.116513 66 1.114053 67 1.113672 68 1.115076 69 1.108055 70 1.098346 71 1.09114 72 1.084017 73 1.075862 74 1.074817 75 1.070505 76 1.061941 77 1.049704 78 1.043634 79 1.032142 80 1.01586 81 1.003792 82 0.994647 83 0.979048 84 0.965487 85 0.948823 86 0.924555 87 0.910533 88 0.891617 89 0.873588 90 0.852826 91 0.828803 92 0.804691 93 0.777225 94 0.750107 95 0.7223 96 0.689905 97 0.654217 98 0.618907 99 0.585196 100 0.551154