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 mr1550 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
vg0705417443 sf0705416444 7 5417443 1.11E-89 3.04E-25
vg0716934795 sf0716933802 7 16934795 1.46E-70 1.28E-08
vg0701513997 sf0701512997 7 1513997 2.36E-70 4.97E-09
vg1019228132 sf1019156688 10 19228132 1.39E-66 5.98E-08
vg0101086387 sf0101085387 1 1086387 1.21E-65 1.33E-11
vg0529267531 sf0529204886 5 29267531 7.58E-65 1.35E-07
vg0716582032 sf0716581039 7 16582032 1.52E-64 4.14E-12
vg0101083709 sf0101082709 1 1083709 1.60E-63 1.08E-11
vg0827342598 sf0827339884 8 27342598 5.75E-62 1.06E-07
vg0622627045 sf0622626048 6 22627045 2.58E-58 2.33E-07
vg0141203398 sf0141202355 1 41203398 2.58E-58 1.63E-07
vg0205960969 sf0205960969 2 5960969 4.30E-58 1.20E-07
vg0630111757 sf0630110759 6 30111757 7.19E-57 2.40E-08
vg0709095039 sf0709094045 7 9095039 4.34E-54 2.52E-09
vg1226792832 sf1226759230 12 26792832 4.66E-54 2.33E-07
vg0215987623 sf0215981753 2 15987623 1.68E-51 2.35E-07
vg1110664454 sf1110658999 11 10664454 2.03E-48 2.13E-11
vg0705418075 sf0705417076 7 5418075 NA 2.42E-14
vg0909235018 sf0909234017 9 9235018 NA 1.94E-09
vg0909238381 sf0909237380 9 9238381 NA 3.16E-09
vg0400004808 sf0400003808 4 4808 NA 3.00E-08
vg0514922521 sf0514865064 5 14922521 NA 3.20E-08
vg0522270472 sf0522207913 5 22270472 NA 8.19E-08
vg0518442916 sf0518382402 5 18442916 NA 1.00E-07
vg0313900900 sf0313899617 3 13900900 NA 1.21E-07
vg0434769084 sf0434583975 4 34769084 NA 2.99E-07
vg0232755756 sf0232749887 2 32755756 NA 1.15E-06
vg0400146964 sf0400145964 4 146964 NA 5.60E-06
vg0433028578 sf0432843465 4 33028578 NA 6.22E-06