## 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-96d0f6-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-96d0f6-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 20:42:59 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 70166807455 69345558730 5508 62621679006 4803708472 1704879830 215285914 0 0 0 5676833 243975396 1049689 0.022739 0.977261 0 0.903038 0.069272 0.024585 0.003105 0.97231 0.96093 0 0.54704 0.495882 0.725092 0.788557 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.279072 1 0.309991 2 0.357791 3 0.415464 4 0.466857 5 0.514662 6 0.579704 7 0.634341 8 0.693062 9 0.74461 10 0.791972 11 0.843608 12 0.892739 13 0.933672 14 0.96696 15 0.99456 16 1.024803 17 1.051889 18 1.068872 19 1.086323 20 1.104138 21 1.121831 22 1.138272 23 1.149184 24 1.154585 25 1.159427 26 1.164585 27 1.16587 28 1.173717 29 1.178211 30 1.182489 31 1.18703 32 1.178368 33 1.178426 34 1.177939 35 1.18171 36 1.179359 37 1.182323 38 1.184382 39 1.177744 40 1.172162 41 1.169216 42 1.175246 43 1.181329 44 1.171977 45 1.180157 46 1.182877 47 1.180716 48 1.179092 49 1.18183 50 1.185436 51 1.181592 52 1.175627 53 1.171074 54 1.168841 55 1.16807 56 1.159001 57 1.153527 58 1.144244 59 1.129875 60 1.125378 61 1.126358 62 1.13128 63 1.131275 64 1.129922 65 1.128246 66 1.121079 67 1.113835 68 1.107792 69 1.103333 70 1.093554 71 1.085149 72 1.081611 73 1.07787 74 1.069153 75 1.055508 76 1.046374 77 1.038713 78 1.034596 79 1.024546 80 1.010281 81 0.995795 82 0.983739 83 0.967263 84 0.960437 85 0.948332 86 0.926872 87 0.917982 88 0.901089 89 0.880626 90 0.855675 91 0.831111 92 0.804989 93 0.777536 94 0.745421 95 0.712413 96 0.678784 97 0.644449 98 0.606627 99 0.571405 100 0.536888