## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SK-BR-3_FFPE_01_RNA_0001_B23LG7FLT4_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: Thu May 28 21:23:52 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 75344628536 74427998074 72779 65850235117 4980918776 3099796002 496975400 0 0 0 10042638 234467890 1526581 0.041072 0.958928 0.000001 0.884751 0.066923 0.041648 0.006677 0.951674 0.940096 0 0.517626 0.58716 0.74194 0.908483 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.272407 1 0.317648 2 0.378152 3 0.445349 4 0.516388 5 0.585534 6 0.65378 7 0.722694 8 0.782861 9 0.834225 10 0.885383 11 0.937589 12 0.986399 13 1.025357 14 1.059917 15 1.090303 16 1.120821 17 1.142894 18 1.157504 19 1.166508 20 1.174425 21 1.194112 22 1.206205 23 1.211898 24 1.215186 25 1.211661 26 1.216368 27 1.213946 28 1.212933 29 1.20405 30 1.202095 31 1.200992 32 1.200878 33 1.203604 34 1.193918 35 1.192645 36 1.191337 37 1.178201 38 1.170272 39 1.159252 40 1.155731 41 1.149221 42 1.146573 43 1.161609 44 1.159375 45 1.158549 46 1.156339 47 1.151172 48 1.152836 49 1.158772 50 1.145753 51 1.146955 52 1.14566 53 1.139074 54 1.14137 55 1.137316 56 1.128542 57 1.119543 58 1.110514 59 1.104507 60 1.099665 61 1.099563 62 1.104405 63 1.097496 64 1.092713 65 1.091057 66 1.098845 67 1.089668 68 1.084629 69 1.075118 70 1.065158 71 1.050953 72 1.04926 73 1.044613 74 1.032571 75 1.017774 76 1.002105 77 0.989507 78 0.985579 79 0.972982 80 0.959134 81 0.942456 82 0.923715 83 0.908474 84 0.886661 85 0.8736 86 0.858143 87 0.847048 88 0.832519 89 0.81659 90 0.797238 91 0.782097 92 0.765185 93 0.74082 94 0.71768 95 0.693255 96 0.671219 97 0.648186 98 0.621407 99 0.588516 100 0.54863