RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354310.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) = 39,417,796 / 39,376,986 read pairs aligned = 39,369,619 total alignments = 83,246,694 secondary alignments = 4,451,912 non-unique alignments = 7,527,701 aligned to genes = 66,931,792 ambiguous alignments = 247,433 no feature assigned = 8,324,170 not aligned = 10,898,286 >>>>>>> Reads genomic origin exonic = 66,931,792 (88.94%) intronic = 5,454,985 (7.25%) intergenic = 2,869,185 (3.81%) overlapping exon = 2,771,791 (3.68%) >>>>>>> Transcript coverage profile 5' bias = 0.25 3' bias = 0.17 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 22,152,414 ACCT : 5.73% AGGT : 4.67% ATCT : 3.79% TCCT : 3.61% AGGA : 3.3% GCCT : 3.28% AGCT : 2.55% AGGC : 2.44% CCCT : 2.32% TTCT : 2.05% AGAT : 2.03%