RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354104.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) = 72,100,340 / 72,056,285 read pairs aligned = 72,045,443 total alignments = 155,246,628 secondary alignments = 11,090,003 non-unique alignments = 17,401,762 aligned to genes = 126,436,936 ambiguous alignments = 504,321 no feature assigned = 9,825,470 not aligned = 5,082,159 >>>>>>> Reads genomic origin exonic = 126,436,936 (92.79%) intronic = 6,367,878 (4.67%) intergenic = 3,457,592 (2.54%) overlapping exon = 4,977,528 (3.65%) >>>>>>> Transcript coverage profile 5' bias = 0.19 3' bias = 0.18 5'-3' bias = 2.1 >>>>>>> Junction analysis reads at junctions = 53,325,136 ACCT : 5.42% TCCT : 4.9% AGGT : 4.63% ATCT : 4.35% AGGA : 3.11% CCCT : 2.73% GCCT : 2.68% AGGC : 2.19% AGCT : 2.1% TTCT : 2.02% AGAA : 1.91%