## 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-d963a2-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-d963a2-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 20:18:02 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 77379789033 76564954409 5672 67998688323 5741760813 2536372348 288127253 0 0 0 5264451 241361675 1378347 0.021346 0.978654 0 0.888118 0.074992 0.033127 0.003763 0.96311 0.952968 0 0.526606 0.589687 0.71083 0.9578 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.29759 1 0.350227 2 0.413651 3 0.48892 4 0.567889 5 0.645195 6 0.705304 7 0.763797 8 0.820473 9 0.861211 10 0.900626 11 0.941031 12 0.988594 13 1.024217 14 1.052253 15 1.07797 16 1.102182 17 1.126683 18 1.140511 19 1.158184 20 1.176418 21 1.185418 22 1.194454 23 1.202187 24 1.205806 25 1.204658 26 1.20529 27 1.201851 28 1.198662 29 1.187123 30 1.181533 31 1.174453 32 1.169691 33 1.167857 34 1.163563 35 1.159272 36 1.155236 37 1.156231 38 1.158128 39 1.152417 40 1.141232 41 1.13636 42 1.139256 43 1.143505 44 1.137221 45 1.136238 46 1.132008 47 1.129743 48 1.124846 49 1.124787 50 1.129709 51 1.122879 52 1.115416 53 1.121895 54 1.130452 55 1.129718 56 1.127145 57 1.124596 58 1.120635 59 1.117245 60 1.108246 61 1.107986 62 1.111791 63 1.109075 64 1.114848 65 1.11546 66 1.114325 67 1.11003 68 1.103991 69 1.095131 70 1.080228 71 1.066988 72 1.058374 73 1.051086 74 1.041542 75 1.030436 76 1.017281 77 0.99852 78 0.989179 79 0.984206 80 0.972176 81 0.960591 82 0.942096 83 0.924294 84 0.912474 85 0.894596 86 0.879059 87 0.866175 88 0.850312 89 0.83129 90 0.809031 91 0.794099 92 0.76901 93 0.738939 94 0.710536 95 0.680024 96 0.650975 97 0.621684 98 0.583032 99 0.546836 100 0.510388