RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354387.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) = 30,788,458 / 30,763,449 read pairs aligned = 30,758,537 total alignments = 66,871,404 secondary alignments = 5,319,497 non-unique alignments = 7,533,256 aligned to genes = 50,622,681 ambiguous alignments = 178,517 no feature assigned = 7,573,315 not aligned = 3,529,367 >>>>>>> Reads genomic origin exonic = 50,622,681 (86.99%) intronic = 4,878,184 (8.38%) intergenic = 2,695,131 (4.63%) overlapping exon = 2,057,971 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.24 5'-3' bias = 1.8 >>>>>>> Junction analysis reads at junctions = 16,259,498 ACCT : 5.22% AGGT : 4.6% ATCT : 3.73% TCCT : 3.39% AGGA : 3.35% TTCT : 3.33% GCCT : 2.99% AGCT : 2.68% CCCT : 2.43% AGGC : 2.27% AGAT : 2.15%