## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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 13:03:09 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 2753045385 2726986315 2363782 2400056821 197304400 95147272 32114040 0 0 0 81857 8016197 43628 0.010108 0.989892 0.000867 0.880113 0.072353 0.034891 0.011776 0.952466 0.94345 0 0.581228 0.568749 0.689316 0.702081 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.305117 1 0.3486 2 0.425254 3 0.509418 4 0.583762 5 0.657586 6 0.7227 7 0.77956 8 0.8315 9 0.873191 10 0.910129 11 0.943316 12 0.981913 13 1.019771 14 1.041487 15 1.065191 16 1.084804 17 1.100733 18 1.107508 19 1.126124 20 1.144831 21 1.157485 22 1.165038 23 1.171752 24 1.182159 25 1.188534 26 1.1936 27 1.190999 28 1.18753 29 1.178973 30 1.159768 31 1.151127 32 1.140343 33 1.14628 34 1.148843 35 1.150857 36 1.150068 37 1.138666 38 1.12906 39 1.123164 40 1.116789 41 1.116372 42 1.121102 43 1.121147 44 1.124293 45 1.126468 46 1.127464 47 1.127205 48 1.121889 49 1.12373 50 1.131492 51 1.129519 52 1.127463 53 1.122715 54 1.125738 55 1.119596 56 1.120203 57 1.120997 58 1.116352 59 1.114047 60 1.111116 61 1.11498 62 1.110051 63 1.104107 64 1.095655 65 1.092734 66 1.093156 67 1.086263 68 1.079283 69 1.077461 70 1.072148 71 1.067889 72 1.060795 73 1.059012 74 1.049544 75 1.041122 76 1.038193 77 1.028362 78 1.0224 79 1.018519 80 1.000316 81 0.983386 82 0.969363 83 0.958842 84 0.94282 85 0.928191 86 0.901964 87 0.890334 88 0.888513 89 0.867842 90 0.8493 91 0.81884 92 0.796875 93 0.772358 94 0.742109 95 0.708753 96 0.669549 97 0.637767 98 0.588826 99 0.546923 100 0.507449