RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354404.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) = 45,243,192 / 45,182,727 read pairs aligned = 45,145,836 total alignments = 97,423,567 secondary alignments = 6,997,648 non-unique alignments = 11,808,304 aligned to genes = 75,937,352 ambiguous alignments = 312,660 no feature assigned = 8,921,364 not aligned = 4,794,239 >>>>>>> Reads genomic origin exonic = 75,937,352 (89.49%) intronic = 5,747,869 (6.77%) intergenic = 3,173,495 (3.74%) overlapping exon = 3,901,100 (4.6%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.22 5'-3' bias = 2.03 >>>>>>> Junction analysis reads at junctions = 30,011,382 ACCT : 5.43% AGGT : 4.53% ATCT : 4.26% TCCT : 4.06% GCCT : 3.42% AGGA : 3.05% CCCT : 2.86% AGCT : 2.45% AGGC : 2.45% TTCT : 2.31% AGAA : 1.74%