## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=16wk_PBS1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/16wk_PBS1_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 09 06:13:46 EDT 2020 ## 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 2637230392 2637119354 60660931 1629964522 613174276 131403794 201915831 0 0 0 10733135 10662182 75384 0.501658 0.498342 0.023003 0.618085 0.232517 0.049829 0.076567 0.850602 0.850566 0 0.434843 0.283279 0.251959 1.077749 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.081883 1 0.136199 2 0.239493 3 0.349584 4 0.428436 5 0.521703 6 0.603298 7 0.665364 8 0.718572 9 0.765572 10 0.807136 11 0.845772 12 0.881858 13 0.917281 14 0.944066 15 0.972208 16 0.993179 17 1.013677 18 1.031034 19 1.0473 20 1.062345 21 1.075744 22 1.091967 23 1.102805 24 1.112619 25 1.127497 26 1.137271 27 1.148917 28 1.163285 29 1.172348 30 1.175228 31 1.186613 32 1.192566 33 1.198908 34 1.212324 35 1.226455 36 1.225564 37 1.230659 38 1.234166 39 1.241116 40 1.242602 41 1.244805 42 1.243032 43 1.244241 44 1.245926 45 1.243084 46 1.243138 47 1.238604 48 1.237025 49 1.235006 50 1.235062 51 1.234271 52 1.232245 53 1.231264 54 1.228561 55 1.226473 56 1.229516 57 1.229195 58 1.226255 59 1.227579 60 1.227519 61 1.225478 62 1.22111 63 1.217264 64 1.21515 65 1.207047 66 1.198956 67 1.189965 68 1.183107 69 1.177236 70 1.170313 71 1.169487 72 1.164519 73 1.158808 74 1.147792 75 1.134571 76 1.126756 77 1.116474 78 1.103246 79 1.093998 80 1.071455 81 1.054727 82 1.043483 83 1.026519 84 1.005398 85 0.984976 86 0.958416 87 0.926214 88 0.888883 89 0.842795 90 0.792304 91 0.742183 92 0.686946 93 0.626765 94 0.556053 95 0.474009 96 0.380956 97 0.284525 98 0.186869 99 0.100335 100 0.050512