RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354191.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) = 38,516,620 / 38,499,364 read pairs aligned = 38,496,987 total alignments = 81,446,660 secondary alignments = 4,430,676 non-unique alignments = 7,326,146 aligned to genes = 65,949,352 ambiguous alignments = 207,323 no feature assigned = 7,615,149 not aligned = 1,287,678 >>>>>>> Reads genomic origin exonic = 65,949,352 (89.65%) intronic = 5,000,221 (6.8%) intergenic = 2,614,928 (3.55%) overlapping exon = 2,294,153 (3.12%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.13 5'-3' bias = 2.05 >>>>>>> Junction analysis reads at junctions = 22,196,643 ACCT : 5.47% AGGT : 4.63% GCCT : 3.61% AGGA : 3.57% ATCT : 3.44% TCCT : 3.13% AGCT : 2.71% AGGC : 2.35% TTCT : 2.26% AGAT : 2.24% CCCT : 2.21%