RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354068.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) = 33,952,192 / 33,925,553 read pairs aligned = 33,899,710 total alignments = 74,218,029 secondary alignments = 6,340,284 non-unique alignments = 9,194,316 aligned to genes = 56,055,718 ambiguous alignments = 234,839 no feature assigned = 7,697,664 not aligned = 2,449,813 >>>>>>> Reads genomic origin exonic = 56,055,718 (87.93%) intronic = 5,411,006 (8.49%) intergenic = 2,286,658 (3.59%) overlapping exon = 3,396,109 (5.33%) >>>>>>> Transcript coverage profile 5' bias = 0.24 3' bias = 0.2 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 20,882,564 ACCT : 5.28% TCCT : 4.48% AGGT : 4.44% ATCT : 4.24% AGGA : 3.08% GCCT : 3% CCCT : 2.96% AGGC : 2.39% AGCT : 2.27% TTCT : 2.05% AGAA : 1.74%