## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT dna_s747.Aligned.sortedByCoord.out.bam --OUTPUT dna_s747_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: Sat May 16 09:54:35 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 86152477358 85075077602 19176394 31413073030 19117070031 30560181843 3965576304 0 0 0 90255466 88887700 6842545 0.503818 0.496182 0.000225 0.369239 0.224708 0.359214 0.046613 0.593948 0.58652 0 0.37248 0.858715 0.813744 1.00639 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.778332 1 0.834824 2 0.864761 3 0.875311 4 0.874304 5 0.875385 6 0.878064 7 0.879993 8 0.882929 9 0.888614 10 0.891879 11 0.895769 12 0.892611 13 0.899555 14 0.903511 15 0.909178 16 0.909415 17 0.91249 18 0.911906 19 0.9198 20 0.924201 21 0.922216 22 0.921844 23 0.927111 24 0.927441 25 0.934058 26 0.939543 27 0.939679 28 0.938867 29 0.945328 30 0.950373 31 0.954098 32 0.960474 33 0.963857 34 0.962255 35 0.961706 36 0.964817 37 0.967038 38 0.97083 39 0.979886 40 0.98722 41 0.995503 42 0.998248 43 1.002589 44 1.005336 45 1.007365 46 1.013889 47 1.020356 48 1.020578 49 1.019912 50 1.022425 51 1.026625 52 1.033666 53 1.031469 54 1.040537 55 1.04534 56 1.050647 57 1.059717 58 1.067958 59 1.073228 60 1.081185 61 1.08646 62 1.084217 63 1.088282 64 1.088831 65 1.087139 66 1.090476 67 1.093453 68 1.093406 69 1.090716 70 1.091707 71 1.096078 72 1.102692 73 1.112143 74 1.117606 75 1.118452 76 1.119912 77 1.11706 78 1.116256 79 1.117183 80 1.115794 81 1.110552 82 1.104949 83 1.105876 84 1.108708 85 1.105757 86 1.107008 87 1.099616 88 1.090776 89 1.082736 90 1.077523 91 1.068134 92 1.056718 93 1.043127 94 1.024012 95 0.998318 96 0.963489 97 0.925621 98 0.877512 99 0.812627 100 0.75019