## 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-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-18a6f2-R1_B23WHYVLT4_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: Thu May 14 23:46:52 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 22771144359 22463543452 3572 20272386910 1462712214 657863766 70576990 0 0 0 4186183 78402066 474262 0.050687 0.949313 0 0.902457 0.065115 0.029286 0.003142 0.967572 0.954502 0 0.632901 0.406362 0.709795 0.604216 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.274456 1 0.301319 2 0.342016 3 0.395097 4 0.435618 5 0.475151 6 0.527931 7 0.573689 8 0.617995 9 0.660768 10 0.708351 11 0.754951 12 0.809882 13 0.854807 14 0.890403 15 0.926392 16 0.955217 17 0.97489 18 0.986535 19 0.997937 20 1.015028 21 1.032739 22 1.054408 23 1.06879 24 1.076223 25 1.08455 26 1.091891 27 1.106469 28 1.128852 29 1.136325 30 1.136524 31 1.144927 32 1.145499 33 1.156898 34 1.158491 35 1.164101 36 1.177846 37 1.179291 38 1.178792 39 1.169529 40 1.165324 41 1.170103 42 1.176848 43 1.181327 44 1.181523 45 1.178991 46 1.174646 47 1.179948 48 1.179967 49 1.184515 50 1.200426 51 1.200159 52 1.195819 53 1.195416 54 1.192166 55 1.186062 56 1.188839 57 1.182791 58 1.176755 59 1.171596 60 1.169964 61 1.173714 62 1.183428 63 1.183015 64 1.185142 65 1.181445 66 1.169454 67 1.158978 68 1.153607 69 1.150187 70 1.141975 71 1.134065 72 1.130597 73 1.12049 74 1.119195 75 1.111817 76 1.098071 77 1.087499 78 1.081619 79 1.066002 80 1.053797 81 1.046788 82 1.038409 83 1.023471 84 1.008433 85 0.992312 86 0.972616 87 0.962112 88 0.947689 89 0.930676 90 0.909784 91 0.878763 92 0.852013 93 0.817031 94 0.782693 95 0.749205 96 0.712401 97 0.673956 98 0.635131 99 0.593557 100 0.551986