RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354166.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) = 47,119,735 / 47,092,084 read pairs aligned = 47,083,896 total alignments = 101,381,944 secondary alignments = 7,170,125 non-unique alignments = 10,608,722 aligned to genes = 78,941,921 ambiguous alignments = 322,740 no feature assigned = 10,482,553 not aligned = 2,996,215 >>>>>>> Reads genomic origin exonic = 78,941,921 (88.28%) intronic = 7,992,235 (8.94%) intergenic = 2,490,318 (2.78%) overlapping exon = 3,449,233 (3.86%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.18 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 26,927,555 ACCT : 5.23% AGGT : 4.7% TCCT : 3.75% ATCT : 3.63% AGGA : 3.44% GCCT : 2.92% AGCT : 2.55% CCCT : 2.54% AGGC : 2.34% TTCT : 2.32% AGAT : 2.06%