## 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_00017_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00017_23LGNLLT4_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: Mon Mar 09 20:52:27 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 24655534298 24334650059 10238 21202985817 1565211123 1428765513 137677368 0 0 0 2633393 76627972 394311 0.033224 0.966776 0 0.871308 0.06432 0.058713 0.005658 0.935629 0.923452 0 0.560298 0.497138 0.716533 0.795325 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.309023 1 0.350665 2 0.406424 3 0.471416 4 0.526505 5 0.574439 6 0.630868 7 0.681753 8 0.739219 9 0.799067 10 0.846385 11 0.888517 12 0.932971 13 0.971564 14 1.007438 15 1.032171 16 1.053029 17 1.075431 18 1.085211 19 1.083466 20 1.091411 21 1.106556 22 1.120874 23 1.137625 24 1.145653 25 1.153846 26 1.156654 27 1.160495 28 1.172837 29 1.182844 30 1.185207 31 1.179101 32 1.174665 33 1.184582 34 1.19098 35 1.203819 36 1.212703 37 1.211175 38 1.205266 39 1.196718 40 1.191872 41 1.193582 42 1.194472 43 1.194743 44 1.195952 45 1.190859 46 1.180634 47 1.178079 48 1.173808 49 1.175576 50 1.170412 51 1.160728 52 1.156384 53 1.151966 54 1.158563 55 1.154106 56 1.153951 57 1.14757 58 1.140137 59 1.132251 60 1.128125 61 1.130226 62 1.12489 63 1.117604 64 1.113189 65 1.103293 66 1.089586 67 1.08056 68 1.070506 69 1.067647 70 1.0587 71 1.047668 72 1.044277 73 1.036269 74 1.02197 75 1.016651 76 1.004432 77 0.99935 78 0.993207 79 0.976036 80 0.968444 81 0.960253 82 0.95386 83 0.944305 84 0.933656 85 0.927524 86 0.919874 87 0.909113 88 0.891088 89 0.868637 90 0.842456 91 0.817449 92 0.795115 93 0.768368 94 0.741501 95 0.712035 96 0.679721 97 0.64582 98 0.613514 99 0.580416 100 0.545894