## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=LERKO_male3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/LERKO_male3_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 04:24:43 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 4797097960 4796783806 28398008 2844317151 1215817277 285199777 423063848 0 26137902 25749636 0.00592 0.592963 0.253465 0.059456 0.088197 0.846428 0.846373 0.503741 0.447574 0.285406 0.353409 0.872742 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.080425 1 0.134958 2 0.226352 3 0.320288 4 0.376538 5 0.44443 6 0.505319 7 0.558394 8 0.610036 9 0.651511 10 0.690051 11 0.72416 12 0.758819 13 0.792473 14 0.82052 15 0.852284 16 0.879986 17 0.907431 18 0.929836 19 0.942532 20 0.955643 21 0.962989 22 0.976331 23 0.991055 24 1.007443 25 1.024493 26 1.037252 27 1.051643 28 1.066506 29 1.078828 30 1.09158 31 1.111921 32 1.130621 33 1.145226 34 1.162106 35 1.17477 36 1.175476 37 1.179483 38 1.18715 39 1.196522 40 1.190554 41 1.189587 42 1.193847 43 1.189788 44 1.188956 45 1.193139 46 1.198862 47 1.206947 48 1.205698 49 1.209263 50 1.213478 51 1.210165 52 1.215454 53 1.226883 54 1.233638 55 1.234527 56 1.240268 57 1.242854 58 1.249774 59 1.257633 60 1.262063 61 1.263634 62 1.267881 63 1.268089 64 1.264476 65 1.256426 66 1.248972 67 1.248947 68 1.242259 69 1.238903 70 1.240136 71 1.243712 72 1.245817 73 1.238235 74 1.237496 75 1.227845 76 1.216437 77 1.220075 78 1.209746 79 1.192821 80 1.187761 81 1.171396 82 1.158831 83 1.150366 84 1.139077 85 1.12532 86 1.10692 87 1.069534 88 1.027151 89 0.985066 90 0.937773 91 0.88403 92 0.824885 93 0.757946 94 0.681898 95 0.589493 96 0.487381 97 0.376752 98 0.252384 99 0.129939 100 0.057628