## 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_00512_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00512_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: Tue Mar 10 00:24:43 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 25304622915 24949262704 22831 21623267352 1705609873 1475275596 145087052 0 0 0 2730352 77522623 208193 0.034022 0.965978 0.000001 0.86669 0.068363 0.059131 0.005815 0.935053 0.921922 0 0.551553 0.480055 0.718416 0.760412 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.270266 1 0.30135 2 0.349477 3 0.409934 4 0.46478 5 0.509028 6 0.568737 7 0.624621 8 0.681411 9 0.744221 10 0.799646 11 0.85451 12 0.910181 13 0.956287 14 0.989225 15 1.014856 16 1.038182 17 1.065953 18 1.081019 19 1.08552 20 1.099918 21 1.117946 22 1.134681 23 1.150439 24 1.153648 25 1.156028 26 1.152414 27 1.151232 28 1.156442 29 1.15873 30 1.169611 31 1.171656 32 1.169894 33 1.170962 34 1.166298 35 1.179196 36 1.183227 37 1.17535 38 1.177682 39 1.174226 40 1.173315 41 1.169959 42 1.18322 43 1.195733 44 1.19682 45 1.20762 46 1.211556 47 1.207498 48 1.208552 49 1.209531 50 1.200288 51 1.196486 52 1.190356 53 1.1833 54 1.179776 55 1.17873 56 1.177613 57 1.172538 58 1.163198 59 1.152866 60 1.143147 61 1.145809 62 1.142527 63 1.131693 64 1.128927 65 1.129642 66 1.121448 67 1.114016 68 1.112809 69 1.110045 70 1.103672 71 1.092211 72 1.087166 73 1.076344 74 1.058491 75 1.050086 76 1.038205 77 1.029478 78 1.028075 79 1.013215 80 0.997462 81 0.982362 82 0.972483 83 0.953502 84 0.937522 85 0.922979 86 0.904573 87 0.893242 88 0.87967 89 0.864431 90 0.844093 91 0.815101 92 0.787428 93 0.758076 94 0.728557 95 0.699218 96 0.668406 97 0.637146 98 0.60626 99 0.572508 100 0.534713