Table 2. RNA—Seq metrics overview.

	X	I	XI
The number of total read pairs refers to the total pair read counts per genotype. The median and mean read pairs per sample refer to the sample specific read pairs, where samples constitute the individual exposures including multiple biological replicates of the same genotype per condition. In addition, the fraction of read pairs with phred >30 with respective mean and median values are shown. Number of environmental exposures indicates the number of environmental perturbations to which the genotypes were exposed. The number of libraries constructed per sample is shown; for the X genotype 25 libraries were constructed, including 2 controls as the exposures were completed over two days. For the I genotype 24 libraries were constructed. For the XI genotype 18 libraries were constructed.
Number of read pairs	3,403,673,296	2,812,630,218	443,120,153
Median read pairs per sample	66,965,781	57,197,308	22,617,799.5
Mean read pairs per sample	68,073,465.92	58,596,462.88	24,617,786.28
Number of reads pairs with phred score >30	2,621,703,528	2,273,042,316	341,213,774
Mean phred score per sequence	32.67	33.29	33.73
Median phred score per sequence	35.00	36.00	35.86
Number of environmental exposures	8	8	6
Number of libraries	25	24	18