RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354232.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) = 40,554,348 / 40,507,349 read pairs aligned = 40,499,637 total alignments = 85,777,893 secondary alignments = 4,716,196 non-unique alignments = 7,866,944 aligned to genes = 69,075,639 ambiguous alignments = 261,942 no feature assigned = 8,254,420 not aligned = 6,272,243 >>>>>>> Reads genomic origin exonic = 69,075,639 (89.33%) intronic = 4,862,558 (6.29%) intergenic = 3,391,862 (4.39%) overlapping exon = 2,897,339 (3.75%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.19 5'-3' bias = 1.83 >>>>>>> Junction analysis reads at junctions = 22,012,731 ACCT : 5.52% AGGT : 4.71% ATCT : 3.89% TCCT : 3.66% GCCT : 3.44% AGGA : 3.4% CCCT : 2.55% AGCT : 2.49% AGGC : 2.4% TTCT : 2.27% AGAT : 2.1%