Table 4. Allele composition of bulk segregant pools based on individual PCR and pooled microarray hybridization.

Population	Scaffold	Position	Map Marker Cluster	PCR-based Proportion N. vitripennis	Array-based Proportion N. vitripennis	Map Markers within 100 kb
st-318,mm+g	22	1,033,000	3.053	0.17	0.12	11
	22	2,810,000	3.065	0.54	0.51	0a
	17	1,078,000	3.071	0.82	0.71	9
	17	1,504,000	3.078	1.00	1.00	10
st-318+g,mm	22	1,033,000	3.053	0.88	0.70	11
	22	2,810,000	3.065	0.58	0.56	0a
	17	1,078,000	3.071	0.24	0.28	9
	17	1,504,000	3.078	1.00	1.00	10

A mutant N. vitripennis strain (st-318,mm) was crossed with a wild-type N. giraulti introgression of the region (st-318^+g,mm^+g) in a N. vitripennis genetic background. Recombinants between the loci were collected into two pools: st-318^+g,mm and st-318,mm^+g. All members of each pool were screened with PCR markers at the listed positions to determine the PCR-based proportion of individuals with each allele. Then, each pool was hybridized to the array and allele proportions were estimated for all map markers. Array-based allele proportion at each PCR marker was determined by averaging proportions for all map markers in a 100-kb window surrounding the PCR marker location. PCR, polymerase chain reaction.

^aBecause no map markers were within 100 kb, we used the 10 closest map markers centered on the position.