## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=LERKO_male2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LERKO_male2_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 ## htsjdk.samtools.metrics.StringHeader # Started on: Tue Apr 30 04:24:06 EDT 2019 ## 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 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 3354689096 3354455922 22619880 2019924371 863903682 165784247 282232362 0 18541668 18232996 0.006743 0.602162 0.257539 0.049422 0.084137 0.859701 0.859641 0.504197 0.453875 0.26733 0.35555 0.801028 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.074627 1 0.125924 2 0.212503 3 0.302946 4 0.359749 5 0.430112 6 0.491449 7 0.545007 8 0.600765 9 0.645535 10 0.683632 11 0.71713 12 0.754808 13 0.79097 14 0.818418 15 0.849335 16 0.876311 17 0.907437 18 0.930639 19 0.942699 20 0.9569 21 0.96596 22 0.978499 23 0.990745 24 1.008892 25 1.020772 26 1.03794 27 1.055338 28 1.071968 29 1.084279 30 1.095013 31 1.111645 32 1.124998 33 1.13445 34 1.144142 35 1.15127 36 1.154558 37 1.162598 38 1.174105 39 1.186684 40 1.197007 41 1.205588 42 1.217064 43 1.215933 44 1.207751 45 1.208874 46 1.210513 47 1.218811 48 1.217389 49 1.220594 50 1.224479 51 1.224378 52 1.237589 53 1.247182 54 1.253011 55 1.25166 56 1.257741 57 1.257234 58 1.256769 59 1.260054 60 1.256436 61 1.25126 62 1.255878 63 1.256321 64 1.250192 65 1.25059 66 1.247696 67 1.243334 68 1.236409 69 1.234196 70 1.236464 71 1.237126 72 1.236061 73 1.233647 74 1.232242 75 1.221666 76 1.211931 77 1.216174 78 1.207453 79 1.192559 80 1.183891 81 1.168812 82 1.158002 83 1.148703 84 1.132086 85 1.1167 86 1.102316 87 1.069134 88 1.030991 89 0.992538 90 0.945052 91 0.892765 92 0.837547 93 0.768523 94 0.692835 95 0.599251 96 0.495972 97 0.384792 98 0.257563 99 0.131674 100 0.058502