## 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-a9fe91-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-a9fe91-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 20:19:03 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 76830009100 76004877996 4134 68658851322 5199169662 1935669744 211183134 0 0 0 10448378 239456849 1182596 0.041809 0.958191 0 0.903348 0.068406 0.025468 0.002779 0.971754 0.961317 0 0.51732 0.598292 0.721876 0.908545 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.272358 1 0.319336 2 0.383486 3 0.463149 4 0.542679 5 0.612083 6 0.675881 7 0.736855 8 0.791053 9 0.841685 10 0.890024 11 0.932303 12 0.969628 13 1.014346 14 1.050085 15 1.068635 16 1.085131 17 1.104701 18 1.123264 19 1.13821 20 1.153954 21 1.16478 22 1.170368 23 1.180389 24 1.185514 25 1.183753 26 1.183879 27 1.181976 28 1.179298 29 1.174525 30 1.172432 31 1.175577 32 1.175548 33 1.179443 34 1.17815 35 1.177574 36 1.177326 37 1.177361 38 1.182539 39 1.181808 40 1.166249 41 1.162339 42 1.168945 43 1.174936 44 1.16955 45 1.173342 46 1.167099 47 1.165026 48 1.159625 49 1.153698 50 1.15189 51 1.142315 52 1.140242 53 1.145492 54 1.153165 55 1.155217 56 1.144635 57 1.138549 58 1.134746 59 1.122723 60 1.118841 61 1.11651 62 1.116827 63 1.110265 64 1.101918 65 1.099506 66 1.093848 67 1.084128 68 1.075506 69 1.068073 70 1.05892 71 1.049228 72 1.040305 73 1.030899 74 1.022286 75 1.014741 76 1.007509 77 0.996139 78 0.982978 79 0.972045 80 0.956105 81 0.946267 82 0.935687 83 0.927008 84 0.918195 85 0.903653 86 0.885948 87 0.873741 88 0.856454 89 0.836312 90 0.813832 91 0.801482 92 0.777083 93 0.751091 94 0.727312 95 0.700384 96 0.6746 97 0.645349 98 0.611468 99 0.579826 100 0.547125