Table 1.

Nucleotide Diversity (π) for SNPs, INDELs (Unpolarized), Insertions (ins), and Deletions (del) in Different Genomic Contexts

Context	π	π indel	π ins	π del
Genome wide	0.00310	0.000356	0.000113 $(0.000112)$	0.000142 $(0.000144)$
Ancestral repeats	0.00432	0.000363	0.000117 $(0.000119)$	0.000175 $(0.000177)$
Intergenic	0.00333	0.000378	0.000121 $(0.000119)$	0.000154 $(0.000157)$
Introns	0.00306	0.000361	0.000116 $(0.000115)$	0.000143 $(0.000145)$
CDS	0.00145	$1.87\times {10}^{-5}$	$3.61\times {10}^{-6}$ $(4.36\times {10}^{-6})$	$5.25\times {10}^{-6}$ $(5.09\times {10}^{-6})$
In-frame	—	$9.43\times {10}^{-6}$	$1.71\times {10}^{-6}$ $(1.86\times {10}^{-6})$	$3.00\times {10}^{-6}$ $(3.04\times {10}^{-6})$
Frameshift	—	$9.28\times {10}^{-6}$	$1.90\times {10}^{-6}$ $(2.17\times {10}^{-6})$	$2.24\times {10}^{-6}$ $(2.27\times {10}^{-6})$
4-Fold	0.00369	—	—	—
0-Fold	0.000586	—	—	—
Nonsense	$2.45\times {10}^{-5}$	—	—	—

Note.—Estimates in parentheses corrected for polarization error.