RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354249.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) = 31,585,753 / 31,558,365 read pairs aligned = 31,547,007 total alignments = 68,219,661 secondary alignments = 5,075,543 non-unique alignments = 7,991,039 aligned to genes = 52,906,605 ambiguous alignments = 242,653 no feature assigned = 6,524,392 not aligned = 1,485,008 >>>>>>> Reads genomic origin exonic = 52,906,605 (89.02%) intronic = 4,419,013 (7.44%) intergenic = 2,105,379 (3.54%) overlapping exon = 2,993,674 (5.04%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.23 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 19,088,914 ACCT : 4.99% AGGT : 4.7% ATCT : 4.08% TCCT : 4.01% AGGA : 3.19% CCCT : 3.03% GCCT : 2.86% AGGC : 2.48% AGCT : 2.41% TTCT : 2.1% AGAA : 1.88%