RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354311.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) = 52,882,898 / 52,839,827 read pairs aligned = 52,830,212 total alignments = 127,120,041 secondary alignments = 21,397,316 non-unique alignments = 21,954,087 aligned to genes = 88,066,390 ambiguous alignments = 383,625 no feature assigned = 8,867,694 not aligned = 3,512,865 >>>>>>> Reads genomic origin exonic = 88,066,390 (90.85%) intronic = 5,110,156 (5.27%) intergenic = 3,757,538 (3.88%) overlapping exon = 3,661,313 (3.78%) >>>>>>> Transcript coverage profile 5' bias = 0.14 3' bias = 0.14 5'-3' bias = 2.58 >>>>>>> Junction analysis reads at junctions = 30,284,187 TCCT : 4.72% AGGT : 4.64% ACCT : 4.63% ATCT : 3.71% AGGA : 3.37% CCCT : 2.73% AGGC : 2.46% AGCT : 2.18% AGAC : 1.93% TTCT : 1.88% GCCT : 1.87%