TABLE 2.
Detection and estimation for QTL simulated in case I
| Effectse
|
Inferred modef
|
||||||||
|---|---|---|---|---|---|---|---|---|---|
| QTL effecta (frequency) | Methodb | Powerc | Positiond | 2a or apat | d or amat | E1 | E2 | E3 | E4 |
| A 0.25 (1.0/0.0) | Bayes | 0.830 | 46.1 (9.1) | 0.26 (0.06) | 0.01 (0.11) | 0.785 | 0.000 | 0.010 | 0.035 |
| IM | 0.840 | 46.4 (12.6) | 0.28 (0.06) | 0.01 (0.13) | 0.775 | 0.000 | 0.035 | 0.030 | |
| A 0.5 (1.0/0.0) | Bayes | 1.000 | 45.7 (3.9) | 0.48 (0.07) | 0.01 (0.10) | 0.995 | 0.005 | 0.000 | 0.000 |
| IM | 1.000 | 45.9 (3.9) | 0.50 (0.06) | 0.00 (0.11) | 0.955 | 0.045 | 0.000 | 0.000 | |
| D 0.25 (1.0/0.0) | Bayes | 0.955 | 46.1 (7.1) | 0.25 (0.06) | 0.24 (0.10) | 0.945 | 0.005 | 0.005 | 0.000 |
| IM | 0.965 | 47.3 (9.5) | 0.26 (0.06) | 0.26 (0.11) | 0.900 | 0.050 | 0.005 | 0.010 | |
| E3 0.25 (1.0/0.0) | Bayes | 0.995 | 45.8 (6.6) | 0.24 (0.04) | — | 0.055 | 0.050 | 0.890 | 0.000 |
| IM | 1.000 | 46.2 (8.2) | 0.26 (0.04) | — | 0.045 | 0.075 | 0.880 | 0.000 | |
| E4 0.25 (1.0/0.0) | Bayes | 0.990 | 46.0 (5.7) | — | 0.25 (0.05) | 0.040 | 0.035 | 0.000 | 0.915 |
| IM | 0.995 | 46.4 (6.4) | — | 0.26 (0.04) | 0.035 | 0.040 | 0.000 | 0.920 | |
| A 0.25 (0.8/0.2) | Bayes | 0.435 | 46.8 (11.4) | 0.19 (0.05) | −0.01 (0.11) | 0.350 | 0.000 | 0.040 | 0.045 |
| IM | 0.270 | 45.3 (13.9) | 0.23 (0.05) | −0.01 (0.13) | 0.205 | 0.010 | 0.035 | 0.020 | |
| A 0.5 (0.8/0.2) | Bayes | 0.930 | 45.8 (7.3) | 0.30 (0.07) | −0.01 (0.10) | 0.840 | 0.005 | 0.035 | 0.050 |
| IM | 0.915 | 46.4 (9.7) | 0.32 (0.07) | −0.01 (0.12) | 0.820 | 0.020 | 0.040 | 0.035 | |
| D 0.25 (0.8/0.2) | Bayes | 0.480 | 45.8 (11.6) | 0.19 (0.05) | 0.10 (0.11) | 0.395 | 0.005 | 0.040 | 0.040 |
| IM | 0.330 | 45.0 (13.9) | 0.22 (0.05) | 0.15 (0.12) | 0.275 | 0.015 | 0.020 | 0.020 | |
| E3 0.25 (0.8/0.2) | Bayes | 0.705 | 45.7 (9.3) | 0.17 (0.05) | — | 0.120 | 0.020 | 0.565 | 0.000 |
| IM | 0.605 | 44.8 (11.5) | 0.22 (0.02) | — | 0.070 | 0.055 | 0.480 | 0.000 | |
| E3 0.5 (0.8/0.2) | Bayes | 0.955 | 45.9 (5.0) | 0.31 (0.07) | — | 0.050 | 0.055 | 0.850 | 0.000 |
| IM | 0.950 | 46.3 (6.0) | 0.32 (0.07) | — | 0.030 | 0.055 | 0.865 | 0.000 | |
| E4 0.25 (0.8/0.2) | Bayes | 0.660 | 47.3 (9.5) | — | 0.17 (0.04) | 0.120 | 0.010 | 0.000 | 0.530 |
| IM | 0.565 | 49.1 (12.1) | — | 0.21 (0.03) | 0.130 | 0.035 | 0.000 | 0.400 | |
| E4 0.5 (0.8/0.2) | Bayes | 0.995 | 46.5 (5.7) | — | 0.29 (0.06) | 0.030 | 0.030 | 0.000 | 0.935 |
| IM | 0.995 | 47.1 (6.5) | — | 0.30 (0.06) | 0.015 | 0.080 | 0.000 | 0.900 | |
A, additive QTL without dominance effect; D, dominant QTL with 2a = d; E3, QTL with exclusive paternal expression with effect apat; E4, QTL with exclusive maternal expression with effect amat (frequency of positive QTL allele in founder lines).
Bayes, Bayesian method; IM, interval-mapping procedure for imprinted QTL.
Proportion of replicates with successful detection of QTL based on the threshold of significance level P = 0.05 in a total of 200 replicates.
Average of estimated positions (centimorgans) over the replicates with successful QTL detection. Standard deviations of estimates are given in parentheses.
Average of estimated effects for simulated QTL over the replicates with successful QTL detection, where 2a and d are relevant to Mendelian QTL and apat or amat is relevant to imprinted QTL. Standard deviations of estimates are given in parentheses.
Proportion of replicates supporting each QTL expression mode as the most probable state in the replicates with successful QTL detection. Accordingly, the sum of the proportions for E1, E2, E3, and E4 was equivalent to the power.