Skip to main content

Table 1 Numbers of genes with B73 and Mo17 positively acting cis regulatory alleles using B73 and Mo17 reference genomes revealed read mapping preferences for reference alleles

From: Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias

  B73 referencea Mo17 referenceb
Total cis-eQTLc 9306 7985
B73 positive cis-eQTL 6341 (68.1%) 2816 (35.3%)
Mo17 positive cis-eQTL 2965 (31.9%) 5169 (64.7%)
  1. RNA-seq were mapped to the B73a or Mo17b reference using STAR with the default criteria as given in Supplemental Information.
  2. c The numbers of genes with cis-eQTL were recorded excluding genes with both cis and trans eQTL