Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1136 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0523492909 sf0523430330 5 23492909 3.86E-54 3.36E-08
vg0804346142 sf0804345145 8 4346142 7.05E-54 1.58E-08
vg0221202871 sf0221197003 2 21202871 1.01E-53 NA
vg0205678863 sf0205678863 2 5678863 1.12E-51 NA
vg0307854597 sf0307853535 3 7854597 2.47E-50 7.81E-06
vg0405358102 sf0405353543 4 5358102 8.78E-50 4.05E-06
vg0815683726 sf0815681012 8 15683726 1.23E-49 1.10E-08
vg0307804168 sf0307803106 3 7804168 1.68E-49 3.63E-07
vg0221682664 sf0221676795 2 21682664 2.25E-47 3.74E-07
vg0319080537 sf0319079297 3 19080537 1.19E-43 5.00E-08
vg0521756317 sf0521693759 5 21756317 NA 3.52E-08
vg0726566560 sf0726565566 7 26566560 NA 1.28E-07
vg0622495913 sf0622494916 6 22495913 NA 1.54E-07
vg0804452573 sf0804451576 8 4452573 NA 2.01E-07
vg0821364762 sf0821362049 8 21364762 NA 3.35E-07
vg1006789704 sf1006805327 10 6789704 NA 4.65E-07
vg0429945987 sf0429760854 4 29945987 NA 5.33E-07
vg1006727798 sf1006743421 10 6727798 NA 6.77E-07
vg0622463232 sf0622462235 6 22463232 NA 7.12E-07
vg0211839911 sf0211839907 2 11839911 NA 1.15E-06
vg0523543573 sf0523480994 5 23543573 NA 2.14E-06
vg0517992463 sf0517931949 5 17992463 NA 2.18E-06
vg0715307926 sf0715306933 7 15307926 NA 2.97E-06
vg0229172293 sf0229166424 2 29172293 NA 4.45E-06
vg0118689086 sf0118688040 1 18689086 NA 4.90E-06