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 mr1798 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
vg0402389835 sf0402385430 4 2389835 4.08E-58 6.71E-33
vg0230266176 sf0230260307 2 30266176 1.73E-17 9.05E-06
vg0403954770 sf0403950376 4 3954770 3.51E-17 6.59E-06
vg0314431461 sf0314430150 3 14431461 2.22E-16 NA
vg1122311857 sf1121845728 11 22311857 5.88E-16 NA
vg0403656258 sf0403651862 4 3656258 4.08E-15 2.49E-06
vg1010719593 sf1010648414 10 10719593 7.32E-15 4.47E-07
vg0403658880 sf0403654484 4 3658880 4.26E-13 4.81E-10
vg0402048808 sf0402044404 4 2048808 5.20E-13 1.44E-10
vg0402823034 sf0402818639 4 2823034 6.56E-11 1.81E-06
vg0402454995 sf0402450592 4 2454995 6.75E-11 2.40E-09
vg0619983787 sf0619982790 6 19983787 1.64E-10 2.98E-07
vg0404609499 sf0404605102 4 4609499 2.06E-10 9.58E-08
vg0402260566 sf0402256161 4 2260566 5.66E-10 1.08E-06
vg0202301166 sf0202301164 2 2301166 6.55E-10 3.94E-06
vg0402458498 sf0402454096 4 2458498 8.54E-10 9.17E-07
vg0224287318 sf0224281449 2 24287318 1.13E-09 1.96E-07
vg0613051893 sf0613050894 6 13051893 8.41E-09 9.94E-08
vg0401915452 sf0401911048 4 1915452 5.87E-08 6.80E-08
vg0405051916 sf0405047355 4 5051916 7.40E-08 2.91E-06
vg0800652241 sf0800651241 8 652241 2.99E-07 2.59E-06
vg0617635655 sf0617634658 6 17635655 NA 1.69E-06
vg0508113074 sf0508113014 5 8113074 NA 2.49E-06
vg0826610630 sf0826607916 8 26610630 NA 2.62E-06
vg0910045511 sf0910044510 9 10045511 NA 2.71E-06