RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354128.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) = 46,032,500 / 45,962,552 read pairs aligned = 45,956,236 total alignments = 97,964,144 secondary alignments = 5,969,092 non-unique alignments = 10,173,868 aligned to genes = 76,203,919 ambiguous alignments = 243,861 no feature assigned = 11,005,406 not aligned = 6,763,126 >>>>>>> Reads genomic origin exonic = 76,203,919 (87.38%) intronic = 6,821,866 (7.82%) intergenic = 4,183,540 (4.8%) overlapping exon = 2,978,549 (3.42%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.18 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 22,900,508 ACCT : 5.45% AGGT : 4.57% ATCT : 3.59% AGGA : 3.53% TCCT : 3.3% GCCT : 3.28% AGCT : 2.72% CCCT : 2.38% AGGC : 2.34% AGAT : 2.27% TTCT : 2.22%