## 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-3270ab-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3270ab-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 20:35:05 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 74568735243 73765276588 9356 66879650931 4906411700 1773345759 205858842 0 0 0 3628033 244603804 1252052 0.014616 0.985384 0 0.906655 0.066514 0.02404 0.002791 0.973169 0.962683 0 0.517755 0.549547 0.715379 0.894078 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.29565 1 0.334291 2 0.388812 3 0.457665 4 0.518309 5 0.570905 6 0.631115 7 0.686833 8 0.747617 9 0.798671 10 0.840956 11 0.88168 12 0.931657 13 0.976668 14 1.010147 15 1.037723 16 1.064378 17 1.089663 18 1.104973 19 1.125885 20 1.143803 21 1.160256 22 1.1784 23 1.192337 24 1.200707 25 1.205003 26 1.207105 27 1.201783 28 1.200656 29 1.199846 30 1.202139 31 1.200468 32 1.191029 33 1.196337 34 1.187066 35 1.188473 36 1.187703 37 1.183235 38 1.184373 39 1.179976 40 1.170603 41 1.173873 42 1.179111 43 1.187875 44 1.182911 45 1.191221 46 1.183805 47 1.180717 48 1.173482 49 1.172012 50 1.175728 51 1.161551 52 1.150611 53 1.151061 54 1.152798 55 1.152646 56 1.146292 57 1.141906 58 1.134471 59 1.122427 60 1.113252 61 1.111867 62 1.112784 63 1.104067 64 1.108348 65 1.104944 66 1.097958 67 1.085788 68 1.083504 69 1.077205 70 1.06415 71 1.051811 72 1.048222 73 1.041196 74 1.032146 75 1.024706 76 1.021624 77 1.012378 78 1.006136 79 0.997347 80 0.984227 81 0.968303 82 0.956889 83 0.94607 84 0.929867 85 0.910622 86 0.889491 87 0.878147 88 0.86063 89 0.842146 90 0.81586 91 0.797144 92 0.770001 93 0.742642 94 0.716176 95 0.684089 96 0.650567 97 0.616852 98 0.580057 99 0.546657 100 0.511735