Table 3.

Pairwise FST estimates for four analyses (with or without clones, genome aligned or unaligned reads).

	FST W&C	95% CI	FST R	95% CI	FST Rcor	95% CI
Potential Clones Included
Genome-aligned
NS vs. MA	0.298	(0.254, 0.351)	0.286	(0.239, 0.340)	0.298	(0.256, 0.350)
NS vs. MD	0.544	(0.477, 0.601)	0.556	(0.488, 0.617)	0.563	(0.498, 0.629)
NS vs. SC	0.518	(0.459, 0.572)	0.517	(0.461, 0.575)	0.521	(0.461, 0.575)
MA vs. MD	0.474	(0.426, 0.518)	0.485	(0.431, 0.536)	0.497	(0.450, 0.548)
MA vs. SC	0.480	(0.425, 0.529)	0.480	(0.429, 0.533)	0.487	(0.435, 0.538)
MD vs. SC	0.622	(0.562, 0.681)	0.617	(0.560, 0.670)	0.622	(0.564, 0.680)
Unaligned
NS vs. MA	0.316	(0.270, 0.371)	0.303	(0.252, 0.361)	0.316	(0.268, 0.371)
NS vs. MD	0.592	(0.534, 0.648)	0.595	(0.534, 0.653)	0.602	(0.547, 0.659)
NS vs. SC	0.560	(0.498, 0.627)	0.559	(0.499, 0.618)	0.561	(0.502, 0.624)
MA vs. MD	0.460	(0.413, 0.507)	0.467	(0.417, 0.519)	0.481	(0.437, 0.533)
MA vs. SC	0.434	(0.387, 0.483)	0.438	(0.386, 0.489)	0.446	(0.397, 0.502)
MD vs. SC	0.637	(0.580, 0.697)	0.632	(0.567, 0.688)	0.637	(0.579, 0.695)
Potential Clones Exclued
Genome-aligned
NS vs. MA	0.230	(0.185, 0.275)	0.218	(0.174, 0.270)	0.231	(0.183, 0.279)
NS vs. MD	0.522	(0.456, 0.590)	0.502	(0.438, 0.571)	0.508	(0.438, 0.578)
NS vs. SC	0.479	(0.422, 0.536)	0.468	(0.411, 0.527)	0.471	(0.415, 0.535)
MA vs. MD	0.431	(0.380, 0.477)	0.437	(0.389, 0.490)	0.451	(0.398, 0.503)
MA vs. SC	0.446	(0.402, 0.492)	0.440	(0.398, 0.485)	0.449	(0.408, 0.496)
MD vs. SC	0.569	(0.506, 0.636)	0.572	(0.504, 0.637)	0.576	(0.516, 0.640)
Unaligned
NS vs. MA	0.218	(0.179, 0.258)	0.201	(0.161, 0.247)	0.221	(0.181, 0.267)
NS vs. MD	0.489	(0.430, 0.545)	0.467	(0.410, 0.525)	0.479	(0.419, 0.538)
NS vs. SC	0.494	(0.438, 0.550)	0.479	(0.431, 0.541)	0.485	(0.428, 0.538)
MA vs. MD	0.397	(0.354, 0.442)	0.395	(0.350, 0.440)	0.413	(0.368, 0.454)
MA vs. SC	0.402	(0.361, 0.446)	0.394	(0.349, 0.436)	0.406	(0.365, 0.450)
MD vs. SC	0.576	(0.520, 0.630)	0.573	(0.522, 0.627)	0.579	(0.530, 0.640)