RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354279.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) = 46,172,871 / 46,099,030 read pairs aligned = 46,093,401 total alignments = 100,905,897 secondary alignments = 8,633,996 non-unique alignments = 11,029,229 aligned to genes = 72,445,730 ambiguous alignments = 382,782 no feature assigned = 15,083,611 not aligned = 4,694,751 >>>>>>> Reads genomic origin exonic = 72,445,730 (82.77%) intronic = 12,974,879 (14.82%) intergenic = 2,108,732 (2.41%) overlapping exon = 3,196,992 (3.65%) >>>>>>> Transcript coverage profile 5' bias = 0.4 3' bias = 0.23 5'-3' bias = 1.64 >>>>>>> Junction analysis reads at junctions = 33,014,458 ACCT : 5% AGGT : 4.65% ATCT : 3.77% AGGA : 3.66% TCCT : 3.5% GCCT : 3.11% AGCT : 2.74% CCCT : 2.73% AGGC : 2.37% TTCT : 2.26% AGAT : 2.22%