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 mr1929 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
vg0222725905 sf0222720036 2 22725905 5.85E-43 1.55E-36
vg0222725103 sf0222719234 2 22725103 1.45E-42 8.52E-37
vg0223077677 sf0223071808 2 23077677 2.75E-12 4.67E-09
vg0223077967 sf0223072098 2 23077967 8.93E-12 2.70E-08
vg0222615084 sf0222609215 2 22615084 2.90E-11 1.66E-07
vg0222879623 sf0222873754 2 22879623 3.78E-11 3.22E-13
vg0221697257 sf0221691388 2 21697257 4.18E-11 1.87E-06
vg0224678499 sf0224672630 2 24678499 6.85E-10 2.20E-07
vg0221650044 sf0221644175 2 21650044 1.93E-09 2.77E-07
vg1112606022 sf1112142225 11 12606022 2.59E-09 5.82E-07
vg0222765370 sf0222759501 2 22765370 3.40E-09 2.25E-06
vg0223737012 sf0223731143 2 23737012 3.81E-09 1.68E-07
vg0222681985 sf0222676116 2 22681985 1.19E-08 9.00E-08
vg0222729132 sf0222723263 2 22729132 2.14E-08 1.20E-06
vg0221239428 sf0221233560 2 21239428 4.30E-08 2.57E-07
vg0222703153 sf0222697284 2 22703153 8.08E-08 3.86E-06
vg0222797604 sf0222791735 2 22797604 3.92E-07 2.69E-06
vg0222802022 sf0222796153 2 22802022 2.78E-06 1.16E-06
vg0223039697 sf0223033828 2 23039697 NA 9.16E-08
vg0222665038 sf0222659169 2 22665038 NA 4.14E-06