## 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-6d9e6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6d9e6f-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 20:18:02 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 73559277077 72784507561 7206 65171433383 5159945224 2201778263 251343485 0 0 0 7403834 240142674 1130818 0.029909 0.970091 0 0.895403 0.070893 0.030251 0.003453 0.966296 0.956118 0 0.508972 0.511955 0.764562 0.751917 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.261917 1 0.296521 2 0.343965 3 0.406309 4 0.471588 5 0.533628 6 0.591698 7 0.63892 8 0.689498 9 0.739658 10 0.78738 11 0.829978 12 0.877198 13 0.919629 14 0.955845 15 0.98993 16 1.01976 17 1.040782 18 1.059249 19 1.075584 20 1.09353 21 1.113139 22 1.128086 23 1.148372 24 1.158353 25 1.164216 26 1.168851 27 1.170515 28 1.169019 29 1.166218 30 1.164124 31 1.162363 32 1.158929 33 1.161132 34 1.156364 35 1.157562 36 1.157799 37 1.155744 38 1.149875 39 1.14886 40 1.146052 41 1.146607 42 1.154858 43 1.169252 44 1.174035 45 1.181622 46 1.179904 47 1.190022 48 1.186781 49 1.182909 50 1.167017 51 1.163926 52 1.159166 53 1.15633 54 1.159574 55 1.157121 56 1.154092 57 1.144678 58 1.136489 59 1.133267 60 1.129513 61 1.135277 62 1.136494 63 1.132551 64 1.131936 65 1.135102 66 1.127811 67 1.120779 68 1.119938 69 1.121092 70 1.113299 71 1.107179 72 1.102618 73 1.100639 74 1.096147 75 1.089925 76 1.07547 77 1.064479 78 1.05701 79 1.042981 80 1.026831 81 1.015696 82 1.004766 83 0.987304 84 0.970713 85 0.952863 86 0.932755 87 0.922169 88 0.906694 89 0.890167 90 0.86692 91 0.8438 92 0.819764 93 0.786879 94 0.758256 95 0.728665 96 0.692741 97 0.655686 98 0.615419 99 0.577503 100 0.54169