RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354381.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) = 29,014,694 / 28,986,770 read pairs aligned = 28,982,148 total alignments = 62,474,425 secondary alignments = 4,472,961 non-unique alignments = 6,864,462 aligned to genes = 48,071,927 ambiguous alignments = 180,159 no feature assigned = 6,788,576 not aligned = 3,511,822 >>>>>>> Reads genomic origin exonic = 48,071,927 (87.63%) intronic = 4,836,409 (8.82%) intergenic = 1,952,167 (3.56%) overlapping exon = 1,859,761 (3.39%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.19 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 16,035,036 ACCT : 5.52% AGGT : 4.65% ATCT : 3.59% AGGA : 3.49% TCCT : 3.44% GCCT : 3.24% AGCT : 2.74% CCCT : 2.43% AGGC : 2.37% AGAT : 2.19% TTCT : 2.13%