RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354291.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) = 29,969,050 / 29,956,669 read pairs aligned = 29,952,683 total alignments = 67,712,871 secondary alignments = 7,787,152 non-unique alignments = 10,685,637 aligned to genes = 42,211,088 ambiguous alignments = 186,362 no feature assigned = 12,967,889 not aligned = 727,703 >>>>>>> Reads genomic origin exonic = 42,211,088 (76.5%) intronic = 5,976,040 (10.83%) intergenic = 6,991,849 (12.67%) overlapping exon = 2,172,805 (3.94%) >>>>>>> Transcript coverage profile 5' bias = 0.2 3' bias = 0.18 5'-3' bias = 2.12 >>>>>>> Junction analysis reads at junctions = 17,572,994 TCCT : 5.42% ACCT : 5.26% ATCT : 4.47% AGGT : 3.97% CCCT : 3.22% GCCT : 2.96% AGGA : 2.63% TCCC : 2.56% GTCT : 2.48% TTCT : 2.42% AGGC : 2.1%