RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354395.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) = 32,326,028 / 32,242,180 read pairs aligned = 32,236,626 total alignments = 68,647,743 secondary alignments = 4,079,535 non-unique alignments = 6,803,335 aligned to genes = 53,048,704 ambiguous alignments = 190,310 no feature assigned = 8,348,918 not aligned = 6,592,144 >>>>>>> Reads genomic origin exonic = 53,048,704 (86.4%) intronic = 5,470,628 (8.91%) intergenic = 2,878,290 (4.69%) overlapping exon = 2,176,128 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.18 5'-3' bias = 1.88 >>>>>>> Junction analysis reads at junctions = 16,371,131 ACCT : 5.31% AGGT : 4.78% ATCT : 3.69% AGGA : 3.55% TCCT : 3.36% GCCT : 3.2% AGCT : 2.67% AGGC : 2.43% CCCT : 2.42% AGAT : 2.3% TTCT : 2.27%