## 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-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-9e2647-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 20:47:04 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 77203371934 76489850798 6000 68778750975 5253295140 2211738744 246059939 0 0 0 3752372 244130537 1203352 0.015138 0.984862 0 0.899188 0.06868 0.028915 0.003217 0.967868 0.958922 0 0.504177 0.576265 0.760598 0.872638 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.287891 1 0.322653 2 0.377168 3 0.443696 4 0.510766 5 0.575914 6 0.632305 7 0.680084 8 0.737518 9 0.780334 10 0.830929 11 0.884223 12 0.936992 13 0.978947 14 1.009081 15 1.037733 16 1.061996 17 1.088119 18 1.097769 19 1.115096 20 1.124497 21 1.136589 22 1.150145 23 1.160134 24 1.161128 25 1.166841 26 1.171789 27 1.171141 28 1.16678 29 1.167766 30 1.164749 31 1.163389 32 1.156556 33 1.157755 34 1.152735 35 1.152178 36 1.154918 37 1.156819 38 1.159548 39 1.158836 40 1.156891 41 1.157881 42 1.158885 43 1.161723 44 1.162285 45 1.162248 46 1.15621 47 1.163873 48 1.16323 49 1.162231 50 1.160921 51 1.157131 52 1.15523 53 1.15386 54 1.15926 55 1.161002 56 1.156983 57 1.153153 58 1.154437 59 1.149941 60 1.147041 61 1.14612 62 1.147391 63 1.138301 64 1.133007 65 1.128979 66 1.115794 67 1.108857 68 1.102827 69 1.095691 70 1.084353 71 1.076816 72 1.071367 73 1.066287 74 1.056357 75 1.050486 76 1.039907 77 1.025578 78 1.009075 79 1.001289 80 0.988065 81 0.976791 82 0.966824 83 0.954695 84 0.941 85 0.922629 86 0.904347 87 0.888826 88 0.871191 89 0.855057 90 0.838341 91 0.820734 92 0.795561 93 0.769916 94 0.743695 95 0.715315 96 0.684845 97 0.650373 98 0.613418 99 0.579096 100 0.536906