Table 1.

Read mapping, alignment and subsequent expression summary for RIL165 and RIL387

Samplea	Number of quality filtered reads	Number of mapped readsb	Number of paired alignments	Maximum FPKMc	Number of expressed genes
RIL165_1	70,769,770	83%	27,884,716	5761	22,558
RIL165_2	62,302,258	75%	21,984,219	6882	22,895
RIL165_3	78,883,890	76%	28,417,469	4868	22,773
RIL387_1	62,399,266	80%	23,331,358	6755	22,633
RIL387_2	63,798,694	78%	23,458,704	8659	22,575
RIL387_3	59,304,854	80%	22,353,073	6349	22,641

^aSamples are numbered per biological replicate

^bSequence reads for each biological replicate were mapped to v2 of the B73 reference genome using TopHat v2.0.9 [103]

^cCufflinks v2.0.2 was used to calculate transcript abundance which is reported as fragments per kilobase pair of exon model per million fragments mapped (FPKM) [33]