## 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-d1f1a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-d1f1a3-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 20:39:01 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 72226704517 71357771450 7156 64964277088 4372241008 1813660671 207585527 0 0 0 5307131 245406366 868772 0.021168 0.978832 0 0.910402 0.061272 0.025416 0.002909 0.971674 0.959985 0 0.555521 0.476649 0.739046 0.766071 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.285693 1 0.317808 2 0.363874 3 0.423126 4 0.477899 5 0.522343 6 0.58177 7 0.636029 8 0.69085 9 0.747706 10 0.800896 11 0.851978 12 0.900088 13 0.946374 14 0.986103 15 1.012176 16 1.033974 17 1.049972 18 1.059772 19 1.074798 20 1.086023 21 1.09681 22 1.109421 23 1.120045 24 1.129047 25 1.135548 26 1.136645 27 1.144315 28 1.158548 29 1.168167 30 1.173647 31 1.176366 32 1.166711 33 1.163283 34 1.153405 35 1.15742 36 1.155179 37 1.155055 38 1.158396 39 1.161991 40 1.158362 41 1.157624 42 1.168358 43 1.182737 44 1.191093 45 1.196784 46 1.197329 47 1.197107 48 1.191716 49 1.195134 50 1.185783 51 1.182075 52 1.177992 53 1.173323 54 1.167569 55 1.162199 56 1.159703 57 1.153505 58 1.140777 59 1.130052 60 1.123895 61 1.123076 62 1.118783 63 1.110644 64 1.107908 65 1.10832 66 1.102618 67 1.101578 68 1.103606 69 1.102344 70 1.092995 71 1.083117 72 1.079111 73 1.074613 74 1.072421 75 1.073179 76 1.068754 77 1.062478 78 1.056983 79 1.046643 80 1.030566 81 1.01465 82 1.001999 83 0.980747 84 0.966274 85 0.951364 86 0.930409 87 0.922299 88 0.907452 89 0.889677 90 0.868031 91 0.84605 92 0.821093 93 0.789073 94 0.758288 95 0.728457 96 0.694736 97 0.660016 98 0.622736 99 0.587443 100 0.547149