## 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_00500_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00500_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: Sat May 16 11:55:25 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 78170932282 77286681944 51605 65329702827 5835886079 5496304609 624736824 0 0 0 9826688 227821625 839861 0.04135 0.95865 0.000001 0.845291 0.07551 0.071116 0.008083 0.9208 0.910384 0 0.512857 0.557635 0.765496 0.837366 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.319532 1 0.353193 2 0.406609 3 0.469481 4 0.520631 5 0.568165 6 0.623626 7 0.682673 8 0.736785 9 0.787931 10 0.834358 11 0.877063 12 0.919903 13 0.954413 14 0.984429 15 1.01627 16 1.048443 17 1.073429 18 1.092466 19 1.103182 20 1.116877 21 1.132876 22 1.144941 23 1.16559 24 1.17054 25 1.17295 26 1.177342 27 1.178864 28 1.178349 29 1.172484 30 1.175084 31 1.169603 32 1.168341 33 1.17116 34 1.167849 35 1.171972 36 1.167862 37 1.161757 38 1.160201 39 1.160293 40 1.159537 41 1.158252 42 1.159723 43 1.168416 44 1.169979 45 1.175057 46 1.170538 47 1.175896 48 1.178502 49 1.178964 50 1.176022 51 1.173257 52 1.168972 53 1.165218 54 1.167865 55 1.164903 56 1.161135 57 1.153307 58 1.142453 59 1.133345 60 1.123668 61 1.123551 62 1.116944 63 1.115093 64 1.110373 65 1.104087 66 1.100204 67 1.088957 68 1.081399 69 1.079407 70 1.070834 71 1.062106 72 1.051535 73 1.044591 74 1.033396 75 1.02631 76 1.014303 77 1.005383 78 1.001299 79 0.994721 80 0.987937 81 0.978833 82 0.973381 83 0.956235 84 0.944119 85 0.934991 86 0.916544 87 0.900839 88 0.882839 89 0.865706 90 0.843706 91 0.820977 92 0.797364 93 0.770205 94 0.742464 95 0.717346 96 0.692641 97 0.667025 98 0.635613 99 0.60301 100 0.563479