## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT Hs746T_FFPE_RNA_0001_23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT Hs746T_FFPE_RNA_0001_23LG7FLT4_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: Fri Feb 27 06:44:01 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 25298329320 24829103536 18188 21849064667 1723778151 1104433091 151809439 0 0 0 2985406 76350617 499720 0.03763 0.96237 0.000001 0.879978 0.069426 0.044481 0.006114 0.949404 0.931794 0 0.507385 0.594265 0.728854 0.958512 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.302387 1 0.34111 2 0.39052 3 0.450778 4 0.51625 5 0.58402 6 0.643744 7 0.705792 8 0.763172 9 0.814554 10 0.865404 11 0.918522 12 0.9664 13 1.006552 14 1.036497 15 1.067174 16 1.083941 17 1.104373 18 1.115806 19 1.13143 20 1.160954 21 1.18722 22 1.202401 23 1.209891 24 1.219984 25 1.221617 26 1.22453 27 1.224871 28 1.22167 29 1.213374 30 1.209958 31 1.209712 32 1.205434 33 1.203523 34 1.202141 35 1.200649 36 1.195108 37 1.192139 38 1.19368 39 1.189581 40 1.186839 41 1.18143 42 1.178933 43 1.178465 44 1.173686 45 1.171994 46 1.163129 47 1.154334 48 1.150573 49 1.151001 50 1.143491 51 1.139104 52 1.135017 53 1.132959 54 1.138068 55 1.137933 56 1.131511 57 1.128099 58 1.120405 59 1.111026 60 1.106934 61 1.101924 62 1.098801 63 1.093209 64 1.089071 65 1.087678 66 1.081481 67 1.070525 68 1.064115 69 1.05915 70 1.054424 71 1.04606 72 1.047451 73 1.037577 74 1.022678 75 1.019312 76 1.009408 77 0.995017 78 0.986522 79 0.97925 80 0.965363 81 0.949612 82 0.936318 83 0.919237 84 0.907325 85 0.897792 86 0.875545 87 0.858875 88 0.846027 89 0.826238 90 0.809177 91 0.787879 92 0.762364 93 0.740042 94 0.714115 95 0.690332 96 0.666293 97 0.639482 98 0.611373 99 0.582574 100 0.547487