## 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-c35cc3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-c35cc3-R1_A23YTGFLT4_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: Wed Jun 03 20:04:47 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 59168878247 58425091230 7670 52180778586 4342564760 1657098801 244641413 0 0 0 5247376 203732988 794162 0.025109 0.974891 0 0.893123 0.074327 0.028363 0.004187 0.96745 0.955288 0 0.581012 0.427804 0.733893 0.681315 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.267198 1 0.29514 2 0.334443 3 0.384471 4 0.430057 5 0.476993 6 0.535392 7 0.588706 8 0.642996 9 0.692702 10 0.737379 11 0.783476 12 0.828036 13 0.867997 14 0.9045 15 0.941385 16 0.974724 17 1.000542 18 1.01743 19 1.036313 20 1.062707 21 1.089107 22 1.109878 23 1.127918 24 1.138006 25 1.147061 26 1.153074 27 1.16037 28 1.168029 29 1.172463 30 1.177556 31 1.178293 32 1.168934 33 1.179785 34 1.176526 35 1.180576 36 1.186488 37 1.184637 38 1.188217 39 1.186601 40 1.179662 41 1.176721 42 1.181597 43 1.184771 44 1.18664 45 1.201713 46 1.201633 47 1.204666 48 1.203401 49 1.196607 50 1.185468 51 1.185838 52 1.176922 53 1.172825 54 1.179239 55 1.176854 56 1.173567 57 1.166894 58 1.154977 59 1.147969 60 1.143675 61 1.141072 62 1.141822 63 1.135819 64 1.140175 65 1.147109 66 1.137382 67 1.130396 68 1.131989 69 1.127653 70 1.116296 71 1.105311 72 1.101604 73 1.099205 74 1.094176 75 1.086852 76 1.076398 77 1.07052 78 1.067776 79 1.053794 80 1.03815 81 1.026962 82 1.009466 83 0.998168 84 0.985937 85 0.970953 86 0.951478 87 0.946383 88 0.931639 89 0.914234 90 0.892157 91 0.868578 92 0.833982 93 0.798035 94 0.761359 95 0.724565 96 0.687381 97 0.650722 98 0.609483 99 0.568654 100 0.528765