RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354351.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) = 40,163,752 / 40,122,610 read pairs aligned = 40,116,751 total alignments = 84,958,960 secondary alignments = 4,672,598 non-unique alignments = 7,877,302 aligned to genes = 66,056,398 ambiguous alignments = 207,353 no feature assigned = 10,555,179 not aligned = 8,409,014 >>>>>>> Reads genomic origin exonic = 66,056,398 (86.22%) intronic = 7,162,990 (9.35%) intergenic = 3,392,189 (4.43%) overlapping exon = 2,691,737 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.17 5'-3' bias = 2.05 >>>>>>> Junction analysis reads at junctions = 19,948,601 ACCT : 5.43% AGGT : 4.66% ATCT : 3.67% AGGA : 3.58% TCCT : 3.36% GCCT : 3.15% AGCT : 2.72% AGGC : 2.39% AGAT : 2.34% CCCT : 2.28% TTCT : 2.2%