## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cIX-T1-TRNA-1_B23WHTKLT4_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 21 04:33:33 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 77075420285 76318260545 4958 69532334030 4969912819 1553266361 262742377 0 0 0 12495695 230995725 1111221 0.051319 0.948681 0 0.911084 0.065121 0.020352 0.003443 0.976205 0.966615 0 0.515777 0.486679 0.719116 0.739453 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.316393 1 0.346712 2 0.395355 3 0.457725 4 0.506671 5 0.542489 6 0.588578 7 0.632997 8 0.681512 9 0.730261 10 0.772153 11 0.81687 12 0.860519 13 0.89906 14 0.932902 15 0.964068 16 0.996289 17 1.016697 18 1.030595 19 1.04504 20 1.065652 21 1.087467 22 1.105363 23 1.114133 24 1.121685 25 1.131237 26 1.135419 27 1.136658 28 1.149958 29 1.155073 30 1.156835 31 1.156252 32 1.157335 33 1.164237 34 1.164159 35 1.175091 36 1.181213 37 1.18214 38 1.185788 39 1.188334 40 1.175569 41 1.182803 42 1.190526 43 1.192826 44 1.198996 45 1.201151 46 1.192489 47 1.196736 48 1.204067 49 1.20873 50 1.206759 51 1.204146 52 1.196771 53 1.191537 54 1.193598 55 1.191443 56 1.173992 57 1.16762 58 1.158017 59 1.154505 60 1.156321 61 1.152694 62 1.145439 63 1.128021 64 1.125324 65 1.128249 66 1.120106 67 1.106299 68 1.095055 69 1.086669 70 1.076124 71 1.068912 72 1.067876 73 1.065481 74 1.058958 75 1.057087 76 1.055681 77 1.04897 78 1.042114 79 1.034157 80 1.019316 81 1.004046 82 0.988641 83 0.969842 84 0.958328 85 0.947563 86 0.933026 87 0.927316 88 0.911068 89 0.890449 90 0.864657 91 0.842942 92 0.81934 93 0.79057 94 0.757531 95 0.725481 96 0.69329 97 0.657183 98 0.617866 99 0.577452 100 0.535323