RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354241.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) = 42,597,475 / 42,560,026 read pairs aligned = 42,546,347 total alignments = 92,455,458 secondary alignments = 7,297,957 non-unique alignments = 12,056,572 aligned to genes = 72,876,762 ambiguous alignments = 257,677 no feature assigned = 6,720,863 not aligned = 4,287,993 >>>>>>> Reads genomic origin exonic = 72,876,762 (91.56%) intronic = 3,984,833 (5.01%) intergenic = 2,736,030 (3.44%) overlapping exon = 3,231,059 (4.06%) >>>>>>> Transcript coverage profile 5' bias = 0.15 3' bias = 0.12 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 22,680,192 AGGT : 5.24% ACCT : 4.95% TCCT : 3.9% AGGA : 3.57% ATCT : 3.51% CCCT : 2.64% AGGC : 2.52% AGCT : 2.15% TTCT : 2.1% AGAA : 2.05% GCCT : 2.03%