## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT V4_0001_RNA_0005_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s19_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: Tue May 19 20:55:20 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 78244813404 77242445887 81600 61606446174 7297601926 7311661987 1026654200 0 0 0 5382371 216152423 1056207 0.024296 0.975704 0.000001 0.797572 0.094477 0.094659 0.013291 0.892049 0.880621 0 0.499649 0.60914 0.755404 0.877468 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.282775 1 0.324028 2 0.384586 3 0.453125 4 0.522981 5 0.589052 6 0.653202 7 0.716531 8 0.774346 9 0.83 10 0.873781 11 0.918939 12 0.964784 13 1.008087 14 1.041131 15 1.067866 16 1.092777 17 1.110034 18 1.120244 19 1.133482 20 1.149833 21 1.163739 22 1.174445 23 1.182304 24 1.192591 25 1.198286 26 1.202731 27 1.205389 28 1.20305 29 1.201524 30 1.195022 31 1.193706 32 1.183258 33 1.182041 34 1.176703 35 1.174082 36 1.17085 37 1.162378 38 1.15545 39 1.154103 40 1.151428 41 1.149391 42 1.150025 43 1.150724 44 1.148108 45 1.151179 46 1.145192 47 1.140074 48 1.139066 49 1.140812 50 1.141719 51 1.138003 52 1.132197 53 1.131933 54 1.136155 55 1.135104 56 1.13072 57 1.126111 58 1.12321 59 1.117218 60 1.115235 61 1.118743 62 1.116322 63 1.110111 64 1.108133 65 1.104997 66 1.099749 67 1.094869 68 1.088148 69 1.079778 70 1.070011 71 1.062283 72 1.058663 73 1.050846 74 1.046095 75 1.039483 76 1.026439 77 1.009295 78 1.007313 79 0.998956 80 0.977774 81 0.957672 82 0.947514 83 0.930558 84 0.91902 85 0.912424 86 0.897804 87 0.884145 88 0.865462 89 0.849004 90 0.82998 91 0.807677 92 0.785847 93 0.760414 94 0.732998 95 0.705826 96 0.676064 97 0.643213 98 0.611387 99 0.576009 100 0.534452