## 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_00479_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00479_B23WHTKLT4_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: Thu May 21 07:11:57 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 77990782344 77217207773 1920 70773137263 4589087355 1667766144 187215091 0 0 0 3372414 246562153 1136597 0.013493 0.986507 0 0.916546 0.059431 0.021598 0.002425 0.975977 0.966297 0 0.491747 0.505475 0.760026 0.801247 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.272057 1 0.306686 2 0.356557 3 0.415042 4 0.468472 5 0.518081 6 0.577978 7 0.626687 8 0.67919 9 0.72967 10 0.772827 11 0.816904 12 0.868921 13 0.911068 14 0.944167 15 0.982954 16 1.009066 17 1.039925 18 1.063671 19 1.08601 20 1.103909 21 1.120031 22 1.135172 23 1.146604 24 1.15338 25 1.163897 26 1.168097 27 1.165238 28 1.165097 29 1.164305 30 1.163442 31 1.161506 32 1.160264 33 1.165691 34 1.162818 35 1.170206 36 1.173158 37 1.171646 38 1.173323 39 1.170081 40 1.171419 41 1.178037 42 1.179206 43 1.184418 44 1.186495 45 1.185601 46 1.178126 47 1.181805 48 1.182152 49 1.187175 50 1.192662 51 1.196059 52 1.19906 53 1.202093 54 1.218061 55 1.222322 56 1.199321 57 1.197554 58 1.187565 59 1.179175 60 1.168631 61 1.16628 62 1.163424 63 1.158515 64 1.157611 65 1.154748 66 1.151417 67 1.140484 68 1.130174 69 1.117206 70 1.105606 71 1.09601 72 1.090647 73 1.081264 74 1.07479 75 1.064252 76 1.051687 77 1.036346 78 1.033464 79 1.022187 80 1.012552 81 0.999424 82 0.986146 83 0.967819 84 0.951369 85 0.933027 86 0.91303 87 0.89413 88 0.872127 89 0.852365 90 0.829049 91 0.801667 92 0.773541 93 0.743369 94 0.714844 95 0.686933 96 0.657444 97 0.62466 98 0.589578 99 0.55752 100 0.519691