## 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-b6fd19-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-b6fd19-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 20:40:02 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 77442799878 76636229839 1774 68667659258 5534079786 2133718980 300770041 0 0 0 6447544 240221795 1260640 0.026138 0.973862 0 0.896021 0.072212 0.027842 0.003925 0.968233 0.958149 0 0.511604 0.587501 0.725626 0.935106 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.294369 1 0.335827 2 0.394614 3 0.456746 4 0.5225 5 0.590274 6 0.65166 7 0.710719 8 0.767562 9 0.810037 10 0.85968 11 0.909225 12 0.96064 13 1.009384 14 1.038744 15 1.063685 16 1.089855 17 1.110559 18 1.123536 19 1.14206 20 1.151314 21 1.168 22 1.183455 23 1.19845 24 1.207491 25 1.212288 26 1.217065 27 1.21999 28 1.218258 29 1.208615 30 1.206885 31 1.207774 32 1.191501 33 1.187203 34 1.183853 35 1.179361 36 1.173514 37 1.167327 38 1.163758 39 1.159995 40 1.15427 41 1.155215 42 1.158228 43 1.159553 44 1.153536 45 1.163243 46 1.160565 47 1.157671 48 1.151294 49 1.151361 50 1.154155 51 1.14669 52 1.139749 53 1.13546 54 1.140286 55 1.136492 56 1.132687 57 1.121833 58 1.115648 59 1.110569 60 1.106204 61 1.104827 62 1.10756 63 1.093834 64 1.089395 65 1.091065 66 1.095792 67 1.095739 68 1.096463 69 1.085003 70 1.076072 71 1.061512 72 1.057992 73 1.047238 74 1.030426 75 1.020975 76 1.012448 77 1.000631 78 0.991908 79 0.975784 80 0.962202 81 0.951602 82 0.941917 83 0.929946 84 0.916569 85 0.906285 86 0.887773 87 0.878783 88 0.863314 89 0.845556 90 0.825918 91 0.808055 92 0.786002 93 0.757359 94 0.726933 95 0.697385 96 0.669091 97 0.635768 98 0.602272 99 0.567501 100 0.52661