Table A1.4.

The probabilities of observing alleles at a specific frequency in the core population and ISC1. We assessed whether or not the SNPs we discovered in our sample of ISC L. donovani were likely to be representative of the variation existing in the wider population of parasites circulating in the ISC. We first assessed the chance of discovering alleles at frequency f as 1-(1-f)^2n in the core population (n=191) and ISC1 (n=12) sample sets (Gutenkunst et al., 2009). As a second approach, we evaluated the chance of sampling at least one derived allele in n sampled chromosomes (as above) assuming these come from a population of size N=1000 following a hypergeometric distribution (Tennessen et al., 2012). Both approaches confirm we have good power (>99% probability) of sampling alleles with population frequencies as low as 1.2% in the core population, but are likely to miss many variants in ISC1.

DOI: http://dx.doi.org/10.7554/eLife.12613.022

Allele Frequency	P(derived allele)=1-(1-f)2n		$\left(\begin{array}{c}M\\ 0\end{array}\right) \left(\begin{array}{c}N-M\\ n\end{array}\right) /\left(\begin{array}{c}N\\ n\end{array}\right)$
			P(derived allele)=1 –
	Core population	ISC1	Core population	ISC1
0.001	0.318	0.024	0.382	0.024
0.002	0.535	0.047	0.618	0.047
0.003	0.683	0.07	0.91	0.07
0.004	0.784	0.092	0.945	0.092
0.005	0.853	0.113	0.966	0.115
0.006	0.9	0.134	0.979	0.136
0.007	0.932	0.155	0.987	0.157
0.008	0.953	0.175	0.992	0.177
0.009	0.968	0.195	0.997	0.197
0.01	0.978	0.214	0.999	0.217
0.012	0.99	0.252	0.999	0.254
0.015	0.997	0.304	0.999	0.307
0.021	0.999	0.399	0.999	0.403
0.024	0.999	0.442	1	0.446
0.029	0.999	0.507	1	0.511
0.038	0.999	0.605	1	0.61
0.039	0.999	0.615	1	0.619
0.04	1	0.625	1	0.629
0.049	1	0.701	1	0.705
0.065	1	0.801	1	0.805
0.092	1	0.901	1	0.904
0.173	1	0.99	1	0.99
0.272	1	1	1	1