RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354240.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) = 69,451,997 / 69,319,447 read pairs aligned = 69,309,176 total alignments = 146,825,075 secondary alignments = 8,053,631 non-unique alignments = 12,740,779 aligned to genes = 112,059,113 ambiguous alignments = 432,309 no feature assigned = 20,739,164 not aligned = 15,621,688 >>>>>>> Reads genomic origin exonic = 112,059,113 (84.38%) intronic = 14,482,353 (10.91%) intergenic = 6,256,811 (4.71%) overlapping exon = 5,657,534 (4.26%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.29 5'-3' bias = 1.67 >>>>>>> Junction analysis reads at junctions = 47,595,351 ACCT : 5.25% AGGT : 4.7% TCCT : 3.52% GCCT : 3.48% ATCT : 3.44% AGGA : 3.32% AGCT : 2.82% CCCT : 2.62% AGGC : 2.46% TTCT : 2.2% AGAT : 2.13%