RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354141.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) = 52,098,285 / 52,057,654 read pairs aligned = 52,052,614 total alignments = 110,898,944 secondary alignments = 6,743,005 non-unique alignments = 11,284,100 aligned to genes = 84,459,474 ambiguous alignments = 316,399 no feature assigned = 14,418,226 not aligned = 3,401,383 >>>>>>> Reads genomic origin exonic = 84,459,474 (85.42%) intronic = 10,142,194 (10.26%) intergenic = 4,276,032 (4.32%) overlapping exon = 3,363,176 (3.4%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.22 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 27,875,792 ACCT : 5.37% AGGT : 4.7% AGGA : 3.55% ATCT : 3.48% TCCT : 3.43% GCCT : 3.18% AGCT : 2.75% CCCT : 2.45% AGGC : 2.4% AGAT : 2.32% TTCT : 2.15%