## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s33.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s33_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 Mar 04 23:06:17 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 26032826565 25735962334 38147 21031342665 2346111365 2091479058 266991099 0 0 0 1473853 73820134 370099 0.019575 0.980425 0.000001 0.817197 0.091161 0.081267 0.010374 0.908357 0.897999 0 0.490303 0.592072 0.759194 0.843587 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.267954 1 0.312028 2 0.37351 3 0.444359 4 0.515422 5 0.584245 6 0.649467 7 0.714893 8 0.770744 9 0.822444 10 0.866991 11 0.917205 12 0.963853 13 1.003465 14 1.031936 15 1.060442 16 1.078427 17 1.092642 18 1.110197 19 1.129332 20 1.141411 21 1.157776 22 1.166453 23 1.172417 24 1.180533 25 1.186469 26 1.189937 27 1.193772 28 1.190079 29 1.185435 30 1.180509 31 1.178519 32 1.172883 33 1.169367 34 1.166116 35 1.16534 36 1.163654 37 1.154999 38 1.149319 39 1.150236 40 1.148577 41 1.146481 42 1.14988 43 1.150899 44 1.150825 45 1.157857 46 1.157428 47 1.154774 48 1.153626 49 1.157521 50 1.164957 51 1.166284 52 1.163018 53 1.161119 54 1.161145 55 1.159858 56 1.151787 57 1.147152 58 1.139955 59 1.130511 60 1.127427 61 1.131225 62 1.126993 63 1.118583 64 1.114315 65 1.112331 66 1.109085 67 1.101562 68 1.092717 69 1.084523 70 1.072796 71 1.064356 72 1.061115 73 1.053517 74 1.046148 75 1.039142 76 1.024474 77 1.006548 78 1.004251 79 0.999268 80 0.982207 81 0.961625 82 0.950041 83 0.932347 84 0.919514 85 0.913011 86 0.899439 87 0.881776 88 0.861805 89 0.842554 90 0.827042 91 0.808289 92 0.786608 93 0.760026 94 0.729306 95 0.697795 96 0.667873 97 0.638056 98 0.606896 99 0.574625 100 0.533652