RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354367.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) = 36,812,997 / 36,790,647 read pairs aligned = 36,787,653 total alignments = 77,810,803 secondary alignments = 4,207,159 non-unique alignments = 7,156,647 aligned to genes = 62,278,552 ambiguous alignments = 191,211 no feature assigned = 7,932,149 not aligned = 3,510,024 >>>>>>> Reads genomic origin exonic = 62,278,552 (88.7%) intronic = 4,993,491 (7.11%) intergenic = 2,938,658 (4.19%) overlapping exon = 2,293,994 (3.27%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.16 5'-3' bias = 2.12 >>>>>>> Junction analysis reads at junctions = 18,914,375 ACCT : 5.43% AGGT : 4.69% ATCT : 3.7% AGGA : 3.56% TCCT : 3.37% GCCT : 3.34% AGCT : 2.71% AGGC : 2.34% AGAT : 2.29% CCCT : 2.27% TTCT : 2.2%