## 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_36.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_36_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 17:59:49 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 24735921151 24451689221 18496 21170705727 1990983031 1149991828 139990139 0 0 0 1522530 77811898 329925 0.019191 0.980809 0.000001 0.865818 0.081425 0.047031 0.005725 0.947243 0.936358 0 0.524298 0.559321 0.778102 0.802332 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.279233 1 0.31588 2 0.369274 3 0.429168 4 0.493587 5 0.558073 6 0.619452 7 0.677901 8 0.729479 9 0.779298 10 0.822619 11 0.873762 12 0.927107 13 0.964545 14 0.994785 15 1.020312 16 1.037176 17 1.053352 18 1.068761 19 1.087103 20 1.09983 21 1.119063 22 1.135391 23 1.146092 24 1.153124 25 1.156149 26 1.164163 27 1.172287 28 1.179195 29 1.177869 30 1.175309 31 1.175517 32 1.165956 33 1.164792 34 1.161953 35 1.163253 36 1.162338 37 1.153841 38 1.143182 39 1.138033 40 1.130943 41 1.12677 42 1.128726 43 1.130042 44 1.127438 45 1.136701 46 1.137249 47 1.135532 48 1.135772 49 1.142075 50 1.148372 51 1.147482 52 1.145738 53 1.146872 54 1.149201 55 1.152501 56 1.154645 57 1.155733 58 1.153823 59 1.14886 60 1.147668 61 1.151518 62 1.151342 63 1.146243 64 1.144354 65 1.146254 66 1.14231 67 1.134315 68 1.126095 69 1.117674 70 1.105721 71 1.098749 72 1.095044 73 1.08472 74 1.077519 75 1.070034 76 1.058157 77 1.040404 78 1.034341 79 1.023664 80 1.006424 81 0.989135 82 0.983373 83 0.968101 84 0.955684 85 0.950356 86 0.938659 87 0.921635 88 0.90137 89 0.883146 90 0.863442 91 0.841071 92 0.81871 93 0.789592 94 0.756536 95 0.72241 96 0.68594 97 0.648243 98 0.610866 99 0.570752 100 0.52706