RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354372.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) = 27,369,383 / 27,351,515 read pairs aligned = 27,348,120 total alignments = 58,297,497 secondary alignments = 3,576,599 non-unique alignments = 5,918,889 aligned to genes = 46,010,813 ambiguous alignments = 166,217 no feature assigned = 5,946,610 not aligned = 1,856,902 >>>>>>> Reads genomic origin exonic = 46,010,813 (88.55%) intronic = 3,901,775 (7.51%) intergenic = 2,044,835 (3.94%) overlapping exon = 1,704,629 (3.28%) >>>>>>> Transcript coverage profile 5' bias = 0.36 3' bias = 0.2 5'-3' bias = 2.1 >>>>>>> Junction analysis reads at junctions = 13,551,106 ACCT : 5.23% AGGT : 4.67% ATCT : 3.73% TCCT : 3.61% AGGA : 3.54% GCCT : 3.03% AGCT : 2.62% CCCT : 2.54% AGGC : 2.34% TTCT : 2.28% AGAT : 2.2%