RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354160.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) = 37,000,964 / 36,979,190 read pairs aligned = 36,975,951 total alignments = 79,722,844 secondary alignments = 5,742,690 non-unique alignments = 9,644,916 aligned to genes = 63,442,726 ambiguous alignments = 215,484 no feature assigned = 5,955,001 not aligned = 1,950,284 >>>>>>> Reads genomic origin exonic = 63,442,726 (91.42%) intronic = 3,350,823 (4.83%) intergenic = 2,604,178 (3.75%) overlapping exon = 2,473,623 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.21 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 21,100,754 ACCT : 5.51% AGGT : 4.51% ATCT : 3.54% GCCT : 3.51% TCCT : 3.47% AGGA : 3.35% AGCT : 2.63% AGGC : 2.33% CCCT : 2.29% TTCT : 2.11% AGAT : 2.07%