## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=LERKO_male4_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LERKO_male4_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 04:27:10 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 4683718120 4683421137 21818080 2824455507 1205719763 255901997 375535009 0 25907768 25482600 0.004659 0.603075 0.257444 0.05464 0.080184 0.86052 0.860465 0.504137 0.437255 0.297901 0.350659 0.887704 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.080814 1 0.135916 2 0.228958 3 0.325206 4 0.386552 5 0.46108 6 0.52423 7 0.578042 8 0.636403 9 0.683943 10 0.722385 11 0.756488 12 0.793463 13 0.82843 14 0.853665 15 0.880402 16 0.903853 17 0.928831 18 0.954509 19 0.967404 20 0.981111 21 0.98926 22 1.003378 23 1.017873 24 1.034104 25 1.0512 26 1.059147 27 1.07306 28 1.087768 29 1.097158 30 1.106951 31 1.123855 32 1.137032 33 1.14563 34 1.155263 35 1.164125 36 1.165051 37 1.169318 38 1.175266 39 1.183429 40 1.192854 41 1.200103 42 1.199381 43 1.194089 44 1.19062 45 1.193366 46 1.200112 47 1.207011 48 1.203551 49 1.210722 50 1.215978 51 1.212031 52 1.216404 53 1.225514 54 1.232405 55 1.238158 56 1.242893 57 1.242556 58 1.246906 59 1.254975 60 1.255494 61 1.253393 62 1.254635 63 1.245161 64 1.239674 65 1.240923 66 1.237451 67 1.235613 68 1.228017 69 1.225016 70 1.229016 71 1.231656 72 1.232907 73 1.222122 74 1.217413 75 1.204909 76 1.190816 77 1.193076 78 1.185054 79 1.17253 80 1.166204 81 1.150208 82 1.136454 83 1.124693 84 1.110728 85 1.09612 86 1.079328 87 1.046942 88 1.006968 89 0.966736 90 0.923615 91 0.870788 92 0.815372 93 0.748566 94 0.671786 95 0.579511 96 0.478092 97 0.369611 98 0.246432 99 0.127584 100 0.058017