## 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-6c4b48-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6c4b48-R1_A23YTGFLT4_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: Wed Jun 03 20:22:07 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 79247989640 78529302965 2462 70637618348 5487776129 2165623457 238282569 0 0 0 7434231 241617999 1332688 0.02985 0.97015 0 0.899506 0.069882 0.027577 0.003034 0.969388 0.960597 0 0.498217 0.596707 0.745924 0.90233 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.265117 1 0.308126 2 0.364672 3 0.431332 4 0.504062 5 0.579338 6 0.648206 7 0.709812 8 0.763369 9 0.81491 10 0.861997 11 0.9056 12 0.950168 13 0.995012 14 1.031414 15 1.062315 16 1.089026 17 1.117338 18 1.137582 19 1.155853 20 1.173259 21 1.184118 22 1.190691 23 1.200586 24 1.205638 25 1.202239 26 1.200632 27 1.201734 28 1.203578 29 1.20629 30 1.2049 31 1.201817 32 1.193407 33 1.1934 34 1.189756 35 1.189839 36 1.191927 37 1.182222 38 1.173279 39 1.164971 40 1.160536 41 1.163524 42 1.161508 43 1.170755 44 1.170404 45 1.181086 46 1.181624 47 1.178803 48 1.174006 49 1.17292 50 1.159958 51 1.156888 52 1.15106 53 1.152625 54 1.153174 55 1.148677 56 1.141839 57 1.136337 58 1.129575 59 1.126225 60 1.116709 61 1.111413 62 1.109485 63 1.103138 64 1.093246 65 1.087904 66 1.088251 67 1.078174 68 1.067603 69 1.056516 70 1.050216 71 1.043207 72 1.039332 73 1.031872 74 1.027494 75 1.021249 76 1.008181 77 0.993859 78 0.990512 79 0.976775 80 0.966831 81 0.955055 82 0.94254 83 0.934025 84 0.920436 85 0.908591 86 0.893057 87 0.883017 88 0.862575 89 0.840316 90 0.816073 91 0.791656 92 0.76991 93 0.7462 94 0.718904 95 0.691259 96 0.662559 97 0.633534 98 0.600429 99 0.571709 100 0.536384