RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354259.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) = 27,563,498 / 27,547,750 read pairs aligned = 27,545,396 total alignments = 58,529,757 secondary alignments = 3,418,509 non-unique alignments = 5,649,810 aligned to genes = 45,876,867 ambiguous alignments = 161,165 no feature assigned = 6,587,530 not aligned = 2,233,346 >>>>>>> Reads genomic origin exonic = 45,876,867 (87.44%) intronic = 4,195,522 (8%) intergenic = 2,392,008 (4.56%) overlapping exon = 1,867,215 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.21 5'-3' bias = 2.03 >>>>>>> Junction analysis reads at junctions = 13,621,676 ACCT : 5.44% AGGT : 4.83% AGGA : 3.58% ATCT : 3.54% TCCT : 3.53% GCCT : 3.03% AGCT : 2.75% CCCT : 2.57% AGGC : 2.44% AGAT : 2.3% TTCT : 2.08%