Table 3.

Marker quality filtering using different thresholds for call rate and $\mathrm{\Delta }ICL$

$\mathrm{\Delta }ICL$ threshold	Marker call rate threshold
	0.80	0.85	0.90	0.95	1.00
0	0.02604 (3668)	0.02573 (3774)	0.02505 (4505)	0.02338 (7411)	0.0263 (29,905)
50	0.01582 (16,329)	0.01571 (16,340)	0.01545 (16,423)	0.01471 (17,526)	0.01461 (34,111)
100	0.00924 (29,888)	0.00916 (29,892)	0.00906 (29,902)	0.0089 (30,076)	0.00723 (39,535)
150	0.00433 (38,521)	0.00433 (38,521)	0.00433 (38,521)	0.0043 (38,535)	0.00287 (43,563)
200	0.00206 (43,557)	0.00206 (43,557)	0.00206 (43,557)	0.002 (43,561)	0.00114 (46,168)
250	0.0007 (46,679)	0.0007 (46,679)	0.0007 (46,679)	0.0007 (46,679)	0.00051 (47,936)
300	0.00037 (48,705)	0.00037 (48,705)	0.00037 (48,705)	0.00037 (48,705)	0.00029 (49,286)

Filtering markers using trios of triploid offspring and diploid parents with predicted sexes using marker call rate thresholds (top row in bold) and thresholds for $\mathrm{\Delta }\text{ICL}$ (left column in italic). The first number in each internal cell is the overall ER for all markers and all trios where there are informative genotypes (i.e. trios where offspring and at least one parent has called genotypes, see Table 2). The number of removed markers is shown in parenthesis.