RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354396.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) = 31,621,771 / 31,440,637 read pairs aligned = 31,403,515 total alignments = 69,129,373 secondary alignments = 6,066,965 non-unique alignments = 9,293,554 aligned to genes = 44,775,556 ambiguous alignments = 195,737 no feature assigned = 14,125,368 not aligned = 5,827,578 >>>>>>> Reads genomic origin exonic = 44,775,556 (76.02%) intronic = 6,671,767 (11.33%) intergenic = 7,453,601 (12.65%) overlapping exon = 2,616,658 (4.44%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.22 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 17,132,230 ACCT : 5.17% ATCT : 4.6% TCCT : 4.51% AGGT : 4.25% GCCT : 3.45% CCCT : 2.87% AGGA : 2.87% TTCT : 2.47% AGCT : 2.24% AGGC : 2.05% GTCT : 2.04%