RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354052.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) = 31,087,757 / 31,067,692 read pairs aligned = 31,064,530 total alignments = 66,004,632 secondary alignments = 3,849,183 non-unique alignments = 6,351,084 aligned to genes = 50,607,204 ambiguous alignments = 187,167 no feature assigned = 8,598,057 not aligned = 2,653,343 >>>>>>> Reads genomic origin exonic = 50,607,204 (85.48%) intronic = 6,522,209 (11.02%) intergenic = 2,075,848 (3.51%) overlapping exon = 2,037,765 (3.44%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.18 5'-3' bias = 2.28 >>>>>>> Junction analysis reads at junctions = 17,036,006 ACCT : 5.42% AGGT : 4.69% TCCT : 3.61% AGGA : 3.59% ATCT : 3.49% GCCT : 2.97% AGCT : 2.69% AGGC : 2.38% AGAT : 2.31% CCCT : 2.3% AGGG : 1.99%