## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_SP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_SP-T1-TRNA-1_B23MHV2LT4_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: Sat May 23 00:22:48 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 74400899641 73526611225 16145 66377979727 5251385428 1679252332 217977593 0 0 0 10327404 237867503 1250514 0.04161 0.95839 0 0.902775 0.071422 0.022839 0.002965 0.974196 0.962749 0 0.545432 0.494231 0.802626 0.664211 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.2553 1 0.287625 2 0.332609 3 0.387467 4 0.447165 5 0.503447 6 0.559059 7 0.611239 8 0.659644 9 0.702751 10 0.746005 11 0.790691 12 0.836313 13 0.880131 14 0.908472 15 0.931005 16 0.951999 17 0.974888 18 0.98751 19 1.001405 20 1.01705 21 1.034122 22 1.051189 23 1.068026 24 1.06854 25 1.073563 26 1.082335 27 1.087248 28 1.102637 29 1.110265 30 1.114653 31 1.121986 32 1.126987 33 1.133628 34 1.134591 35 1.140543 36 1.144157 37 1.144373 38 1.145245 39 1.145499 40 1.147643 41 1.150887 42 1.151767 43 1.15679 44 1.163585 45 1.170576 46 1.176672 47 1.180785 48 1.175463 49 1.182383 50 1.198958 51 1.198144 52 1.19848 53 1.194017 54 1.190037 55 1.183971 56 1.181457 57 1.176459 58 1.170941 59 1.172727 60 1.175175 61 1.180462 62 1.179157 63 1.175143 64 1.167096 65 1.160271 66 1.152058 67 1.154897 68 1.155655 69 1.149132 70 1.141535 71 1.135306 72 1.127941 73 1.116204 74 1.111196 75 1.102141 76 1.091663 77 1.084112 78 1.074666 79 1.064205 80 1.052984 81 1.046076 82 1.039562 83 1.029505 84 1.016471 85 1.00143 86 0.978224 87 0.96515 88 0.955117 89 0.944189 90 0.926577 91 0.890856 92 0.868507 93 0.834409 94 0.79986 95 0.769656 96 0.736449 97 0.711588 98 0.673808 99 0.631139 100 0.586584