RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354355.markdup.sorted.bam gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf counting algorithm = uniquely-mapped-reads protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 37,924,481 / 37,900,771 read pairs aligned = 37,897,593 total alignments = 80,698,360 secondary alignments = 4,873,108 non-unique alignments = 8,289,965 aligned to genes = 62,889,147 ambiguous alignments = 211,817 no feature assigned = 9,044,281 not aligned = 3,767,248 >>>>>>> Reads genomic origin exonic = 62,889,147 (87.43%) intronic = 5,704,834 (7.93%) intergenic = 3,339,447 (4.64%) overlapping exon = 2,402,038 (3.34%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.16 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 19,111,827 ACCT : 5.24% AGGT : 4.74% ATCT : 3.74% AGGA : 3.63% TCCT : 3.38% GCCT : 3.17% AGCT : 2.66% CCCT : 2.44% AGGC : 2.37% AGAT : 2.31% TTCT : 2.27%