Table 3. Summary statistics describing patterns of differentiation in fully sorted regions vs. all other regions in pairwise comparisons of the subspecies of M. musculus.

Subspecies	Subspecies	Chromosome type	Window typea	nb	Average size of region (bp) (SD)	Average no. of SNPs (SD)	${\overline{F}}_{st}$ (SD)	${\overline{D}}_{xy}$ (SD)	$\overline{\delta }$ (SD)	${\overline{\pi }}_1^c$ (SD)	${\overline{\pi }}_2^c$ (SD)
M. m. castaneus	M. m. domesticus	Autosomes	Fully sorted	223	159,193 (38,840)	15.05** (9.17)	0.48*** (0.16)	0.59*** (0.13)	0.59*** (0.13)	0.15*** (0.10)	0.11*** (0.07)
		Autosomes	All others	321	157,243 (46,855)	19.36** (12.56)	0.20*** (0.13)	0.43 *** (0.10)	0.39*** (0.11)	0.29*** (0.09)	0.20*** (0.09)
		X	Fully sorted	5	175,000 (0)	5.20 (1.92)	0.80 (0.12)	0.85 (0.09)	0.85 (0.09)	0.06 (0.06)	0.05 (0.04)
M. m. castaneus	M. m. musculus	Autosomes	Fully sorted	317	172,003** (52,573)	16.54 (10.86)	0.47*** (0.17)	0.60*** (0.13)	0.60*** (0.13)	0.20*** (0.10)	0.07*** (0.06)
		Autosomes	All others	287	154,355** (52,334)	18.20 (12.42)	0.19*** (0.14)	0.42*** (0.11)	0.38*** (0.13)	0.28*** (0.09)	0.21*** (0.10)
		X	Fully sorted	3	175,000 (0)	3.67 (1.15)	1.00 (0.00)	1.00 (0.00)	1.00 (0.00)	0.00 (0.00)	0.00 (0.00)
M. m. domesticus	M. m. musculus	Autosomes	Fully sorted	624	178,766 *** (55,386)	13.93 (9.50)	0.57*** (0.17)	0.66*** (0.13)	0.66*** (0.13)	0.12*** (0.07)	0.08*** (0.06)
		Autosomes	All others	234	140,171*** (51,005)	14.50 (10.45)	0.27*** (0.16)	0.48*** (0.12)	0.44*** (0.14)	0.22*** (0.09)	0.23*** (0.10)
		X	Fully sorted	10	16,000 (24,152)	5.50 (1.27)	0.70 (0.18)	0.76 (0.15)	0.76 (0.15)	0.07 (0.06)	0.05 (0.06)

^*P < 0.05, ** P < 10⁻³, *** P < 10⁻⁷ in two-sided t-tests comparing highly differentiated autosomal regions and all other autosomal regions in each pairwise comparison.

^aFully sorted regions are defined as those in which: $\frac{\#fixed\hspace{0.17em}differences}{\#fixed\hspace{0.17em}differences+\#shared\hspace{0.17em}polymorphisms}=1$ (see Materials and Methods).

^bNumber of delimited regions.

^c${\overline{\pi }}_1$ and ${\overline{\pi }}_2$ refer to nucleotide diversity (Nei and Li 1979) in the first and second subspecies, respectively.