RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354180.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) = 31,556,184 / 31,538,928 read pairs aligned = 31,535,627 total alignments = 67,075,290 secondary alignments = 3,980,178 non-unique alignments = 6,581,649 aligned to genes = 52,544,695 ambiguous alignments = 190,639 no feature assigned = 7,484,759 not aligned = 2,198,286 >>>>>>> Reads genomic origin exonic = 52,544,695 (87.53%) intronic = 5,401,780 (9%) intergenic = 2,082,979 (3.47%) overlapping exon = 2,081,688 (3.47%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.21 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 18,351,268 ACCT : 5.35% AGGT : 4.73% AGGA : 3.64% ATCT : 3.47% TCCT : 3.34% GCCT : 3.29% AGCT : 2.82% CCCT : 2.45% AGGC : 2.42% AGAT : 2.33% TTCT : 2.11%