RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354386.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) = 66,895,681 / 66,857,980 read pairs aligned = 66,849,125 total alignments = 144,113,613 secondary alignments = 10,359,952 non-unique alignments = 16,946,433 aligned to genes = 113,868,354 ambiguous alignments = 515,524 no feature assigned = 11,959,955 not aligned = 3,763,335 >>>>>>> Reads genomic origin exonic = 113,868,354 (90.5%) intronic = 8,023,914 (6.38%) intergenic = 3,936,041 (3.13%) overlapping exon = 4,952,816 (3.94%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.23 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 39,083,663 ACCT : 5.43% AGGT : 4.39% TCCT : 4.12% ATCT : 4.09% GCCT : 3.58% AGGA : 3.08% CCCT : 2.84% AGCT : 2.3% AGGC : 2.23% TTCT : 2.18% TCCC : 1.78%