RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354406.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) = 35,646,823 / 35,628,472 read pairs aligned = 35,625,729 total alignments = 76,108,967 secondary alignments = 4,833,672 non-unique alignments = 8,082,847 aligned to genes = 60,179,478 ambiguous alignments = 201,343 no feature assigned = 7,285,622 not aligned = 3,358,803 >>>>>>> Reads genomic origin exonic = 60,179,478 (89.2%) intronic = 4,591,958 (6.81%) intergenic = 2,693,664 (3.99%) overlapping exon = 2,019,412 (2.99%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.18 5'-3' bias = 2.19 >>>>>>> Junction analysis reads at junctions = 19,150,496 ACCT : 5.45% AGGT : 4.69% AGGA : 3.57% ATCT : 3.55% TCCT : 3.45% GCCT : 3.24% AGCT : 2.7% CCCT : 2.39% AGAT : 2.36% AGGC : 2.35% TTCT : 2.16%