## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s26.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s26_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: Tue May 19 19:38:49 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 77908703542 76949443698 193789 62467633405 7076377316 6506388837 898850351 0 0 0 5451737 217792677 1212683 0.02442 0.97558 0.000003 0.811801 0.091961 0.084554 0.011681 0.903762 0.892635 0 0.492934 0.596404 0.757139 0.863174 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.279986 1 0.320806 2 0.380707 3 0.449177 4 0.51892 5 0.586558 6 0.648189 7 0.710427 8 0.76458 9 0.818036 10 0.861045 11 0.906994 12 0.950514 13 0.991979 14 1.023176 15 1.050975 16 1.076662 17 1.093948 18 1.106106 19 1.120157 20 1.133505 21 1.150798 22 1.163117 23 1.173722 24 1.185411 25 1.192088 26 1.199114 27 1.202871 28 1.201387 29 1.197834 30 1.191994 31 1.189801 32 1.184276 33 1.181067 34 1.178542 35 1.178471 36 1.177148 37 1.170177 38 1.163329 39 1.163818 40 1.162292 41 1.159621 42 1.159434 43 1.16093 44 1.158542 45 1.158813 46 1.154401 47 1.151909 48 1.15122 49 1.152973 50 1.158351 51 1.157403 52 1.15447 53 1.154691 54 1.156472 55 1.154167 56 1.148279 57 1.143797 58 1.137674 59 1.128249 60 1.125969 61 1.130054 62 1.126431 63 1.118644 64 1.114585 65 1.113086 66 1.109302 67 1.102494 68 1.094041 69 1.084149 70 1.073638 71 1.064787 72 1.059068 73 1.048843 74 1.040362 75 1.033121 76 1.020184 77 1.001315 78 0.999164 79 0.993651 80 0.975527 81 0.955264 82 0.945456 83 0.928447 84 0.914586 85 0.907857 86 0.894088 87 0.876505 88 0.856942 89 0.838912 90 0.822911 91 0.803196 92 0.781127 93 0.755865 94 0.728974 95 0.70143 96 0.672472 97 0.639909 98 0.608513 99 0.574996 100 0.534056