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

BMC Genomics

Table 3 Median percentages of reads from B73 and Mo17 that mapped to splice junctions relative to all exons for genes with B73 or Mo17 positive eQTL

	B73 reads	Mo17 reads	All reads^c
B73 + eQTL	15.2^a	15.3	15.2
Mo17 + eQTL	15.6^b	15.8	15.7

^aAmong genes upregulated by B73 alleles, the proportion of reads that mapped to splice sites was significantly higher for Mo17 derived reads than B73 derived reads. Wilcoxon signed rank test, V = 5,474,100, p-value = 4.947e-12
^bAmong genes upregulated by Mo17 alleles, the proportion of reads that mapped to splice sites was significantly higher for Mo17 derived reads than B73 derived reads. Wilcoxon signed rank test, V = 1,269,200, p-value = 0.019
^cThe percentage of all reads that mapped to splice sites was significantly lower in genes upregulated by B73 alleles compared to genes upregulated by Mo17 alleles. Wilcoxon rank sum test, W = 23,696,329, p-value = 4.518e-4

ISSN: 1471-2164