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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