RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354122.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) = 47,503,427 / 47,469,385 read pairs aligned = 47,457,110 total alignments = 103,108,919 secondary alignments = 8,136,107 non-unique alignments = 12,584,288 aligned to genes = 80,039,500 ambiguous alignments = 321,738 no feature assigned = 9,186,051 not aligned = 4,500,566 >>>>>>> Reads genomic origin exonic = 80,039,500 (89.7%) intronic = 5,846,675 (6.55%) intergenic = 3,339,376 (3.74%) overlapping exon = 3,163,504 (3.55%) >>>>>>> Transcript coverage profile 5' bias = 0.25 3' bias = 0.24 5'-3' bias = 1.62 >>>>>>> Junction analysis reads at junctions = 23,976,346 ACCT : 5.11% AGGT : 4.6% ATCT : 4.17% TCCT : 4.13% AGGA : 3.21% GCCT : 2.95% CCCT : 2.94% AGCT : 2.3% AGGC : 2.21% TTCT : 2.19% AGAA : 1.9%