## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT RT4_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT RT4_FFPE_RNA_0001_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: Thu May 28 21:19:52 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 75795256144 74879729245 56699 64577735998 5558236053 4149912505 593787990 0 0 0 9775434 226481211 1423595 0.041376 0.958624 0.000001 0.862419 0.074229 0.055421 0.00793 0.936648 0.925335 0 0.506028 0.544408 0.785115 0.774817 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.294203 1 0.332174 2 0.38186 3 0.440013 4 0.501126 5 0.562504 6 0.623188 7 0.675142 8 0.72974 9 0.78013 10 0.829646 11 0.876374 12 0.917464 13 0.951205 14 0.977007 15 0.999281 16 1.020258 17 1.041651 18 1.058352 19 1.072167 20 1.092926 21 1.112018 22 1.134675 23 1.153029 24 1.165694 25 1.168669 26 1.168676 27 1.174991 28 1.177751 29 1.174625 30 1.171646 31 1.170662 32 1.166112 33 1.167302 34 1.162932 35 1.159868 36 1.156057 37 1.155809 38 1.15731 39 1.160858 40 1.159965 41 1.154504 42 1.14734 43 1.149632 44 1.152067 45 1.152881 46 1.141412 47 1.136627 48 1.136131 49 1.146112 50 1.153368 51 1.151985 52 1.154734 53 1.158669 54 1.158989 55 1.154483 56 1.147099 57 1.144543 58 1.144398 59 1.14434 60 1.138778 61 1.138948 62 1.141036 63 1.136628 64 1.130234 65 1.123104 66 1.123896 67 1.114991 68 1.107083 69 1.096543 70 1.084855 71 1.075322 72 1.067104 73 1.057737 74 1.053221 75 1.050259 76 1.035198 77 1.023905 78 1.018643 79 1.011191 80 0.998557 81 0.985 82 0.978228 83 0.963718 84 0.950936 85 0.944239 86 0.934954 87 0.925552 88 0.907062 89 0.890283 90 0.868251 91 0.847503 92 0.828295 93 0.805512 94 0.775273 95 0.744195 96 0.711852 97 0.676932 98 0.643997 99 0.610209 100 0.564737