## 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-150e73-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-150e73-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 20:35:00 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 72575460523 71642422858 9630 64456995367 5102803977 1843583736 239030148 0 0 0 5849081 240071332 1333089 0.023784 0.976216 0 0.899704 0.071226 0.025733 0.003336 0.97093 0.958448 0 0.564195 0.539492 0.665454 0.879973 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.262673 1 0.306731 2 0.372526 3 0.442219 4 0.512492 5 0.583201 6 0.640798 7 0.69666 8 0.755861 9 0.802081 10 0.851243 11 0.906811 12 0.961498 13 1.006286 14 1.02991 15 1.050071 16 1.077518 17 1.101623 18 1.119163 19 1.139822 20 1.16229 21 1.175872 22 1.178597 23 1.182203 24 1.190037 25 1.187217 26 1.182374 27 1.179324 28 1.176631 29 1.179306 30 1.183794 31 1.179313 32 1.166105 33 1.169626 34 1.166615 35 1.168348 36 1.167649 37 1.167362 38 1.172609 39 1.166939 40 1.163335 41 1.165403 42 1.173264 43 1.175172 44 1.171938 45 1.185631 46 1.182465 47 1.177555 48 1.172617 49 1.16888 50 1.166399 51 1.159839 52 1.146235 53 1.146181 54 1.149461 55 1.148913 56 1.141083 57 1.133303 58 1.127765 59 1.121113 60 1.120576 61 1.123014 62 1.132874 63 1.12048 64 1.11942 65 1.118495 66 1.109384 67 1.104839 68 1.100265 69 1.094833 70 1.081369 71 1.061663 72 1.058643 73 1.055593 74 1.048191 75 1.044398 76 1.036744 77 1.024696 78 1.013315 79 1.004232 80 0.989771 81 0.973195 82 0.952114 83 0.936858 84 0.918852 85 0.903147 86 0.88382 87 0.871505 88 0.860112 89 0.842919 90 0.823168 91 0.80883 92 0.782406 93 0.750742 94 0.715717 95 0.681228 96 0.651545 97 0.618577 98 0.574431 99 0.537416 100 0.499844