## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_7.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_7_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: Mon Mar 09 17:59:59 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 24695884199 24393010033 11314 21054770497 2034807522 1149467078 153953622 0 0 0 5804536 73486677 300001 0.073205 0.926795 0 0.863148 0.083418 0.047123 0.006311 0.946565 0.934957 0 0.532459 0.589957 0.739273 0.870839 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.279185 1 0.3156 2 0.372225 3 0.435409 4 0.503657 5 0.571759 6 0.638792 7 0.702732 8 0.757126 9 0.807366 10 0.853814 11 0.901523 12 0.949843 13 0.988563 14 1.017534 15 1.041633 16 1.0667 17 1.084529 18 1.098653 19 1.11621 20 1.131173 21 1.149067 22 1.1618 23 1.177089 24 1.185288 25 1.190139 26 1.197158 27 1.202319 28 1.205719 29 1.206024 30 1.201169 31 1.198975 32 1.189088 33 1.184876 34 1.177755 35 1.173348 36 1.170183 37 1.159539 38 1.147113 39 1.142508 40 1.130488 41 1.124809 42 1.130367 43 1.131253 44 1.125467 45 1.132889 46 1.130411 47 1.125623 48 1.124048 49 1.129024 50 1.133209 51 1.129678 52 1.12907 53 1.129316 54 1.13124 55 1.134843 56 1.135804 57 1.135185 58 1.133928 59 1.129423 60 1.13082 61 1.135119 62 1.1329 63 1.128069 64 1.126426 65 1.12633 66 1.122756 67 1.117317 68 1.109895 69 1.102756 70 1.091636 71 1.082845 72 1.08045 73 1.069709 74 1.061858 75 1.056176 76 1.043903 77 1.02282 78 1.015472 79 1.00682 80 0.991431 81 0.973901 82 0.968268 83 0.954036 84 0.943212 85 0.938043 86 0.923854 87 0.905951 88 0.885526 89 0.865851 90 0.845563 91 0.822693 92 0.801145 93 0.774061 94 0.74378 95 0.711823 96 0.675356 97 0.638303 98 0.601688 99 0.561001 100 0.516548