RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354384.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) = 56,137,570 / 56,076,345 read pairs aligned = 56,069,686 total alignments = 122,057,020 secondary alignments = 9,843,105 non-unique alignments = 16,731,113 aligned to genes = 94,862,845 ambiguous alignments = 299,716 no feature assigned = 9,490,222 not aligned = 5,289,045 >>>>>>> Reads genomic origin exonic = 94,862,845 (90.91%) intronic = 4,011,818 (3.84%) intergenic = 5,478,404 (5.25%) overlapping exon = 3,548,376 (3.4%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.2 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 26,780,016 ACCT : 5.39% AGGT : 4.46% TCCT : 3.85% ATCT : 3.78% AGGA : 3.38% GCCT : 3.2% CCCT : 2.46% AGCT : 2.38% AGGC : 2.26% TTCT : 2.26% AGAT : 1.96%