RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354112.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) = 37,369,237 / 37,337,032 read pairs aligned = 37,331,193 total alignments = 79,003,454 secondary alignments = 4,297,185 non-unique alignments = 7,179,887 aligned to genes = 61,284,155 ambiguous alignments = 195,309 no feature assigned = 10,062,646 not aligned = 7,406,477 >>>>>>> Reads genomic origin exonic = 61,284,155 (85.9%) intronic = 6,906,568 (9.68%) intergenic = 3,156,078 (4.42%) overlapping exon = 2,669,920 (3.74%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.18 5'-3' bias = 1.86 >>>>>>> Junction analysis reads at junctions = 19,800,143 ACCT : 5.4% AGGT : 4.68% ATCT : 3.62% AGGA : 3.58% TCCT : 3.41% GCCT : 3.23% AGCT : 2.75% AGGC : 2.41% CCCT : 2.34% AGAT : 2.31% TTCT : 2.11%