RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354218.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) = 42,972,955 / 42,946,710 read pairs aligned = 42,942,617 total alignments = 91,467,467 secondary alignments = 5,547,802 non-unique alignments = 9,164,767 aligned to genes = 71,532,385 ambiguous alignments = 287,964 no feature assigned = 10,053,922 not aligned = 5,791,955 >>>>>>> Reads genomic origin exonic = 71,532,385 (87.68%) intronic = 6,472,712 (7.93%) intergenic = 3,581,210 (4.39%) overlapping exon = 3,002,672 (3.68%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.19 5'-3' bias = 1.75 >>>>>>> Junction analysis reads at junctions = 23,732,209 ACCT : 5.33% AGGT : 4.79% ATCT : 3.85% TCCT : 3.48% AGGA : 3.4% GCCT : 3.24% CCCT : 2.72% AGCT : 2.61% AGGC : 2.45% TTCT : 2.22% AGAT : 2.04%