## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT tih_rna_sample_00086_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00086_23KKJ7LT4_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: Sat May 16 11:55:03 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 74751760287 73263997871 238036 52967438028 7284934741 11804427539 1206959527 0 0 0 3300936 201929771 999224 0.016084 0.983916 0.000003 0.722967 0.099434 0.161122 0.016474 0.822401 0.806033 0 0.567239 0.523835 0.707469 0.900068 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.363802 1 0.400739 2 0.459156 3 0.517829 4 0.571231 5 0.624131 6 0.685728 7 0.740362 8 0.79764 9 0.847594 10 0.891596 11 0.934476 12 0.970775 13 1.008158 14 1.035444 15 1.060497 16 1.071854 17 1.082339 18 1.083858 19 1.090779 20 1.105071 21 1.116175 22 1.126974 23 1.130035 24 1.140521 25 1.143202 26 1.148639 27 1.157152 28 1.157903 29 1.144285 30 1.135737 31 1.141529 32 1.144992 33 1.152377 34 1.150369 35 1.155541 36 1.15679 37 1.14908 38 1.151511 39 1.14775 40 1.142677 41 1.14468 42 1.14782 43 1.155535 44 1.153323 45 1.152688 46 1.145358 47 1.142301 48 1.138262 49 1.138867 50 1.138433 51 1.137558 52 1.134201 53 1.136943 54 1.14392 55 1.141951 56 1.134194 57 1.128518 58 1.126707 59 1.120745 60 1.115202 61 1.117795 62 1.118775 63 1.111751 64 1.111394 65 1.117124 66 1.118653 67 1.111279 68 1.104046 69 1.090991 70 1.078634 71 1.06932 72 1.061762 73 1.05492 74 1.047569 75 1.041193 76 1.030693 77 1.017318 78 1.010733 79 1.007122 80 0.998381 81 0.987771 82 0.97253 83 0.957631 84 0.940282 85 0.920427 86 0.901381 87 0.884502 88 0.870533 89 0.852385 90 0.837419 91 0.817672 92 0.791673 93 0.764865 94 0.742369 95 0.719106 96 0.693409 97 0.663181 98 0.626515 99 0.589258 100 0.54548