## 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-ec2fd6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ec2fd6-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 20:29:01 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 67603787337 66848412494 4350 60473297111 4273687764 1885876307 215546962 0 0 0 3375572 231349655 949270 0.014381 0.985619 0 0.904633 0.063931 0.028211 0.003224 0.968564 0.957742 0 0.529624 0.482356 0.772608 0.725082 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.258626 1 0.287196 2 0.325999 3 0.3816 4 0.44224 5 0.50689 6 0.56356 7 0.615026 8 0.662304 9 0.714915 10 0.766028 11 0.812371 12 0.861813 13 0.909597 14 0.941879 15 0.969852 16 0.997614 17 1.021043 18 1.036096 19 1.056822 20 1.07904 21 1.094366 22 1.100856 23 1.115923 24 1.117524 25 1.125979 26 1.131129 27 1.131687 28 1.137104 29 1.139372 30 1.141706 31 1.143461 32 1.140263 33 1.146303 34 1.146142 35 1.155204 36 1.158535 37 1.156716 38 1.159431 39 1.160585 40 1.158664 41 1.158287 42 1.162719 43 1.164151 44 1.169429 45 1.177274 46 1.17473 47 1.178375 48 1.185395 49 1.18943 50 1.188368 51 1.187126 52 1.177999 53 1.171583 54 1.170684 55 1.166989 56 1.16493 57 1.161921 58 1.155813 59 1.149838 60 1.145138 61 1.143542 62 1.140121 63 1.134241 64 1.133203 65 1.142236 66 1.13905 67 1.144647 68 1.148375 69 1.147459 70 1.144792 71 1.13832 72 1.128824 73 1.121246 74 1.119232 75 1.112441 76 1.100156 77 1.087015 78 1.077709 79 1.063244 80 1.051052 81 1.034466 82 1.022599 83 1.0068 84 0.990056 85 0.971198 86 0.950134 87 0.937606 88 0.91514 89 0.892149 90 0.871206 91 0.8449 92 0.822429 93 0.795347 94 0.767471 95 0.734375 96 0.700454 97 0.665226 98 0.624762 99 0.585038 100 0.539014