## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00375_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00375_23LGNLLT4_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: Mon Mar 09 20:52:06 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 24085740683 23747591421 20102 21125790641 1347233282 1153893108 120654288 0 0 0 2522623 79768870 443265 0.030655 0.969345 0.000001 0.889597 0.056731 0.04859 0.005081 0.946329 0.933043 0 0.512681 0.498603 0.780872 0.780328 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.309304 1 0.342947 2 0.394955 3 0.448493 4 0.49115 5 0.531651 6 0.589281 7 0.643388 8 0.700745 9 0.754786 10 0.803211 11 0.842505 12 0.886819 13 0.928024 14 0.961091 15 0.995223 16 1.02559 17 1.045401 18 1.061114 19 1.070202 20 1.085834 21 1.101554 22 1.12052 23 1.13778 24 1.147517 25 1.156815 26 1.161183 27 1.161847 28 1.159208 29 1.15802 30 1.167952 31 1.170184 32 1.177712 33 1.182777 34 1.183365 35 1.181013 36 1.176815 37 1.17178 38 1.172646 39 1.172173 40 1.178024 41 1.179854 42 1.184364 43 1.193771 44 1.196601 45 1.211408 46 1.210963 47 1.210973 48 1.208791 49 1.195654 50 1.180657 51 1.173778 52 1.164142 53 1.155096 54 1.154199 55 1.153207 56 1.149444 57 1.1467 58 1.14203 59 1.13347 60 1.123111 61 1.122374 62 1.125158 63 1.119283 64 1.119813 65 1.120663 66 1.112292 67 1.103369 68 1.094352 69 1.093314 70 1.080614 71 1.068952 72 1.060792 73 1.054272 74 1.044021 75 1.0386 76 1.030058 77 1.020981 78 1.017826 79 1.009252 80 1.002395 81 0.990592 82 0.982549 83 0.972383 84 0.959944 85 0.945396 86 0.929624 87 0.921445 88 0.903557 89 0.885476 90 0.864469 91 0.843897 92 0.816543 93 0.788286 94 0.761168 95 0.728767 96 0.697717 97 0.663593 98 0.631169 99 0.595825 100 0.553159