## 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-89f3a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-89f3a3-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 20:21:02 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 77590076565 76833312336 4364 68620080392 5480273610 2428706273 304247697 0 0 0 7046020 241073693 1214025 0.028398 0.971602 0 0.893103 0.071327 0.03161 0.00396 0.96443 0.955024 0 0.504238 0.583628 0.731471 0.892171 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.315862 1 0.357459 2 0.40849 3 0.46703 4 0.534436 5 0.600063 6 0.659686 7 0.716128 8 0.771902 9 0.820328 10 0.869617 11 0.918867 12 0.966683 13 1.006274 14 1.037207 15 1.061486 16 1.085344 17 1.100645 18 1.112704 19 1.126748 20 1.141711 21 1.159893 22 1.176172 23 1.19138 24 1.195841 25 1.199012 26 1.202141 27 1.20778 28 1.21261 29 1.216632 30 1.217325 31 1.219132 32 1.197289 33 1.188366 34 1.186272 35 1.183686 36 1.1767 37 1.171499 38 1.170948 39 1.165169 40 1.164848 41 1.170853 42 1.169041 43 1.158649 44 1.155996 45 1.159369 46 1.152181 47 1.148313 48 1.143622 49 1.141065 50 1.13436 51 1.126998 52 1.120871 53 1.121352 54 1.12295 55 1.125136 56 1.119819 57 1.114941 58 1.111259 59 1.107098 60 1.10464 61 1.107893 62 1.110816 63 1.102021 64 1.100638 65 1.100712 66 1.096402 67 1.0885 68 1.082305 69 1.069508 70 1.05655 71 1.043001 72 1.036191 73 1.029999 74 1.028666 75 1.023993 76 1.014607 77 1.005292 78 1.000337 79 0.990477 80 0.97551 81 0.962522 82 0.950805 83 0.941138 84 0.926419 85 0.914075 86 0.893224 87 0.881971 88 0.862506 89 0.844062 90 0.821739 91 0.806665 92 0.783417 93 0.756088 94 0.728302 95 0.701857 96 0.674805 97 0.645221 98 0.6125 99 0.582525 100 0.546779