## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT aih-tih-sc-965752-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-965752-R1_A23WJ53LT4_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: Tue May 19 21:20:04 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 72566177225 71695300788 1766 65611147850 4381756141 1520548087 181846944 0 0 0 10377763 244021654 1106332 0.040793 0.959207 0 0.915139 0.061116 0.021208 0.002536 0.976255 0.964539 0 0.531542 0.50878 0.745553 0.754256 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.285752 1 0.319623 2 0.367949 3 0.420329 4 0.473767 5 0.522168 6 0.584964 7 0.640172 8 0.697533 9 0.745665 10 0.791821 11 0.837201 12 0.879696 13 0.918101 14 0.956373 15 0.978675 16 1.002308 17 1.031036 18 1.047693 19 1.066318 20 1.080805 21 1.097957 22 1.11756 23 1.130212 24 1.139133 25 1.144274 26 1.149917 27 1.156378 28 1.156314 29 1.157078 30 1.167794 31 1.174946 32 1.171547 33 1.176221 34 1.171575 35 1.172061 36 1.173279 37 1.177816 38 1.178508 39 1.177939 40 1.173041 41 1.170361 42 1.174533 43 1.185802 44 1.184396 45 1.193141 46 1.192716 47 1.192551 48 1.194104 49 1.200498 50 1.188584 51 1.184455 52 1.17691 53 1.169067 54 1.165195 55 1.15735 56 1.152123 57 1.147771 58 1.133371 59 1.123648 60 1.119223 61 1.119292 62 1.127411 63 1.124289 64 1.122325 65 1.124433 66 1.130178 67 1.121708 68 1.117447 69 1.112645 70 1.096047 71 1.085642 72 1.077671 73 1.072419 74 1.066829 75 1.061977 76 1.052412 77 1.044907 78 1.042991 79 1.032503 80 1.021319 81 1.009149 82 0.997979 83 0.984891 84 0.971796 85 0.954119 86 0.933254 87 0.918534 88 0.897753 89 0.877263 90 0.860622 91 0.847747 92 0.819605 93 0.792714 94 0.762744 95 0.732761 96 0.702622 97 0.667559 98 0.629371 99 0.590712 100 0.552279