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 mr1123 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
vg0222679274 sf0222673405 2 22679274 2.86E-60 4.85E-27
vg0222687716 sf0222681847 2 22687716 5.19E-52 1.38E-27
vg0526722696 sf0526660054 5 26722696 6.41E-36 1.24E-07
vg0518201525 sf0518141011 5 18201525 9.54E-34 1.89E-07
vg0906971590 sf0906970590 9 6971590 4.88E-32 2.87E-08
vg0110298482 sf0110297458 1 10298482 9.30E-32 NA
vg0500435853 sf0500435853 5 435853 9.78E-31 6.44E-09
vg0818212763 sf0818210050 8 18212763 4.00E-30 4.29E-09
vg1110425815 sf1110420360 11 10425815 7.06E-30 3.81E-08
vg0907026290 sf0907025290 9 7026290 4.63E-28 1.92E-09
vg0222732157 sf0222726288 2 22732157 9.84E-28 3.78E-11
vg0222718166 sf0222712297 2 22718166 3.10E-27 4.12E-10
vg0703826736 sf0703825737 7 3826736 6.18E-26 3.71E-08
vg0316147114 sf0316145761 3 16147114 2.31E-25 1.21E-08
vg0616706040 sf0616705042 6 16706040 5.57E-24 5.20E-09
vg0222722554 sf0222716685 2 22722554 NA 1.20E-11
vg0224793205 sf0224787336 2 24793205 NA 1.58E-09
vg0626215270 sf0626214273 6 26215270 NA 2.85E-09
vg0709372324 sf0709371330 7 9372324 NA 3.54E-09
vg0222271516 sf0222265647 2 22271516 NA 3.90E-09
vg0820869390 sf0820866677 8 20869390 NA 1.47E-08
vg0222952563 sf0222946694 2 22952563 NA 1.52E-08
vg1204507349 sf1204506337 12 4507349 NA 1.86E-08
vg0307804640 sf0307803578 3 7804640 NA 4.09E-08
vg0224791280 sf0224785411 2 24791280 NA 4.30E-08
vg0431376032 sf0431190928 4 31376032 NA 4.48E-08
vg0819598853 sf0819596140 8 19598853 NA 4.84E-08
vg0141554830 sf0141553787 1 41554830 NA 7.30E-08
vg0421291212 sf0421119266 4 21291212 NA 1.25E-07
vg0311437556 sf0311436274 3 11437556 NA 4.04E-07
vg0804869267 sf0804868270 8 4869267 NA 1.26E-06