## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_bhK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bhK-T1-TRNA-1_B23MHV2LT4_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: Fri May 22 21:18:43 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 74971178175 74033686285 11764 67516200571 4761550871 1577418720 178504359 0 0 0 11056939 244323988 1620378 0.043296 0.956704 0 0.911966 0.064316 0.021307 0.002411 0.976282 0.964074 0 0.532622 0.526496 0.77355 0.749701 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.304945 1 0.338892 2 0.386614 3 0.444044 4 0.495926 5 0.542516 6 0.598046 7 0.647839 8 0.693772 9 0.736054 10 0.780387 11 0.821573 12 0.85988 13 0.895101 14 0.923183 15 0.949546 16 0.974289 17 0.996077 18 1.008955 19 1.02114 20 1.037345 21 1.055759 22 1.074535 23 1.091789 24 1.105535 25 1.111274 26 1.120736 27 1.133618 28 1.147436 29 1.151593 30 1.156935 31 1.158964 32 1.154081 33 1.160134 34 1.154354 35 1.160257 36 1.163615 37 1.159223 38 1.154319 39 1.151638 40 1.149432 41 1.148973 42 1.152999 43 1.161711 44 1.158512 45 1.162162 46 1.159692 47 1.160117 48 1.164511 49 1.170109 50 1.171221 51 1.166476 52 1.165104 53 1.16469 54 1.16499 55 1.162682 56 1.15934 57 1.158679 58 1.150082 59 1.143707 60 1.142264 61 1.14056 62 1.143001 63 1.140448 64 1.140424 65 1.146009 66 1.154801 67 1.154557 68 1.152836 69 1.148011 70 1.134815 71 1.120097 72 1.115839 73 1.111256 74 1.104777 75 1.100558 76 1.088815 77 1.079911 78 1.073372 79 1.055648 80 1.038468 81 1.023842 82 1.019669 83 1.003314 84 0.982377 85 0.96534 86 0.942521 87 0.92941 88 0.924013 89 0.908195 90 0.888186 91 0.852831 92 0.825836 93 0.800768 94 0.7708 95 0.738279 96 0.705341 97 0.683754 98 0.649339 99 0.60987 100 0.569507