RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354167.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) = 27,184,429 / 27,169,038 read pairs aligned = 27,165,458 total alignments = 57,747,406 secondary alignments = 3,393,939 non-unique alignments = 5,347,993 aligned to genes = 45,421,498 ambiguous alignments = 149,784 no feature assigned = 6,461,483 not aligned = 3,282,499 >>>>>>> Reads genomic origin exonic = 45,421,498 (87.55%) intronic = 4,005,263 (7.72%) intergenic = 2,456,220 (4.73%) overlapping exon = 2,028,546 (3.91%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.23 5'-3' bias = 1.66 >>>>>>> Junction analysis reads at junctions = 13,495,509 ACCT : 5.63% AGGT : 4.49% ATCT : 3.92% TCCT : 3.85% AGGA : 3.27% GCCT : 3.24% AGCT : 2.61% CCCT : 2.59% AGGC : 2.36% AGAT : 2.04% TTCT : 1.97%