RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354263.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) = 31,739,100 / 31,702,146 read pairs aligned = 31,691,248 total alignments = 67,886,239 secondary alignments = 4,444,993 non-unique alignments = 7,157,317 aligned to genes = 54,084,209 ambiguous alignments = 182,103 no feature assigned = 6,010,572 not aligned = 5,614,372 >>>>>>> Reads genomic origin exonic = 54,084,209 (90%) intronic = 3,363,418 (5.6%) intergenic = 2,647,154 (4.4%) overlapping exon = 2,202,253 (3.66%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.19 5'-3' bias = 2.13 >>>>>>> Junction analysis reads at junctions = 17,883,484 ACCT : 5.44% AGGT : 4.66% ATCT : 3.62% TCCT : 3.58% AGGA : 3.43% GCCT : 3.12% AGCT : 2.69% AGGC : 2.4% CCCT : 2.36% TTCT : 2.24% AGAT : 2.18%