RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354156.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) = 31,285,813 / 31,266,266 read pairs aligned = 31,263,886 total alignments = 66,202,406 secondary alignments = 3,650,327 non-unique alignments = 6,012,280 aligned to genes = 51,603,353 ambiguous alignments = 171,049 no feature assigned = 8,137,511 not aligned = 1,318,855 >>>>>>> Reads genomic origin exonic = 51,603,353 (86.38%) intronic = 5,672,063 (9.49%) intergenic = 2,465,448 (4.13%) overlapping exon = 1,982,629 (3.32%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.16 5'-3' bias = 2.24 >>>>>>> Junction analysis reads at junctions = 16,710,064 ACCT : 5.37% AGGT : 4.69% AGGA : 3.63% ATCT : 3.63% TCCT : 3.37% GCCT : 3.1% AGCT : 2.74% AGGC : 2.42% AGAT : 2.4% CCCT : 2.38% TTCT : 2.26%