## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=WTF_2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/WTF_2_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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 09 10:54:32 EDT 2020 ## 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 NUM_R1_TRANSCRIPT_STRAND_READS NUM_R2_TRANSCRIPT_STRAND_READS NUM_UNEXPLAINED_READS PCT_R1_TRANSCRIPT_STRAND_READS PCT_R2_TRANSCRIPT_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 1669203975 1669057458 268117084 860859569 240151528 126011120 173918157 0 0 0 27954 14248820 20529 0.001958 0.998042 0.16064 0.515776 0.143885 0.075498 0.104201 0.65966 0.659602 0 0.741951 0.047491 0.543975 0.095343 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.039011 1 0.052905 2 0.093544 3 0.16085 4 0.231538 5 0.349421 6 0.468571 7 0.573182 8 0.653225 9 0.697302 10 0.720348 11 0.751431 12 0.822028 13 0.856016 14 0.894676 15 0.913242 16 0.920144 17 0.947149 18 0.967984 19 0.996695 20 1.033357 21 1.055801 22 1.072719 23 1.086147 24 1.092706 25 1.104944 26 1.115647 27 1.160501 28 1.164632 29 1.154915 30 1.179133 31 1.181355 32 1.187904 33 1.190522 34 1.20048 35 1.219986 36 1.223816 37 1.224518 38 1.197509 39 1.197014 40 1.21844 41 1.234379 42 1.251404 43 1.257512 44 1.243419 45 1.217148 46 1.20552 47 1.183135 48 1.182362 49 1.194527 50 1.201815 51 1.171181 52 1.170023 53 1.19763 54 1.205446 55 1.196265 56 1.185309 57 1.183186 58 1.206456 59 1.231162 60 1.235688 61 1.211408 62 1.162235 63 1.17827 64 1.187177 65 1.187436 66 1.146658 67 1.126161 68 1.11854 69 1.110942 70 1.108308 71 1.118628 72 1.12086 73 1.106087 74 1.081247 75 1.061558 76 1.05961 77 1.07792 78 1.079478 79 1.0707 80 1.062209 81 1.039612 82 1.02938 83 1.037992 84 1.037272 85 1.055907 86 1.041026 87 1.016063 88 1.013987 89 1.016006 90 1.010905 91 1.002125 92 0.985101 93 0.928561 94 0.877477 95 0.830338 96 0.770562 97 0.668155 98 0.495498 99 0.281997 100 0.095165