## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bhK-T1-TRNA-1_B23WHTKLT4_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 21 04:34:30 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 78562352925 77743573757 1692 70680091036 5201335263 1665882523 196263243 0 0 0 13013376 242379369 1112787 0.050954 0.949046 0 0.909144 0.066904 0.021428 0.002524 0.976048 0.965875 0 0.497735 0.503121 0.76502 0.720206 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.306717 1 0.341058 2 0.384659 3 0.433304 4 0.479189 5 0.523098 6 0.575654 7 0.62441 8 0.67057 9 0.714025 10 0.75803 11 0.805548 12 0.850411 13 0.89124 14 0.921237 15 0.945338 16 0.968034 17 0.99171 18 1.008816 19 1.026229 20 1.048585 21 1.071281 22 1.094015 23 1.103181 24 1.109877 25 1.111957 26 1.116717 27 1.12624 28 1.129425 29 1.130226 30 1.132867 31 1.136744 32 1.130556 33 1.137801 34 1.1409 35 1.150896 36 1.160504 37 1.1575 38 1.15928 39 1.160177 40 1.161461 41 1.162678 42 1.167604 43 1.176517 44 1.177586 45 1.184374 46 1.18097 47 1.180798 48 1.180327 49 1.183136 50 1.184905 51 1.179281 52 1.176952 53 1.177107 54 1.177921 55 1.177714 56 1.177525 57 1.178462 58 1.168815 59 1.164066 60 1.161126 61 1.163572 62 1.168589 63 1.161984 64 1.154143 65 1.150985 66 1.159218 67 1.159554 68 1.158515 69 1.150987 70 1.134617 71 1.122757 72 1.117068 73 1.109259 74 1.106579 75 1.100376 76 1.084042 77 1.067647 78 1.057227 79 1.042357 80 1.02886 81 1.016249 82 1.01233 83 0.999165 84 0.984279 85 0.966426 86 0.940506 87 0.923564 88 0.910258 89 0.891849 90 0.872843 91 0.84387 92 0.819584 93 0.797001 94 0.7672 95 0.738658 96 0.706544 97 0.680889 98 0.64529 99 0.607312 100 0.568544