## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT EndoN_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT EndoN_FFPE_L02_RNA_01_B23LG7FLT4_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: Sat May 16 08:39:07 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 2611502049 2514553801 153662 1710038364 201378349 531663273 71320153 0 0 0 602150 7933369 58714 0.070546 0.929454 0.000061 0.680056 0.080085 0.211434 0.028363 0.760142 0.731922 0 0.855217 0.330799 0.502427 0.538701 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.345624 1 0.393507 2 0.44907 3 0.508174 4 0.560232 5 0.614928 6 0.660606 7 0.69751 8 0.732585 9 0.783253 10 0.811671 11 0.841877 12 0.882539 13 0.931359 14 0.968165 15 0.982736 16 1.000595 17 0.999378 18 0.994285 19 1.007235 20 1.02865 21 1.038496 22 1.035513 23 1.045381 24 1.055634 25 1.057015 26 1.054673 27 1.060716 28 1.068506 29 1.058952 30 1.05595 31 1.066414 32 1.078862 33 1.08797 34 1.08088 35 1.08521 36 1.095871 37 1.103684 38 1.111059 39 1.110044 40 1.138617 41 1.167531 42 1.170749 43 1.183958 44 1.202599 45 1.206147 46 1.198133 47 1.185105 48 1.171132 49 1.164178 50 1.153259 51 1.147324 52 1.144438 53 1.138849 54 1.134366 55 1.13557 56 1.143093 57 1.148647 58 1.142754 59 1.136258 60 1.153185 61 1.153508 62 1.148678 63 1.145252 64 1.154943 65 1.164215 66 1.160634 67 1.138521 68 1.126028 69 1.134558 70 1.122611 71 1.109274 72 1.104066 73 1.092053 74 1.096002 75 1.10152 76 1.110881 77 1.114225 78 1.108414 79 1.093449 80 1.084838 81 1.064909 82 1.051386 83 1.034711 84 1.018461 85 1.000422 86 0.995326 87 0.979569 88 0.962395 89 0.94472 90 0.918595 91 0.893317 92 0.866019 93 0.832119 94 0.798766 95 0.752725 96 0.701134 97 0.648543 98 0.60144 99 0.54271 100 0.48844