## 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-28eb14-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-28eb14-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 20:36:04 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 76935444556 76197742292 5954 69107125513 4951995614 1919850276 218764935 0 0 0 6706507 241200178 1138003 0.027053 0.972947 0 0.906945 0.064989 0.025196 0.002871 0.971933 0.962614 0 0.517716 0.516089 0.758521 0.789688 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.274107 1 0.303761 2 0.346286 3 0.400301 4 0.459575 5 0.518048 6 0.576423 7 0.635863 8 0.686975 9 0.734468 10 0.776724 11 0.817402 12 0.864447 13 0.90677 14 0.946337 15 0.980166 16 1.015154 17 1.038192 18 1.059445 19 1.083697 20 1.105542 21 1.129686 22 1.146227 23 1.159192 24 1.163523 25 1.164842 26 1.169544 27 1.173199 28 1.17817 29 1.17929 30 1.176928 31 1.176111 32 1.179452 33 1.18178 34 1.181251 35 1.183714 36 1.18327 37 1.182133 38 1.185284 39 1.186636 40 1.179481 41 1.175364 42 1.175206 43 1.183679 44 1.178611 45 1.175739 46 1.174712 47 1.176843 48 1.173989 49 1.171985 50 1.160601 51 1.163184 52 1.16686 53 1.165028 54 1.166793 55 1.16573 56 1.156727 57 1.147553 58 1.148333 59 1.141374 60 1.135379 61 1.131047 62 1.131119 63 1.126258 64 1.127241 65 1.129692 66 1.120376 67 1.116116 68 1.111409 69 1.10435 70 1.102146 71 1.089022 72 1.080809 73 1.071921 74 1.068307 75 1.062175 76 1.051691 77 1.043246 78 1.032764 79 1.024485 80 1.011102 81 0.998494 82 0.984717 83 0.971052 84 0.959754 85 0.950637 86 0.933509 87 0.923518 88 0.906888 89 0.88813 90 0.869799 91 0.848125 92 0.820745 93 0.787452 94 0.758225 95 0.728113 96 0.696125 97 0.661872 98 0.622677 99 0.586366 100 0.545318