## 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-776623-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-776623-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 21:07:54 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 73556341140 72647220877 3840 65618135527 4804799578 1970466781 253815151 0 0 0 11129059 236528845 1152286 0.044937 0.955063 0 0.903244 0.066139 0.027124 0.003494 0.969382 0.957401 0 0.644158 0.498391 0.58196 0.933675 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.294749 1 0.328718 2 0.379951 3 0.443522 4 0.499236 5 0.553726 6 0.622306 7 0.686543 8 0.753505 9 0.808454 10 0.862202 11 0.920415 12 0.972274 13 1.014869 14 1.043264 15 1.069804 16 1.090685 17 1.108063 18 1.121892 19 1.129024 20 1.144521 21 1.163241 22 1.178665 23 1.201602 24 1.223655 25 1.233905 26 1.234908 27 1.238074 28 1.244389 29 1.240665 30 1.240842 31 1.237499 32 1.228205 33 1.228768 34 1.222364 35 1.231614 36 1.236004 37 1.226056 38 1.219322 39 1.206899 40 1.1922 41 1.181897 42 1.178857 43 1.184256 44 1.186459 45 1.199304 46 1.198423 47 1.191031 48 1.181662 49 1.179142 50 1.189693 51 1.185919 52 1.179892 53 1.173436 54 1.175491 55 1.16944 56 1.16151 57 1.158617 58 1.14686 59 1.134355 60 1.126655 61 1.121337 62 1.118271 63 1.105891 64 1.097453 65 1.093305 66 1.085161 67 1.087095 68 1.085139 69 1.074364 70 1.062936 71 1.050101 72 1.039704 73 1.032697 74 1.019011 75 1.005273 76 0.991027 77 0.974978 78 0.9649 79 0.956264 80 0.941812 81 0.926378 82 0.916008 83 0.906316 84 0.892381 85 0.878756 86 0.857979 87 0.848297 88 0.832464 89 0.812548 90 0.785493 91 0.75591 92 0.723871 93 0.687462 94 0.65603 95 0.627121 96 0.595503 97 0.566596 98 0.536301 99 0.506024 100 0.472674