## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21_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 21:56:50 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 2795883347 2772797282 300 2470896529 201902141 86792356 13205956 0 0 0 128383 8100715 41447 0.015601 0.984399 0 0.891121 0.072815 0.031301 0.004763 0.963936 0.955976 0 0.563571 0.543049 0.68164 0.755191 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.309711 1 0.346553 2 0.40561 3 0.470656 4 0.537896 5 0.614158 6 0.684648 7 0.738329 8 0.789637 9 0.828806 10 0.866681 11 0.904154 12 0.940791 13 0.977607 14 1.009535 15 1.043883 16 1.072314 17 1.084224 18 1.091344 19 1.111463 20 1.129586 21 1.144436 22 1.153642 23 1.165019 24 1.179679 25 1.187506 26 1.195764 27 1.199859 28 1.200035 29 1.192135 30 1.179665 31 1.172731 32 1.161183 33 1.168447 34 1.168088 35 1.16902 36 1.172234 37 1.16216 38 1.154721 39 1.146874 40 1.134038 41 1.130972 42 1.139922 43 1.144444 44 1.143409 45 1.14165 46 1.140949 47 1.141277 48 1.137295 49 1.139882 50 1.150497 51 1.150395 52 1.14884 53 1.145621 54 1.147696 55 1.147571 56 1.152178 57 1.152211 58 1.146733 59 1.143444 60 1.141569 61 1.144566 62 1.138619 63 1.130625 64 1.120877 65 1.116734 66 1.115729 67 1.10746 68 1.100787 69 1.095879 70 1.090612 71 1.088397 72 1.088978 73 1.084292 74 1.077125 75 1.065958 76 1.055391 77 1.039038 78 1.029497 79 1.021956 80 0.998467 81 0.976544 82 0.960909 83 0.944819 84 0.922483 85 0.900228 86 0.870929 87 0.862738 88 0.860338 89 0.836321 90 0.815203 91 0.784223 92 0.759136 93 0.734634 94 0.705999 95 0.676786 96 0.6461 97 0.62318 98 0.581398 99 0.542495 100 0.501162