## 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-a51633-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-a51633-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 20:42:03 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 78345950208 77403853988 10012 69395996574 5361078536 2337706263 309062603 0 0 0 5985996 241795869 1463463 0.024158 0.975842 0 0.896544 0.069261 0.030201 0.003993 0.965806 0.954192 0 0.530027 0.580393 0.720262 0.89567 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.29072 1 0.341006 2 0.406772 3 0.481962 4 0.558929 5 0.624004 6 0.683089 7 0.740555 8 0.792201 9 0.841368 10 0.884684 11 0.929279 12 0.969906 13 1.000537 14 1.020655 15 1.037602 16 1.057243 17 1.076859 18 1.087966 19 1.101444 20 1.114699 21 1.12803 22 1.136946 23 1.142168 24 1.146046 25 1.143898 26 1.145244 27 1.147681 28 1.148797 29 1.146632 30 1.147492 31 1.147527 32 1.146629 33 1.148936 34 1.149824 35 1.152888 36 1.146523 37 1.143907 38 1.154473 39 1.157591 40 1.15868 41 1.165938 42 1.175486 43 1.180063 44 1.181741 45 1.18614 46 1.184259 47 1.182537 48 1.174978 49 1.172219 50 1.166011 51 1.160191 52 1.154319 53 1.150739 54 1.154233 55 1.154122 56 1.145239 57 1.144049 58 1.141372 59 1.133774 60 1.131863 61 1.132511 62 1.136026 63 1.127342 64 1.130252 65 1.129672 66 1.120825 67 1.109708 68 1.100073 69 1.09216 70 1.082147 71 1.06624 72 1.059069 73 1.048905 74 1.039868 75 1.032702 76 1.021871 77 1.005165 78 0.994947 79 0.985546 80 0.972196 81 0.958178 82 0.938833 83 0.922749 84 0.911868 85 0.897149 86 0.881971 87 0.874285 88 0.859715 89 0.841422 90 0.824157 91 0.811358 92 0.791872 93 0.761875 94 0.736498 95 0.711171 96 0.68703 97 0.663801 98 0.633471 99 0.600329 100 0.56346