RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354297.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) = 179,477,962 / 179,182,277 read pairs aligned = 179,130,875 total alignments = 392,664,657 secondary alignments = 34,004,418 non-unique alignments = 41,113,842 aligned to genes = 272,896,516 ambiguous alignments = 1,281,608 no feature assigned = 68,383,258 not aligned = 14,198,237 >>>>>>> Reads genomic origin exonic = 272,896,516 (79.96%) intronic = 60,072,824 (17.6%) intergenic = 8,310,434 (2.44%) overlapping exon = 15,755,018 (4.62%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.17 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 112,639,441 ACCT : 5.11% AGGT : 4.61% ATCT : 3.63% AGGA : 3.61% TCCT : 3.46% GCCT : 3.11% AGCT : 2.74% CCCT : 2.53% AGGC : 2.37% AGAT : 2.29% TTCT : 2.22%