## 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_00067_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00067_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 20:21:07 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 23399395861 22466893498 26284 19636082546 1488873327 1212295361 129615980 0 0 0 6105932 70513543 428485 0.079692 0.920308 0.000001 0.874001 0.06627 0.053959 0.005769 0.94027 0.902799 0 0.564289 0.513978 0.692791 0.840178 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.277428 1 0.321782 2 0.374089 3 0.437202 4 0.504399 5 0.566995 6 0.621172 7 0.671015 8 0.723928 9 0.772081 10 0.819596 11 0.870311 12 0.920237 13 0.965258 14 0.992625 15 1.021402 16 1.045149 17 1.070719 18 1.097367 19 1.107412 20 1.116175 21 1.127459 22 1.139772 23 1.161173 24 1.172905 25 1.173789 26 1.176565 27 1.1753 28 1.179734 29 1.184426 30 1.186315 31 1.180599 32 1.176333 33 1.179745 34 1.171249 35 1.182251 36 1.190634 37 1.186134 38 1.185481 39 1.17717 40 1.172295 41 1.173498 42 1.183004 43 1.197175 44 1.201387 45 1.206609 46 1.207282 47 1.207622 48 1.204182 49 1.199681 50 1.18399 51 1.177172 52 1.171568 53 1.153625 54 1.148296 55 1.141407 56 1.129319 57 1.124874 58 1.116239 59 1.103032 60 1.104371 61 1.108264 62 1.107262 63 1.096862 64 1.098496 65 1.09608 66 1.091745 67 1.084263 68 1.083415 69 1.088123 70 1.080034 71 1.066051 72 1.066132 73 1.062885 74 1.052255 75 1.049059 76 1.046562 77 1.040053 78 1.03084 79 1.020588 80 1.008274 81 0.994813 82 0.978019 83 0.960182 84 0.949398 85 0.935389 86 0.912901 87 0.8943 88 0.876592 89 0.855228 90 0.834666 91 0.816449 92 0.787085 93 0.7552 94 0.726685 95 0.697012 96 0.669199 97 0.641192 98 0.602987 99 0.565795 100 0.527403