RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354189.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) = 46,432,967 / 46,419,069 read pairs aligned = 46,411,582 total alignments = 98,680,789 secondary alignments = 5,828,753 non-unique alignments = 9,364,018 aligned to genes = 79,643,448 ambiguous alignments = 287,049 no feature assigned = 8,805,015 not aligned = 2,357,498 >>>>>>> Reads genomic origin exonic = 79,643,448 (90.05%) intronic = 5,659,393 (6.4%) intergenic = 3,145,622 (3.56%) overlapping exon = 3,140,764 (3.55%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.15 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 24,433,218 ACCT : 5.37% AGGT : 4.86% ATCT : 3.79% TCCT : 3.71% AGGA : 3.6% GCCT : 3.06% AGCT : 2.61% CCCT : 2.45% AGGC : 2.3% AGAT : 2.09% TTCT : 2.03%