RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354258.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) = 113,813,918 / 113,735,862 read pairs aligned = 113,711,237 total alignments = 248,352,025 secondary alignments = 20,802,245 non-unique alignments = 31,490,268 aligned to genes = 192,093,773 ambiguous alignments = 753,767 no feature assigned = 21,296,539 not aligned = 11,235,276 >>>>>>> Reads genomic origin exonic = 192,093,773 (90.02%) intronic = 12,791,682 (5.99%) intergenic = 8,504,857 (3.99%) overlapping exon = 9,332,208 (4.37%) >>>>>>> Transcript coverage profile 5' bias = 0.18 3' bias = 0.17 5'-3' bias = 2.06 >>>>>>> Junction analysis reads at junctions = 67,932,498 ACCT : 5.22% TCCT : 4.56% ATCT : 4.38% AGGT : 4.35% AGGA : 3.07% CCCT : 2.98% GCCT : 2.36% AGGC : 2.27% AGCT : 2.07% TTCT : 1.94% AGAA : 1.72%