RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354237.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) = 47,669,839 / 47,627,367 read pairs aligned = 47,612,868 total alignments = 102,191,557 secondary alignments = 6,894,351 non-unique alignments = 10,774,188 aligned to genes = 80,864,859 ambiguous alignments = 262,963 no feature assigned = 9,612,743 not aligned = 5,377,254 >>>>>>> Reads genomic origin exonic = 80,864,859 (89.38%) intronic = 6,952,575 (7.68%) intergenic = 2,660,168 (2.94%) overlapping exon = 3,898,836 (4.31%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.22 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 28,975,106 AGGT : 4.86% ACCT : 4.84% ATCT : 4.76% TCCT : 4.28% AGGA : 3.45% AGCT : 2.82% GCCT : 2.64% AGGC : 2.35% CCCT : 2.29% AGAT : 1.94% TTCT : 1.83%