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. 2010 Dec 24;28(5):1675–1686. doi: 10.1093/molbev/msq348

Table 3.

Nucleotide Variation within M. domesticus and M. musculus.

Locus/Sample	n	All^a	Coding^a	Silent^a Sites	Hap.^b	S^c	π (%)		θ (%)		Tajima’s D^d	D_XY^e (%)
Locus/Sample	n	All^a	Coding^a	Silent^a Sites	Hap.^b	S^c	All	Silent^d	All	Silent^d	Tajima’s D^d	All	Silent^d
4933436I01Rik
Mus domesticus	32	1,649	1,287	416	7	6	0.038	0.03	0.090	0.119	−1.504*	1.58	1.94
M. musculus	39	1,649	1,287	416	3	3	0.015	—	0.043	—	—	1.76	2.16
Magea9
M. domesticus	32	794	729	110	3	2	0.109	—	0.063	—	—	2.75	3.64
M. musculus	44	799	708	112	2	1	0.056	—	0.029	—	—	2.47	2.68
Tsga8
M. domesticus	26	981	804	335	11	12	0.210	0.202	0.321	0.391	−1.37	1.77	2.12
M. musculus	22	1,101	924	368	4	7	0.072	0.049	0.174	0.149	−1.52*	2.05	1.63
Pbsn
M. domesticus	31	1,995	522	1,297	7	8	0.068	0.041	0.100	0.058	−0.689	1.18	1.39
M. musculus	27	2,649	522	1,951	5	5	0.017	0.019	0.049	0.053	−1.714*	1.07	1.14
Tsx
M. domesticus	28	3,740	432	3,078	8	9	0.040	0.032	0.062	0.05	−1.075	1.34	1.40
M. musculus	26	3,751	432	3,089	8	6	0.049	0.060	0.042	0.051	0.510	1.32	1.41

^a

Based on aligned regions, excluding indel variation.

^b

Number of unambiguously resolved haplotypes considering all sites.

^c

Total number of polymorphic sites.

^d

Based on noncoding and 4-fold degenerate synonymous coding sites, excluding conserved regions flanking introns (20 bp) and indel variation.

^e

Average percent of nucleotide substitutions per site based on comparison with M. spretus.

P < 0.05 based on 10,000 coalescent simulations.