## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=SECOND_READ_TRANSCRIPTION_STRAND INPUT=G167_M2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/G167_M2_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: Sun Jul 15 18:08:48 EDT 2018 ## 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 2582053190 2581877046 69186690 1764157985 564284938 34023551 150259475 0 14590342 15748 0.026797 0.683285 0.218556 0.013178 0.058198 0.901841 0.90178 0.998922 0.493481 0.287211 0.144252 1.968416 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.074131 1 0.118401 2 0.205088 3 0.304601 4 0.380605 5 0.484156 6 0.579698 7 0.66576 8 0.751087 9 0.82023 10 0.878512 11 0.927684 12 0.971234 13 1.009916 14 1.048208 15 1.082249 16 1.111286 17 1.136449 18 1.160671 19 1.181137 20 1.203205 21 1.220986 22 1.240611 23 1.252792 24 1.260589 25 1.268514 26 1.275052 27 1.294428 28 1.306526 29 1.318992 30 1.325558 31 1.332776 32 1.339506 33 1.344412 34 1.346343 35 1.348986 36 1.344678 37 1.340693 38 1.328397 39 1.328611 40 1.329169 41 1.333887 42 1.334675 43 1.327467 44 1.318067 45 1.311965 46 1.30889 47 1.304884 48 1.297091 49 1.289089 50 1.281729 51 1.272955 52 1.269394 53 1.271811 54 1.268036 55 1.263661 56 1.260559 57 1.255209 58 1.257063 59 1.255631 60 1.251186 61 1.237988 62 1.228537 63 1.220128 64 1.207606 65 1.195682 66 1.179941 67 1.171029 68 1.158448 69 1.145585 70 1.133621 71 1.124242 72 1.110466 73 1.085735 74 1.069133 75 1.044727 76 1.021437 77 0.997884 78 0.978019 79 0.957573 80 0.939299 81 0.923457 82 0.900835 83 0.873329 84 0.841606 85 0.803739 86 0.76133 87 0.711488 88 0.655813 89 0.602159 90 0.549793 91 0.492966 92 0.433884 93 0.373395 94 0.310384 95 0.247039 96 0.187465 97 0.129475 98 0.078953 99 0.042536 100 0.026043