RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354100.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) = 42,907,737 / 42,873,796 read pairs aligned = 42,864,362 total alignments = 92,994,472 secondary alignments = 7,212,939 non-unique alignments = 11,525,659 aligned to genes = 73,128,212 ambiguous alignments = 262,473 no feature assigned = 7,325,431 not aligned = 3,021,345 >>>>>>> Reads genomic origin exonic = 73,128,212 (90.89%) intronic = 4,641,559 (5.77%) intergenic = 2,683,872 (3.34%) overlapping exon = 2,656,827 (3.3%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.23 5'-3' bias = 1.79 >>>>>>> Junction analysis reads at junctions = 22,030,480 AGGT : 5.03% ACCT : 5.02% AGGA : 3.6% TCCT : 3.6% ATCT : 3.52% GCCT : 2.68% AGCT : 2.62% AGGC : 2.47% CCCT : 2.44% AGAT : 2.1% TTCT : 2.02%