RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354388.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) = 35,521,193 / 35,498,986 read pairs aligned = 35,495,677 total alignments = 76,513,013 secondary alignments = 5,492,834 non-unique alignments = 9,115,514 aligned to genes = 56,459,338 ambiguous alignments = 217,474 no feature assigned = 10,263,156 not aligned = 2,656,229 >>>>>>> Reads genomic origin exonic = 56,459,338 (84.62%) intronic = 5,405,562 (8.1%) intergenic = 4,857,594 (7.28%) overlapping exon = 2,326,555 (3.49%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.28 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 22,751,411 ACCT : 5.42% AGGT : 4.55% TCCT : 3.9% ATCT : 3.59% GCCT : 3.57% AGGA : 3.23% CCCT : 2.66% AGCT : 2.6% AGGC : 2.44% TTCT : 2.18% AGAT : 2.01%