## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-377071-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-377071-R1_A23YTGFLT4_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: Wed Jun 03 20:16:56 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 76965054414 76132579890 5596 67895701627 5660685880 2280430602 295756185 0 0 0 3763471 241372347 1267191 0.015353 0.984647 0 0.891809 0.074353 0.029953 0.003885 0.966162 0.955711 0 0.503144 0.542589 0.779448 0.794253 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.271173 1 0.304607 2 0.349067 3 0.408964 4 0.476623 5 0.541345 6 0.601493 7 0.659116 8 0.718597 9 0.771734 10 0.816121 11 0.861083 12 0.909176 13 0.952171 14 0.978932 15 1.001328 16 1.034153 17 1.055546 18 1.070134 19 1.083427 20 1.098245 21 1.113336 22 1.125999 23 1.13641 24 1.148395 25 1.15379 26 1.158148 27 1.16319 28 1.166351 29 1.168193 30 1.172382 31 1.168026 32 1.156724 33 1.159007 34 1.155353 35 1.15244 36 1.15262 37 1.153842 38 1.167238 39 1.168854 40 1.169954 41 1.171284 42 1.176484 43 1.185546 44 1.187171 45 1.201816 46 1.199721 47 1.200241 48 1.197387 49 1.19866 50 1.184874 51 1.182184 52 1.177699 53 1.177278 54 1.174215 55 1.163916 56 1.155528 57 1.150337 58 1.14274 59 1.134565 60 1.127398 61 1.128944 62 1.136747 63 1.136329 64 1.138219 65 1.133095 66 1.123306 67 1.111956 68 1.107725 69 1.10035 70 1.089899 71 1.08253 72 1.074544 73 1.066683 74 1.059683 75 1.055746 76 1.048135 77 1.039047 78 1.036322 79 1.026293 80 1.008447 81 0.994756 82 0.983101 83 0.970492 84 0.956954 85 0.941346 86 0.918311 87 0.901337 88 0.880662 89 0.864022 90 0.84542 91 0.830438 92 0.807789 93 0.779448 94 0.746197 95 0.712113 96 0.67922 97 0.64958 98 0.615207 99 0.580394 100 0.543486