RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354144.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) = 32,687,334 / 32,659,377 read pairs aligned = 32,655,055 total alignments = 69,605,442 secondary alignments = 4,258,731 non-unique alignments = 7,112,599 aligned to genes = 53,017,987 ambiguous alignments = 186,025 no feature assigned = 9,034,700 not aligned = 5,777,527 >>>>>>> Reads genomic origin exonic = 53,017,987 (85.44%) intronic = 6,192,600 (9.98%) intergenic = 2,842,100 (4.58%) overlapping exon = 2,276,300 (3.67%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.18 5'-3' bias = 1.88 >>>>>>> Junction analysis reads at junctions = 17,942,087 ACCT : 5.54% AGGT : 4.78% AGGA : 3.64% ATCT : 3.58% TCCT : 3.38% GCCT : 3.18% AGCT : 2.71% AGAT : 2.44% CCCT : 2.43% AGGC : 2.38% TTCT : 2.17%