Table 1 SNPs identified as associated with the phenotypic trait by different methods and approaches.
From: Data modeling as a main source of discrepancies in single and multiple marker association methods
SNP (P-value) | SNP (HQ-score) | SMA Additive effect (SE)3 | ||||
|---|---|---|---|---|---|---|
Chromosome | SMA raw1 | SMA corrected (QxPak) | Blossoc raw1 | Blossoc corrected | raw | corrected |
1 | 196 (52.2)2 | 196 (33.0) | 200 (215.7) | 200 (75.4) | 0.74 (0.05) | 0.71 (0.06) |
323 (16.9)* | 331 (10.4) | - | - | 0.40 (0.05) | -0.69 (0.10) | |
415 (23.5) | 402 (17.6) | 416 (98.1) | 402 (52.2) | 0.46 (0.05) | -0.78 (0.09) | |
778 (14.9) | 778 (11.5) | 778 (51.7)* | 778 (20.2) | 0.40 (0.05) | 0.40 (0.06) | |
2 | 1271 (15.8) | 1270 (14.4) | 1268 (94.6) | 1267 (31.1) | 0.36 (0.04) | 0.43 (0.05) |
1483 (28.3) | 1483 (15.4) | 1483 (113.2) | 1487 (31.2) | -0.50 (0.04) | -0.45 (0.05) | |
3 | 2149 (17.2) | 2133 (9.3) | 2134 (65.8) | - | -0.39 (0.04) | 0.35 (0.06) |
- | - | 2598 (37.9)* | 2601 (17.6) | - | - | |
4 | 3048 (35.9) | 3033 (27.4) | 3032 (237.4) | 3032 (104.4) | 0.54 (0.04) | 0.59 (0.05) |
3765 (44.9) | 3765 (23.4) | 3765 (183) | 3765 (47.5) | 0.62 (0.04) | 0.55 (0.05) | |
3953 (17.0) | - | 3952 (103.2) | 3952 (15.6) | 0.37 (0.04) | - | |
5 | 4935 (23.7) | 4935 (29.8) | 4940 (94.8) | 4935 (68.7) | -0.47 (0.05) | -0.63 (0.05) |
Total # SNPs | 33/15 | 10 | 49/19 | 10 | ||