RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354265.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) = 50,331,865 / 50,302,897 read pairs aligned = 50,295,572 total alignments = 113,335,126 secondary alignments = 12,700,364 non-unique alignments = 15,445,862 aligned to genes = 81,489,453 ambiguous alignments = 233,628 no feature assigned = 12,478,984 not aligned = 2,699,334 >>>>>>> Reads genomic origin exonic = 81,489,453 (86.72%) intronic = 7,991,507 (8.5%) intergenic = 4,487,477 (4.78%) overlapping exon = 4,026,144 (4.28%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.13 5'-3' bias = 2.16 >>>>>>> Junction analysis reads at junctions = 22,937,847 ACCT : 5.03% AGGT : 4.58% AGGA : 3.62% ATCT : 3.61% TCCT : 3.35% GCCT : 3% AGCT : 2.83% TTCT : 2.38% CCCT : 2.37% AGAT : 2.3% AGGC : 2.29%