RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354083.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) = 30,485,767 / 30,467,542 read pairs aligned = 30,464,423 total alignments = 64,636,701 secondary alignments = 3,683,392 non-unique alignments = 6,035,287 aligned to genes = 52,458,795 ambiguous alignments = 189,767 no feature assigned = 5,669,561 not aligned = 2,290,827 >>>>>>> Reads genomic origin exonic = 52,458,795 (90.25%) intronic = 3,783,219 (6.51%) intergenic = 1,886,342 (3.25%) overlapping exon = 2,060,500 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.19 5'-3' bias = 1.88 >>>>>>> Junction analysis reads at junctions = 16,760,098 ACCT : 5.44% AGGT : 4.68% ATCT : 3.94% TCCT : 3.64% AGGA : 3.23% GCCT : 3.15% AGCT : 2.52% TTCT : 2.47% CCCT : 2.47% AGGC : 2.36% AGAT : 1.97%