RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354397.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) = 120,988,440 / 120,784,066 read pairs aligned = 120,756,260 total alignments = 260,955,046 secondary alignments = 19,182,540 non-unique alignments = 32,320,132 aligned to genes = 197,286,625 ambiguous alignments = 678,304 no feature assigned = 29,208,659 not aligned = 11,959,526 >>>>>>> Reads genomic origin exonic = 197,286,625 (87.1%) intronic = 19,977,517 (8.82%) intergenic = 9,231,142 (4.08%) overlapping exon = 11,024,286 (4.87%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.25 5'-3' bias = 1.68 >>>>>>> Junction analysis reads at junctions = 65,274,198 ACCT : 5.05% AGGT : 4.58% TCCT : 3.81% ATCT : 3.74% GCCT : 3.57% AGGA : 3.21% CCCT : 2.76% AGCT : 2.73% AGGC : 2.4% TTCT : 2.3% AGAT : 2%