RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354371.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) = 38,763,882 / 38,729,948 read pairs aligned = 38,726,639 total alignments = 84,718,154 secondary alignments = 7,224,324 non-unique alignments = 10,042,492 aligned to genes = 64,829,228 ambiguous alignments = 236,288 no feature assigned = 8,187,693 not aligned = 4,452,184 >>>>>>> Reads genomic origin exonic = 64,829,228 (88.79%) intronic = 5,374,012 (7.36%) intergenic = 2,813,681 (3.85%) overlapping exon = 2,562,872 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.25 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 20,415,271 ACCT : 5.35% AGGT : 4.53% ATCT : 3.65% TCCT : 3.53% GCCT : 3.43% AGGA : 3.21% TTCT : 2.76% CCCT : 2.67% AGCT : 2.65% AGGC : 2.34% AGAT : 2.05%