RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354157.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) = 37,416,554 / 37,380,459 read pairs aligned = 37,376,452 total alignments = 79,494,439 secondary alignments = 4,697,426 non-unique alignments = 7,798,287 aligned to genes = 63,881,160 ambiguous alignments = 221,293 no feature assigned = 7,274,929 not aligned = 4,679,217 >>>>>>> Reads genomic origin exonic = 63,881,160 (89.78%) intronic = 4,673,302 (6.57%) intergenic = 2,601,627 (3.66%) overlapping exon = 2,283,841 (3.21%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.15 5'-3' bias = 2.32 >>>>>>> Junction analysis reads at junctions = 19,322,187 ACCT : 5.46% AGGT : 4.73% ATCT : 3.57% TCCT : 3.5% AGGA : 3.47% GCCT : 2.92% TTCT : 2.74% AGCT : 2.6% AGGC : 2.4% CCCT : 2.29% AGAT : 2.16%