## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_wQ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_wQ-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 00:22:50 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 76226340434 75297863493 16167 68769391285 4508301451 1816817041 203337549 0 0 0 5162671 246446753 1700746 0.020519 0.979481 0 0.913298 0.059873 0.024128 0.0027 0.973171 0.961317 0 0.535723 0.485347 0.774099 0.707098 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.307945 1 0.339197 2 0.381606 3 0.429234 4 0.472511 5 0.514489 6 0.56791 7 0.613308 8 0.660822 9 0.708033 10 0.760822 11 0.81247 12 0.85732 13 0.895209 14 0.924217 15 0.948281 16 0.96825 17 0.983688 18 0.999992 19 1.017272 20 1.028731 21 1.040085 22 1.05963 23 1.073949 24 1.081354 25 1.085262 26 1.09326 27 1.103613 28 1.117698 29 1.124107 30 1.125317 31 1.128816 32 1.13219 33 1.140931 34 1.1385 35 1.144694 36 1.152492 37 1.15518 38 1.160653 39 1.163181 40 1.162036 41 1.166597 42 1.173946 43 1.182344 44 1.182297 45 1.180922 46 1.17742 47 1.175479 48 1.174106 49 1.172201 50 1.178104 51 1.175518 52 1.17562 53 1.169856 54 1.174178 55 1.174589 56 1.17922 57 1.177457 58 1.163176 59 1.154146 60 1.155704 61 1.157215 62 1.152863 63 1.144849 64 1.140397 65 1.146034 66 1.142198 67 1.137191 68 1.135038 69 1.127966 70 1.117263 71 1.109269 72 1.107275 73 1.104233 74 1.105806 75 1.105683 76 1.096163 77 1.095801 78 1.090231 79 1.08081 80 1.067636 81 1.055777 82 1.044817 83 1.019076 84 0.999185 85 0.981284 86 0.957396 87 0.942834 88 0.927606 89 0.913627 90 0.89777 91 0.876924 92 0.85184 93 0.822209 94 0.789825 95 0.756009 96 0.723791 97 0.690275 98 0.652282 99 0.614964 100 0.572164