RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354309.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) = 38,648,215 / 38,624,577 read pairs aligned = 38,621,994 total alignments = 82,481,459 secondary alignments = 5,208,667 non-unique alignments = 8,459,072 aligned to genes = 64,561,136 ambiguous alignments = 238,311 no feature assigned = 8,809,143 not aligned = 1,853,064 >>>>>>> Reads genomic origin exonic = 64,561,136 (87.99%) intronic = 6,167,367 (8.41%) intergenic = 2,641,776 (3.6%) overlapping exon = 2,247,279 (3.06%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.22 5'-3' bias = 2.03 >>>>>>> Junction analysis reads at junctions = 20,588,908 ACCT : 5.26% AGGT : 4.76% ATCT : 3.62% AGGA : 3.59% TCCT : 3.42% GCCT : 3.15% AGCT : 2.71% CCCT : 2.56% AGAT : 2.37% AGGC : 2.36% TTCT : 2.14%