## 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-f26674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f26674-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 20:20:03 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 73947553672 73106067716 6222 66523062190 4688445599 1701212967 193340738 0 0 0 3171542 246894291 1069286 0.012683 0.987317 0 0.909953 0.064132 0.02327 0.002645 0.974085 0.963 0 0.50988 0.544597 0.753747 0.79899 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.299857 1 0.335501 2 0.383452 3 0.439745 4 0.495844 5 0.539885 6 0.597875 7 0.647893 8 0.706083 9 0.757832 10 0.798254 11 0.839811 12 0.887811 13 0.928894 14 0.959719 15 0.993655 16 1.024573 17 1.045354 18 1.060048 19 1.078337 20 1.097889 21 1.112781 22 1.129661 23 1.147559 24 1.149095 25 1.149237 26 1.144276 27 1.139542 28 1.143174 29 1.149285 30 1.155348 31 1.153707 32 1.137445 33 1.134376 34 1.128081 35 1.126078 36 1.127798 37 1.12906 38 1.129341 39 1.125005 40 1.126198 41 1.127832 42 1.13325 43 1.136949 44 1.140522 45 1.159454 46 1.161117 47 1.168204 48 1.171089 49 1.176419 50 1.180954 51 1.179996 52 1.17655 53 1.181235 54 1.186602 55 1.178498 56 1.175084 57 1.173115 58 1.161243 59 1.157455 60 1.150706 61 1.15006 62 1.150035 63 1.150566 64 1.150199 65 1.150419 66 1.138912 67 1.125048 68 1.121387 69 1.117799 70 1.112061 71 1.101603 72 1.097616 73 1.092336 74 1.084452 75 1.071685 76 1.061278 77 1.055758 78 1.057242 79 1.044388 80 1.030012 81 1.015853 82 1.008169 83 0.995999 84 0.984049 85 0.972394 86 0.955945 87 0.940384 88 0.91805 89 0.897745 90 0.868707 91 0.83921 92 0.813475 93 0.779718 94 0.741968 95 0.707158 96 0.675329 97 0.644258 98 0.609512 99 0.577681 100 0.54345