## 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-2e5fe9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2e5fe9-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 20:45:00 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 77385739606 76546169305 2218 68781351492 5629855427 1894645765 240314403 0 0 0 4808860 243540021 1441001 0.019363 0.980637 0 0.89856 0.073548 0.024752 0.003139 0.972109 0.961562 0 0.494207 0.611465 0.747605 0.934123 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.278901 1 0.323379 2 0.386652 3 0.460208 4 0.528783 5 0.594485 6 0.654106 7 0.714617 8 0.778182 9 0.827059 10 0.873964 11 0.919526 12 0.961902 13 0.998405 14 1.036825 15 1.061068 16 1.087749 17 1.110948 18 1.125583 19 1.146843 20 1.165186 21 1.185317 22 1.198422 23 1.207804 24 1.206078 25 1.199686 26 1.197978 27 1.195489 28 1.194987 29 1.193144 30 1.187423 31 1.184415 32 1.17635 33 1.174347 34 1.176194 35 1.17678 36 1.180235 37 1.178318 38 1.180008 39 1.177838 40 1.178818 41 1.178779 42 1.182149 43 1.179971 44 1.170835 45 1.177873 46 1.172524 47 1.168505 48 1.164466 49 1.167824 50 1.161979 51 1.155125 52 1.152539 53 1.148457 54 1.148384 55 1.146717 56 1.138481 57 1.133615 58 1.126307 59 1.111002 60 1.105099 61 1.102576 62 1.105482 63 1.104929 64 1.105896 65 1.108698 66 1.100445 67 1.087492 68 1.076773 69 1.06606 70 1.058102 71 1.050962 72 1.042142 73 1.032315 74 1.021917 75 1.012691 76 1.006157 77 0.992053 78 0.989208 79 0.982135 80 0.963209 81 0.949803 82 0.939692 83 0.926444 84 0.912598 85 0.900437 86 0.883222 87 0.868358 88 0.8485 89 0.829409 90 0.810407 91 0.791857 92 0.768977 93 0.742519 94 0.713797 95 0.686158 96 0.659505 97 0.636828 98 0.605549 99 0.575369 100 0.541623