RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354102.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) = 30,076,716 / 30,054,357 read pairs aligned = 30,051,643 total alignments = 65,234,475 secondary alignments = 5,103,402 non-unique alignments = 7,138,623 aligned to genes = 49,286,293 ambiguous alignments = 171,429 no feature assigned = 7,688,363 not aligned = 3,301,137 >>>>>>> Reads genomic origin exonic = 49,286,293 (86.51%) intronic = 5,449,698 (9.57%) intergenic = 2,238,665 (3.93%) overlapping exon = 1,926,888 (3.38%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.21 5'-3' bias = 2.04 >>>>>>> Junction analysis reads at junctions = 15,160,237 ACCT : 5.53% AGGT : 4.75% ATCT : 3.68% AGGA : 3.62% TCCT : 3.6% GCCT : 3.17% AGCT : 2.73% CCCT : 2.39% AGGC : 2.35% AGAT : 2.27% TTCT : 2.12%