## htsjdk.samtools.metrics.StringHeader # picard.analysis.CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND INPUT=CV_CO3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/CV_CO3_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 04:27:43 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 4968076500 4968004894 15770000 3760789174 910191412 46173154 235088707 0 93876 91135227 0.003174 0.757002 0.183211 0.009294 0.047321 0.940213 0.940199 0.001029 0.426129 0.549263 0.309645 1.712688 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.151487 1 0.290343 2 0.470312 3 0.586598 4 0.636634 5 0.708698 6 0.771872 7 0.829281 8 0.884202 9 0.928672 10 0.953929 11 0.984543 12 1.015787 13 1.031121 14 1.056626 15 1.074687 16 1.085459 17 1.095852 18 1.105845 19 1.118812 20 1.130304 21 1.142134 22 1.152938 23 1.158533 24 1.162614 25 1.178833 26 1.186639 27 1.193794 28 1.205251 29 1.212667 30 1.22402 31 1.237933 32 1.240213 33 1.236618 34 1.237728 35 1.241903 36 1.238233 37 1.242344 38 1.249923 39 1.256141 40 1.258401 41 1.267301 42 1.267642 43 1.264309 44 1.262389 45 1.265269 46 1.267691 47 1.256679 48 1.246277 49 1.235057 50 1.228705 51 1.218046 52 1.204557 53 1.203542 54 1.20673 55 1.199111 56 1.195903 57 1.188886 58 1.188579 59 1.180676 60 1.177076 61 1.17511 62 1.163004 63 1.164649 64 1.170992 65 1.155204 66 1.130907 67 1.11486 68 1.10301 69 1.09367 70 1.090741 71 1.097864 72 1.10353 73 1.078611 74 1.05853 75 1.033792 76 1.005267 77 0.986669 78 0.975336 79 0.964278 80 0.944966 81 0.929669 82 0.908997 83 0.887059 84 0.868542 85 0.849609 86 0.820518 87 0.793995 88 0.761885 89 0.718086 90 0.677507 91 0.627768 92 0.583368 93 0.539091 94 0.484132 95 0.422996 96 0.361104 97 0.286102 98 0.197274 99 0.104768 100 0.039717