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Table 4 Number of genes with B73 and Mo17 positively acting, cis-regulatory alleles detected in different analyses

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

Methods STAR-StringTie TopHat2-Cufflinks Salmon
cis-eQTL only default criteria relaxed criteria most relaxed criteria default criteria relaxed criteria most relaxed criteria default criteria
Total 9306 9256 9260 11,908 11,720 11,643 7855
B73 positive cis-eQTL 6341 (68.1%) 6203 (67.0%) 6172 (66.6%) 9905 (83.2%) 9639 (82.1%) 9504 (81.6%) 4959 (63.1%)
Mo17 positive cis-eQTL 2965 (31.9%) 3053 (33.0%) 3088 (33.3%) 2003 (16.8%) 2081 (17.8%) 2139 (18.4%) 2896 (36.9%)