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Fig. S1 Alternative model for predicting the proportion of informative reads: incorporating the finite length of mRNA sequence.

Fig. S2 The location of a SNP within a sequence affects its probability of being sampled in a random sampling strategy.

Fig. S3 The number of informative reads per gene, as well as the magnitude of AI, affect the accuracy of AI estimates.

Fig. S4 Distribution of significant AI in F1 hybrids.

Table S1 Genes and intergenic regions with significant AI (binomial test, p<0.05).

Table S2 Comparisons between 454 sequencing and Pyrosequencing AI estimates.

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