RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354196.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) = 54,271,593 / 54,200,545 read pairs aligned = 54,183,176 total alignments = 115,220,285 secondary alignments = 6,748,147 non-unique alignments = 11,548,081 aligned to genes = 87,743,121 ambiguous alignments = 265,878 no feature assigned = 15,315,608 not aligned = 8,087,236 >>>>>>> Reads genomic origin exonic = 87,743,121 (85.14%) intronic = 10,289,725 (9.98%) intergenic = 5,025,883 (4.88%) overlapping exon = 4,251,535 (4.13%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.17 5'-3' bias = 2.03 >>>>>>> Junction analysis reads at junctions = 25,064,274 ACCT : 5.31% AGGT : 4.81% AGGA : 3.67% ATCT : 3.63% TCCT : 3.34% GCCT : 2.94% AGCT : 2.83% CCCT : 2.43% AGGC : 2.43% AGAT : 2.41% TTCT : 2.17%