RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354178.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) = 46,933,012 / 46,877,524 read pairs aligned = 46,861,052 total alignments = 103,700,501 secondary alignments = 9,889,965 non-unique alignments = 12,245,016 aligned to genes = 75,869,105 ambiguous alignments = 287,596 no feature assigned = 12,590,690 not aligned = 2,147,306 >>>>>>> Reads genomic origin exonic = 75,869,105 (85.77%) intronic = 9,696,728 (10.96%) intergenic = 2,893,962 (3.27%) overlapping exon = 3,763,576 (4.25%) >>>>>>> Transcript coverage profile 5' bias = 0.49 3' bias = 0.2 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 28,165,505 ACCT : 5.27% AGGT : 4.7% ATCT : 3.65% TCCT : 3.44% AGGA : 3.4% GCCT : 3.32% AGCT : 2.77% CCCT : 2.63% AGGC : 2.42% AGAT : 2.13% TTCT : 2.1%