RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354197.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) = 43,685,919 / 43,663,152 read pairs aligned = 43,655,439 total alignments = 94,007,562 secondary alignments = 6,658,491 non-unique alignments = 10,516,551 aligned to genes = 74,543,795 ambiguous alignments = 287,933 no feature assigned = 7,993,083 not aligned = 1,796,643 >>>>>>> Reads genomic origin exonic = 74,543,795 (90.32%) intronic = 5,294,511 (6.41%) intergenic = 2,698,572 (3.27%) overlapping exon = 3,211,938 (3.89%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.22 5'-3' bias = 2.04 >>>>>>> Junction analysis reads at junctions = 25,747,278 ACCT : 5.32% AGGT : 4.54% TCCT : 4.2% ATCT : 4.18% AGGA : 3.18% GCCT : 3.03% CCCT : 2.63% AGCT : 2.44% AGGC : 2.33% TTCT : 2.08% AGAA : 1.83%