The in silico sampling experiments demonstrate the necessity of high sequencing depth for increasing QTL detection in bulked segregant analysis.
Although the in silico sample size was small, this finding is consistent with a domestication bottleneck in A. altilis with respect to its wild progenitor, A. camansi (Zerega et al., 2005).
Comparison of mapped reads from our sequence data to in silico sampling of the reference genome finds a similarly strong correlation across all 1,514 families of the database after removing five outliers (see below).
We created 6,105 in silico intercross samples by imputation of genotypes for all pairwise combinations of 111 M.
All datasets represented perfect replicates by definition as they were generated in silico by sampling from a common pool.
There are 1,566 occurrences of an AP-1 motif within 150-bps of a GR motif in the genome, much higher than expected (p=3×10-53) calcusingd using in silico random sampling in the genome.
All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes.
Instead of in silico bootstrapping simulation, samples belonging to different visits of the same patient and even the same samples were assayed, i.e., "bootstrapped" experimentally, for testing.
Exome enrichment, sequencing and in silico analysis of samples was performed as previously described [ 18, 19].
The less stringent protocol here applied has allowed us to recognize 585 NumtS, over 95% of which have been validated here for the first time, either by bench approaches (PCR and sequencing) or in silico on eight samples collected within the international HapMap project.
