## 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_00473_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00473_B23WHTKLT4_2_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 21 05:55:05 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 79137745349 78380771893 664 71676170917 5145077204 1384994195 174528913 0 0 0 2640080 249005480 1228786 0.010491 0.989509 0 0.914461 0.065642 0.01767 0.002227 0.980103 0.970728 0 0.498552 0.547296 0.731676 0.86843 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.294328 1 0.333217 2 0.384558 3 0.448358 4 0.505616 5 0.555593 6 0.614223 7 0.666524 8 0.722364 9 0.772652 10 0.822327 11 0.867851 12 0.909552 13 0.950778 14 0.977698 15 1.001937 16 1.028516 17 1.059576 18 1.075215 19 1.092821 20 1.109986 21 1.128613 22 1.146371 23 1.161966 24 1.172924 25 1.180562 26 1.187414 27 1.189436 28 1.192838 29 1.194367 30 1.192988 31 1.190111 32 1.18657 33 1.186257 34 1.194279 35 1.19797 36 1.198669 37 1.200729 38 1.200338 39 1.194112 40 1.193756 41 1.192578 42 1.195319 43 1.194402 44 1.190358 45 1.194421 46 1.190475 47 1.188823 48 1.181564 49 1.181116 50 1.177923 51 1.175391 52 1.169182 53 1.167233 54 1.170455 55 1.174153 56 1.17004 57 1.169573 58 1.159618 59 1.147188 60 1.146154 61 1.143473 62 1.147719 63 1.144336 64 1.143646 65 1.145354 66 1.132569 67 1.114792 68 1.104933 69 1.096956 70 1.085232 71 1.073519 72 1.065064 73 1.055915 74 1.046269 75 1.035677 76 1.024708 77 1.011765 78 1.005542 79 1.001369 80 0.978708 81 0.959968 82 0.945334 83 0.931798 84 0.920784 85 0.905257 86 0.882654 87 0.866694 88 0.847489 89 0.824285 90 0.806247 91 0.78893 92 0.76155 93 0.735603 94 0.706954 95 0.679128 96 0.649627 97 0.620345 98 0.585784 99 0.553601 100 0.521319