## 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_00276_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00276_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 20:05:07 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 23967488868 23597679230 23818 20249840249 1529716948 1610006169 208092046 0 0 0 4402178 74165465 482695 0.05603 0.94397 0.000001 0.858128 0.064825 0.068227 0.008818 0.922953 0.908713 0 0.548096 0.473474 0.729912 0.724582 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.343574 1 0.379263 2 0.42779 3 0.479207 4 0.518336 5 0.556089 6 0.609687 7 0.664984 8 0.714493 9 0.753165 10 0.787595 11 0.824952 12 0.863906 13 0.901379 14 0.93268 15 0.960624 16 0.982918 17 1.009899 18 1.016419 19 1.028045 20 1.052915 21 1.07303 22 1.09435 23 1.105016 24 1.112629 25 1.123075 26 1.130953 27 1.136816 28 1.149211 29 1.154033 30 1.151782 31 1.152095 32 1.153481 33 1.155282 34 1.158894 35 1.167949 36 1.171788 37 1.165162 38 1.162228 39 1.162578 40 1.166533 41 1.166227 42 1.167413 43 1.169411 44 1.17222 45 1.164499 46 1.152088 47 1.149874 48 1.147221 49 1.144815 50 1.153865 51 1.147429 52 1.144077 53 1.142167 54 1.154947 55 1.157172 56 1.147995 57 1.139563 58 1.13352 59 1.129832 60 1.126169 61 1.12047 62 1.119163 63 1.121119 64 1.125028 65 1.124456 66 1.11837 67 1.10933 68 1.103827 69 1.097233 70 1.08763 71 1.078156 72 1.077391 73 1.075152 74 1.06541 75 1.059152 76 1.056032 77 1.052898 78 1.046541 79 1.043914 80 1.039195 81 1.027541 82 1.015374 83 0.999485 84 0.992918 85 0.983543 86 0.969916 87 0.961539 88 0.941575 89 0.923233 90 0.899278 91 0.878323 92 0.851924 93 0.823552 94 0.796841 95 0.767005 96 0.731662 97 0.698252 98 0.660783 99 0.619875 100 0.579194