High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array

Table 4 Consistency rate between genotyping by sequencing and by array for the 4 individuals used to discover the InDels, for the three probe types and for the two different genotypes observed from sequencing: presence (P) or absence (A)

Probe Types	Genotype by sequencing	B73	F2	C103	PH207	All Lines
BP^a	A	0.98	0.98	0.98	0.97	0.98
	P	0.97	0.97	0.97	0.96	0.97
	ALL^a	0.97	0.97	0.97	0.97	0.97
OTV	A	0.85	0.89	0.80	0.78	0.83
	P	0.93	0.97	0.96	0.96	0.96
	ALL	0.90	0.95	0.91	0.90	0.92
MONO	A	0.77	0.81	0.82	0.81	0.80
	P	0.90	0.98	0.94	0.94	0.95
	ALL	0.82	0.94	0.89	0.88	0.88
ALL	A	0.80	0.86	0.84	0.82	0.82
	P	0.92	0.97	0.94	0.95	0.95
	ALL	0.85	0.95	0.90	0.89	0.90

^aNote that consistency rate of hemizygous genotypes (heterozygous for presence / absence) were not displayed in the table for BP probes but considered to estimate global consistency rate (ALL). Note that the absence of probe sequence due to absence of hybridization or no alignment on draft sequence of BP probes were considered as missing data. Missing data were not included in the comparison for all probes

ISSN: 1471-2164