## 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-cece97-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-cece97-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 20:22:13 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 71510249176 70598893153 5104 63586440081 4599161822 2161393386 251892760 0 0 0 7321124 239737935 1028215 0.029633 0.970367 0 0.900672 0.065145 0.030615 0.003568 0.965817 0.953508 0 0.563922 0.544783 0.709819 0.843147 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.307532 1 0.345505 2 0.399619 3 0.461445 4 0.523389 5 0.582255 6 0.638562 7 0.692152 8 0.744445 9 0.787115 10 0.829822 11 0.872895 12 0.913943 13 0.953839 14 0.995884 15 1.02209 16 1.047027 17 1.064261 18 1.072555 19 1.088143 20 1.10051 21 1.109444 22 1.123687 23 1.133156 24 1.145633 25 1.151417 26 1.154094 27 1.156391 28 1.168186 29 1.167038 30 1.161931 31 1.160862 32 1.156749 33 1.158498 34 1.150889 35 1.155448 36 1.156001 37 1.151431 38 1.159209 39 1.157835 40 1.154358 41 1.160627 42 1.164758 43 1.164437 44 1.158251 45 1.164641 46 1.152824 47 1.146445 48 1.140807 49 1.14076 50 1.139506 51 1.130934 52 1.121135 53 1.124186 54 1.129653 55 1.137022 56 1.140317 57 1.14482 58 1.143601 59 1.141475 60 1.140673 61 1.139438 62 1.133756 63 1.119375 64 1.123755 65 1.119572 66 1.116595 67 1.104534 68 1.106852 69 1.10324 70 1.093271 71 1.079802 72 1.073501 73 1.066118 74 1.061776 75 1.057398 76 1.058327 77 1.052701 78 1.045554 79 1.03436 80 1.020874 81 1.011256 82 0.999819 83 0.985209 84 0.976278 85 0.965356 86 0.949809 87 0.938452 88 0.917424 89 0.896432 90 0.862211 91 0.843488 92 0.81263 93 0.774336 94 0.74047 95 0.711676 96 0.680492 97 0.643086 98 0.60393 99 0.564775 100 0.523625