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 mr1934 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
vg0524494561 sf0524431982 5 24494561 1.55E-140 2.20E-29
vg1209153210 sf1209150619 12 9153210 1.17E-94 NA
vg0135932584 sf0135931541 1 35932584 6.32E-91 NA
vg0232358240 sf0232352371 2 32358240 1.14E-90 NA
vg0129939389 sf0129938344 1 29939389 2.02E-90 NA
vg0524793384 sf0524730799 5 24793384 NA 1.76E-16
vg1221775967 sf1221742514 12 21775967 NA 1.47E-06
vg0504761403 sf0504761380 5 4761403 NA 1.50E-06
vg0524300922 sf0524238341 5 24300922 NA 1.79E-06
vg0404665726 sf0404661165 4 4665726 NA 2.75E-06
vg0230082779 sf0230076910 2 30082779 NA 3.29E-06
vg1221620847 sf1221587394 12 21620847 NA 3.53E-06
vg0916030541 sf0916029540 9 16030541 NA 3.71E-06
vg1118780293 sf1118314101 11 18780293 NA 4.18E-06
vg0726108448 sf0726107454 7 26108448 NA 4.44E-06
vg0821968306 sf0821965593 8 21968306 NA 4.80E-06
vg1012400571 sf1012329386 10 12400571 NA 4.84E-06