Fig. 1
From: Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
Depiction of a correlation test to determine if preferential alignment affected gene transcript estimates. a A chromosomal region whose genes transcripts are all inferred to be correlated across RILs indicates preferential read alignment. A hypothetical region has five linked genes (A-E) that are in complete linkage disequilibrium within the B73 x Mo17 RIL population. Individual members of the RIL population are arbitrarily labelled 1–97. Preferential read alignment causes the B73 allele to have a positive effect on all genes’ transcript abundance estimates relative to the Mo17 allele, leading to one group of coexpressed genes. b A chromosomal region with two groups of genes coexpressed across RILs indicates unbiased read alignments across the regions’ genes. Relative to Mo17, B73 alleles increase transcript abundances for genes A, C, and D and decrease transcript abundances for genes B and E. Genes A, C, and D are coexpressed, and genes B and E are also coexpressed