## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=Ezh12F_3_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/Ezh12F_3_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 10:56:57 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 1441225950 1441052998 261971639 721018661 230720684 96894705 130447309 0 0 0 25585 12338204 19245 0.002069 0.997931 0.181792 0.500342 0.160106 0.067239 0.090522 0.660447 0.660368 0 0.733273 0.038743 0.561321 0.079365 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.036679 1 0.045462 2 0.081066 3 0.146696 4 0.211687 5 0.317078 6 0.448563 7 0.551548 8 0.627767 9 0.680013 10 0.722755 11 0.766426 12 0.836423 13 0.869266 14 0.90188 15 0.918197 16 0.930196 17 0.954179 18 0.975472 19 0.997329 20 1.029666 21 1.053106 22 1.071421 23 1.07826 24 1.08368 25 1.097102 26 1.109463 27 1.139805 28 1.13818 29 1.133885 30 1.163205 31 1.175623 32 1.184764 33 1.181333 34 1.187013 35 1.19912 36 1.205883 37 1.201832 38 1.188024 39 1.204611 40 1.221575 41 1.220217 42 1.233695 43 1.241308 44 1.215924 45 1.193278 46 1.184725 47 1.16683 48 1.170351 49 1.181256 50 1.183503 51 1.152231 52 1.14987 53 1.180071 54 1.192 55 1.191141 56 1.182145 57 1.176301 58 1.200198 59 1.229971 60 1.232437 61 1.19455 62 1.152496 63 1.160383 64 1.163459 65 1.164197 66 1.136529 67 1.132931 68 1.13663 69 1.126436 70 1.125563 71 1.138309 72 1.142289 73 1.133697 74 1.111339 75 1.09007 76 1.096039 77 1.103538 78 1.097663 79 1.082121 80 1.067247 81 1.056607 82 1.050045 83 1.063876 84 1.070011 85 1.088376 86 1.069393 87 1.051623 88 1.046693 89 1.03749 90 1.031353 91 1.031213 92 1.012472 93 0.957053 94 0.911929 95 0.870253 96 0.799573 97 0.671351 98 0.473174 99 0.252182 100 0.083527